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1
Lalani, Samir, Sehajroop Gadh, Justin Elfman, Sandeep Singh, and Hui Li. "Abstract 4351: Differential dependency mapping of chimeric RNAs across cancer reveals a new landscape of functional fusion transcripts." Cancer Research 84, no. 6_Supplement (March 22, 2024): 4351. http://dx.doi.org/10.1158/1538-7445.am2024-4351.
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Abstract Chimeric RNAs are RNA transcripts containing sequences originating from multiple distinct genetic loci and can form through a variety of mechanisms such as DNA rearrangement, cis-splicing of adjacent genes, or RNA trans-splicing. Chimeras have long been known to be a hallmark of cancer and due to their unique properties are promising targets for precision medicine. Appropriately, fusion proteins transcribed from chimeras such as BCR-ABL1 and TPM3-NTRK1 have been shown to be effective targets. Due to these past successes, there exists an opportunity to identify new chimeras as therapeutic targets. While modern chimera prediction software allows for the fast and accurate identification of chimeric RNAs from RNA sequencing data, investigations separating therapeutically relevant transcripts from “transcriptional noise” remain lacking. In this study we performed an in-silico functional screen of chimeras across cell lines representing a wide variety of cancers. We used state-of-the-art chimeric RNA prediction software to create a database of chimeric RNAs across 1017 cell lines from The Cancer Cell Line Encyclopedia. For each chimera we assessed factors such as frequency, recurrence, breakpoint coordinates, frame, and coding potential. To identify specific functional transcripts, we integrated publicly available shRNA knockdown data with our predictions and developed an in-silico functional analysis pipeline comparing differential knockdown effects between chimera and corresponding parental transcripts. For each transcript we assessed the average fold change of chimera-mapping probes, a function score defined as the difference between the fold change of chimera-mapping and parent-specific probes, and a p-value assessing the confidence of our functional score. From our initial screen of 127,819 transcripts, we identified 1088 high-confidence functional chimeras. We successfully identified nearly all known functional chimeras screened including PAX3-FOXO1, EWSR1-FLI1, and TCF3-PBX1. We also identified previously unknown chimeras that that we predict have a function in cell growth and proliferation. Overall, the results of our study reveal a new landscape of functionally relevant chimeric transcripts in cancer. Follow-up studies can further investigate these transcripts to determine their potential as therapeutic targets. Citation Format: Samir Lalani, Sehajroop Gadh, Justin Elfman, Sandeep Singh, Hui Li. Differential dependency mapping of chimeric RNAs across cancer reveals a new landscape of functional fusion transcripts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4351.
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Rowsell, Joanna, Renata da Silva Camargo, William B. Langdon, Maria A. Stalteri, and Andrew P. Harrison. "Uncovering the expression patterns of chimeric transcripts using surveys of Affymetrix GeneChips." Journal of Integrative Bioinformatics 7, no. 3 (December 1, 2010): 300–330. http://dx.doi.org/10.1515/jib-2010-137.
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Summary Background: A chimeric transcript is a single RNA sequence which results from the transcription of two adjacent genes. Recent studies estimate that at least 4% of tandem human gene pairs may form chimeric transcripts. Affymetrix GeneChip data are used to study the expression patterns of tens of thousands of genes and the probe sequences used in these microarrays can potentially map to exotic RNA sequences such as chimeras.Results: We have studied human chimeras and investigated their expression patterns using large surveys of Affymetrix microarray data obtained from the Gene Expression Omnibus. We show that for six probe sets, a unique probe mapping to a transcript produced by one of the adjacent genes can be used to identify the expression patterns of readthrough transcripts. Furthermore, unique probes mapping to an intergenic exon present only in the MASK-BP3 chimera can be used directly to study the expression levels of this transcript.Conclusions: We have attempted to implement a new method for identifying tandem chimerism. In this analysis unambiguous probes are needed to measure run-off transcription and probes that map to intergenic exons are particularly valuable for identifying the expression of chimeras.
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Amundarain, Ane, Luis Vitores Valcárcel, Raquel Ordoñez, Leire Garate, Estíbaliz Miranda, Xabier Cendoya, Maria Jose Calasanz, et al. "Lncrnas As New Partners of Novel Chimeric Transcripts in Multiple Myeloma." Blood 134, Supplement_1 (November 13, 2019): 4356. http://dx.doi.org/10.1182/blood-2019-122568.
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Deregulation of long non-coding RNAs (lncRNAs) is a common feature of cancer, including Multiple Myeloma (MM). In our previous studies, we detected 11,495 and 40,511 previously non-annotated lncRNAs during normal humoral immune response and MM patient samples, respectively. These results support an important role for the lncRNAs transcriptome in this hematological malignancy. lncRNAs are genes that differ from coding genes in that they do not give rise to a protein. Nevertheless, lncRNA could undergo the same genetic alterations as coding genes. In this study, we hypothesize that lncRNAs can be involved in the principal genetic alterations occurring in MM such as chromosomal translocations, affecting the Immunoglobulin loci (IG) and in the majority of which the fusion partner still remains unknown. In order to unveil the role of lncRNAs in fusion transcripts occurring in MM, we analyzed the strand specific RNA-seq (ssRNA-seq) data obtained from 35 samples from different subpopulations of B cells (Naïve, Centroblast, Centrocyte, Memory and Plasma cells (PCs)), purified PCs from 32 MM patients and 3 MM cell lines. Chimeric transcripts were detected with the STAR-Fusion software, identifying 1,347 novel fusion transcripts ranging from 1 to 142 chimeric transcripts per sample. Strikingly, healthy PC samples (from tonsils and bone marrow) yielded the highest number of fusion transcripts, while other B cell subpopulations showed overall low numbers and MM samples turned out highly variable. 96% of all fusion transcripts detected in healthy PCs occurred with IG genes and harbored few reads per transcript, suggesting that the hyperactive transcription of the IG loci in PCs may be the cause for their formation and are probably not involved in the pathogenesis of the disease. We also found that HLA fusion transcripts were abundant in Naïve B cells, disappearing progressively during the humoral immune response (Figure 1). Interestingly, fusion transcripts identified in different B cell subpopulations were not detected in MM samples. Next, we focus on myeloma samples and identified 362 chimeric transcripts (312 unique) expressed specifically in MM (ranging from 2 to 24 chimeric transcripts per sample), most of them (84%) identified for the first time. 69% of these transcripts partnered with the IG genes, while the other fusions involved two non-IG genes. Interestingly, as we hypothesized, 26,5% of the chimeric transcripts in MM occurred with lncRNA as a partner, increasing the relevance of lncRNAs in this disease. Furthermore, using the read distribution per chimeric transcript, we identified a prevalent reciprocal transcript or a prevalent transcript expressed with >1 FFPM in 47% of MM samples, suggesting that they could derived from underlying genomic rearrangements. Besides these prevalent transcripts, we observed that 40% of the non-IG fusion transcripts occurred between adjacent genes, defining novel MM-transcriptional read-throughs, possibly caused by the oncogenic stress suffered by MM cells. Some of these chimeric transcripts were validated in different cell lines of MM by conventional PCR and sequencing. In summary, our findings show that ssRNA-seq data is an adequate strategy for the detection of chimeric transcripts in MM, being able to detect highly expressed chimeric transcripts that probably were derived from an underlying genomic rearrangements and also new categories of chimeric transcripts. In addition, our study reveals a complex landscape of fusion transcripts in the MM, many of them including a lncRNA, which could be potential therapeutic targets for the development of new treatment strategies for MM. Disclosures Paiva: Amgen, Bristol-Myers Squibb, Celgene, Janssen, Merck, Novartis, Roche, and Sanofi; unrestricted grants from Celgene, EngMab, Sanofi, and Takeda; and consultancy for Celgene, Janssen, and Sanofi: Consultancy, Honoraria, Research Funding, Speakers Bureau. San-Miguel:Amgen, Bristol-Myers Squibb, Celgene, Janssen, MSD, Novartis, Roche, Sanofi, and Takeda: Consultancy, Honoraria.
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Alterman, R. B., C. Sprecher, R. Graves, W. F. Marzluff, and A. I. Skoultchi. "Regulated expression of a chimeric histone gene introduced into mouse fibroblasts." Molecular and Cellular Biology 5, no. 9 (September 1985): 2316–24. http://dx.doi.org/10.1128/mcb.5.9.2316-2324.1985.
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The regulated expression of a mouse histone gene was studied by DNA-mediated gene transfer. A chimeric H3 histone gene was constructed by fusing the 5' and 3' portions of two different mouse H3 histone genes. Transfection of the chimeric gene into mouse fibroblasts resulted in the production of chimeric mRNA at levels nearly equal to that of the total endogenous H3 histone mRNAs. Most chimeric RNA transcripts had correct 5' and 3' termini, and the chimeric mRNA was translated into an H3.1 protein that accumulated in the nucleus of the transfected cells. Expression of the chimeric gene was studied under several conditions in which the rate of transcription and the stability of endogenous H3 transcripts change. Chimeric mRNA levels were regulated in parallel with endogenous H3 mRNAs, suggesting that cis-acting regulatory sequences lie within or near individual histone genes. In addition to correctly initiated and terminated chimeric mRNA, we also detected a novel H3 transcript containing an additional 250 bases at the 3' end. Surprisingly, the longer transcript is polyadenylated and accumulates in the cytoplasm.
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Alterman, R. B., C. Sprecher, R. Graves, W. F. Marzluff, and A. I. Skoultchi. "Regulated expression of a chimeric histone gene introduced into mouse fibroblasts." Molecular and Cellular Biology 5, no. 9 (September 1985): 2316–24. http://dx.doi.org/10.1128/mcb.5.9.2316.
Full textAbstract:
The regulated expression of a mouse histone gene was studied by DNA-mediated gene transfer. A chimeric H3 histone gene was constructed by fusing the 5' and 3' portions of two different mouse H3 histone genes. Transfection of the chimeric gene into mouse fibroblasts resulted in the production of chimeric mRNA at levels nearly equal to that of the total endogenous H3 histone mRNAs. Most chimeric RNA transcripts had correct 5' and 3' termini, and the chimeric mRNA was translated into an H3.1 protein that accumulated in the nucleus of the transfected cells. Expression of the chimeric gene was studied under several conditions in which the rate of transcription and the stability of endogenous H3 transcripts change. Chimeric mRNA levels were regulated in parallel with endogenous H3 mRNAs, suggesting that cis-acting regulatory sequences lie within or near individual histone genes. In addition to correctly initiated and terminated chimeric mRNA, we also detected a novel H3 transcript containing an additional 250 bases at the 3' end. Surprisingly, the longer transcript is polyadenylated and accumulates in the cytoplasm.
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Claxton, DF, P. Liu, HB Hsu, P. Marlton, J. Hester, F. Collins, AB Deisseroth, JD Rowley, and MJ Siciliano. "Detection of fusion transcripts generated by the inversion 16 chromosome in acute myelogenous leukemia." Blood 83, no. 7 (April 1, 1994): 1750–56. http://dx.doi.org/10.1182/blood.v83.7.1750.1750.
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Abstract Pericentric inversion of chromosome 16 [inv(16)(p13q22)] and the related t(16;16)(p13;q22) are seen in a subset of acute myelogenous leukemia (AML) phenotypically and prognostically differing from other cases. We have recently shown that inv(16) results in fusion of CBFB/PEBP2B, a gene encoded at 16q22 to MYH11, a smooth muscle myosin heavy chain gene encoded at 16p13. Chimeric transcripts consisting of upstream CBFB fused to downstream MYH11 coding sequences result from this fusion. In this study we have examined a series of 37 of these cases using reverse transcriptase-polymerase chain reaction (RT-PCR) to detect expression of a hybrid CBFB/MYH11 transcript. Chimeric cDNAs were detected in all but 1 of 37 leukemias with typical inv(16) or t(16;16). Such chimeric products were not seen in a case with inv(16)(p13q24) (ie, a variant q arm breakpoint) or any of 10 cases of AML without these chromosomal changes. Four different chimeric transcripts were found, representing differing fusion points within MYH11 spliced to position 495 of CBFB. Primer sets are described for efficient amplification of these different cDNA forms. Amplification of cDNA showed that all but 17 codons of the CBFB coding sequence are included in the abnormal transcripts. RT-PCR was shown to be highly sensitive and potentially useful for detection of leukemic cells during morphologic remission.
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Claxton, DF, P. Liu, HB Hsu, P. Marlton, J. Hester, F. Collins, AB Deisseroth, JD Rowley, and MJ Siciliano. "Detection of fusion transcripts generated by the inversion 16 chromosome in acute myelogenous leukemia." Blood 83, no. 7 (April 1, 1994): 1750–56. http://dx.doi.org/10.1182/blood.v83.7.1750.bloodjournal8371750.
Full textAbstract:
Pericentric inversion of chromosome 16 [inv(16)(p13q22)] and the related t(16;16)(p13;q22) are seen in a subset of acute myelogenous leukemia (AML) phenotypically and prognostically differing from other cases. We have recently shown that inv(16) results in fusion of CBFB/PEBP2B, a gene encoded at 16q22 to MYH11, a smooth muscle myosin heavy chain gene encoded at 16p13. Chimeric transcripts consisting of upstream CBFB fused to downstream MYH11 coding sequences result from this fusion. In this study we have examined a series of 37 of these cases using reverse transcriptase-polymerase chain reaction (RT-PCR) to detect expression of a hybrid CBFB/MYH11 transcript. Chimeric cDNAs were detected in all but 1 of 37 leukemias with typical inv(16) or t(16;16). Such chimeric products were not seen in a case with inv(16)(p13q24) (ie, a variant q arm breakpoint) or any of 10 cases of AML without these chromosomal changes. Four different chimeric transcripts were found, representing differing fusion points within MYH11 spliced to position 495 of CBFB. Primer sets are described for efficient amplification of these different cDNA forms. Amplification of cDNA showed that all but 17 codons of the CBFB coding sequence are included in the abnormal transcripts. RT-PCR was shown to be highly sensitive and potentially useful for detection of leukemic cells during morphologic remission.
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Fujieda, S., Y. Q. Lin, A. Saxon, and K. Zhang. "Multiple types of chimeric germ-line Ig heavy chain transcripts in human B cells: evidence for trans-splicing of human Ig RNA." Journal of Immunology 157, no. 8 (October 15, 1996): 3450–59. http://dx.doi.org/10.4049/jimmunol.157.8.3450.
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Abstract Germ-line transcripts from Ig heavy chain loci precede the occurrence of isotype switching and are thought to play an important though still controversial role in Ig class switching. In this study, we employed a reverse transcriptase-PCR approach to detect human chimeric Ig germ-line mRNA transcripts. Multiple types of chimeric Ig germ-line transcripts (Imu-Cepsilon, Iepsilon-Cmu, Imu-Cgamma4, Igamma-Cmu, Igamma-Cepsilon, Iepsilon-Cgamma, and Igamma4-Calpha1 transcripts) were readily detected in human B cells stimulated with IL-4 alone. Sequence analysis revealed that all of these chimeric Ig germ-line transcripts represented the I exons from one Ig locus spliced to the CH exons from another locus by using consensus sequences for splicing donor and acceptor sites, indicating that they were generated through splicing machinery. In the case of stimulation of human resting B cells with IL-4 alone, the chimeric Ig germ-line transcripts are likely derived from a trans-splicing mechanism, as the extensive searching did not find evidence that Ig class-switch recombination had occurred, which alternatively could give rise to chimeric Ig mRNA by mechanisms other than trans-splicing. Similarly, an EBV-transformed gamma2 rearranged B cell line, GM1500, which produces IgG2 and contains both gamma2 productive and epsilon germ-line transcripts, also expressed chimeric germ-line RNA (Iepsilon-Cgamma2) and epsilon-productive transcripts (VDJ-Cepsilon). This line had no further sequential Sgamma2-Sepsilon rearrangements, providing evidence that the productive VDJ-Cepsilon mRNA was derived from a transcriptionally active unrearranged epsilon gene locus by trans-splicing. Taken together, these results provide possible evidence that trans-splicing of germ-line Ig RNA transcripts occurs in human B cells.
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Zoubek, A., B. Dockhorn-Dworniczak, O. Delattre, H. Christiansen, F. Niggli, I. Gatterer-Menz, T. L. Smith, H. Jürgens, H. Gadner, and H. Kovar. "Does expression of different EWS chimeric transcripts define clinically distinct risk groups of Ewing tumor patients?" Journal of Clinical Oncology 14, no. 4 (April 1996): 1245–51. http://dx.doi.org/10.1200/jco.1996.14.4.1245.
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PURPOSE Because of the high heterogeneity of EWS gene fusions with FLI1 and ERG genes due to variable chromosomal breakpoint locations in Ewing tumors (ET) (14 different chimeric transcripts identified so far), we evaluated the clinical impact of the expression of diverse fusion transcripts in ET patients. PATIENTS AND METHODS In a European multicenter study, 147 ET were analyzed by reverse-transcriptase polymerase chain reaction (RT-PCR) and the molecular data statistically compared with all clinical data available. RESULTS Most tumors expressed chimeric transcripts with fusion of EWS exon 7 to FLI1 exon 6 (75 of 147) (type I) or five (39 of 147) and EWS exon 10 to FLI1 exon 5 (eight of 147) or 6 (five of 147). In five cases, chimerism between EWS exon 9 and FLI1 exons 4 and EWS exon 7 and FLI1 exon 7 or 8 was observed. Fifteen cases of EWS-ERG rearrangement were identified. In 85 of these patients treated in the European Cooperative Ewing Sarcoma Studies, molecular results were analyzed in comparison to age, sex, tumor localization, tumor volume, and disease extension. No significant correlation between the various fusion types and these features were observed. Relapse-free survival (RFS) for the 31 patients with localized disease and fusion type I tended to be longer compared with the 24 patients with localized tumors bearing other chimeric transcripts (P = .04). CONCLUSION Results suggest a possible advantage in PFS for patients with localized disease and fusion type I transcripts, although this will require prospective validation with a larger number of patients and longer follow-up periods.
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Katsuya, Hiroo, Paola Miyazato, Saiful Islam, Benjy Jek Yang Tan, Yuki Inada, Misaki Matsuo, Takaharu Ueno, et al. "The Presence and Possible Role of Virus-Host Chimeric Transcripts in Adult T-Cell Leukemia-Lymphoma." Blood 134, Supplement_1 (November 13, 2019): 2779. http://dx.doi.org/10.1182/blood-2019-124361.
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The retrovirus human T-cell leukemia virus type 1 (HTLV-1) integrates into the host genome and persists for the lifetime of the host. There are tens of thousands of different infected clones in a HTLV-1 carrier and each clone can be identified by its unique viral integration site. Only about 5% of infected people develop the hematological malignancy, adult T-cell leukemia-lymphoma (ATL). However, it is unclear how a certain infected clone, among various different ones, is selected as a malignant clone. It has been reported that viral integration alters transcripts of the cellular host genes adjacent to the integration site, even generating truncated or virus-host chimeric transcripts. Because each infected clone has a unique viral integration site, each clone possibly has unique virus-host chimeric transcripts, which were not present in the host before infection. Therefore, we hypothesized that the integrated provirus generates virus-host chimeric transcripts that may play a role in the clonal selection of the HTLV-1-infected cell. We previously reported HTLV-1 DNA-capture-seq using biotinylated DNA-probes for the viral genome, to increase the sensitivity and efficiency of viral-sequences detection. In this study, we used HTLV-1 RNA-capture-seq for PBMCs samples from ATL patients to test the hypothesis in a highly sensitive manner. The results showed the presence of chimeric transcripts in 19 out of 30 ATL patients. We next quantified the abundance of chimeric transcripts by droplet digital PCR, and found that the expression levels of chimeric transcripts were similar to those of viral RNAs containing splice junction of HBZ, in 5 of 19 chimeric transcripts positive ATL cases, although the levels varied among different ATL cases. To identify the whole sequences of the chimeric transcripts, we performed Oxford Nanopore sequencing. This approach revealed that the HTLV-1 provirus generates various splicing chimeric transcripts with the host genes in both viral sense and antisense orientations. The transcriptional start site of most of the sense chimeric transcripts was the R region of the 5'- or 3'-long terminal repeats (LTRs) in the proviral sequences, indicating that the chimeric transcripts were generated using the viral promoters because the LTRs work as a promoter for the viral transcripts. Given the structure of the chimeric transcripts with the viral promotors, the expression of the fused host genes could be enhanced by generating the chimeric transcripts. We evaluated the mRNA expression of the fused host genes of the chimeric transcripts by RNA-seq, and the results correlated with those obtained by ddPCR. To clarify the impact of viral integration on the clonal expansion, we analyzed HTLV-1-infected Jurkat cells. The clonality analysis of infected cells by HTLV-1 DNA-capture-seq showed that some infected clones were remarkably expanded for 4-6 months culture. We also confirmed that some of them harbored virus-host chimeric transcripts by HTLV-1 RNA-capture-seq. This study revealed the expression levels and the structures of virus-host chimeric transcripts in ATL patients. We are currently investigating the functional role of chimeric transcripts in the clonal proliferation of infected cells in vitro. Disclosures Uchimaru: Daiichi Sankyo Co., Ltd..: Research Funding. Kimura:Novartis: Honoraria, Research Funding; Ohara Pharmaceutical Co.: Research Funding.
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Davies, J. P., and A. R. Grossman. "Sequences controlling transcription of the Chlamydomonas reinhardtii beta 2-tubulin gene after deflagellation and during the cell cycle." Molecular and Cellular Biology 14, no. 8 (August 1994): 5165–74. http://dx.doi.org/10.1128/mcb.14.8.5165-5174.1994.
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In Chlamydomonas reinhardtii, transcripts from the beta 2-tubulin gene (tubB2), as well as those from other tubulin-encoding genes, accumulate immediately after flagellar excision as well as at a specific time in the cell cycle. Control of tubB2 transcript accumulation following deflagellation is regulated, at least partially, at the transcriptional level. We have fused the tubB2 promoter to the arylsulfatase (ars) reporter gene, introduced this construct into C. reinhardtii, and compared expression of the chimeric gene with that of the endogenous tubB2 gene. After flagellar excision, transcripts from the tubB2/ars chimeric gene accumulate with kinetics similar to those of transcripts from the endogenous tubB2 gene. The tubB2/ars transcripts also accumulate in a cell cycle-specific manner; however, chimeric transcripts are more abundant earlier in the cell cycle than the endogenous tubB2 transcripts. To elucidate transcriptional control of tubB2, we have mutated or removed sequences in the tubB2 promoter and examined the effect on transcription. The tubB2 promoter shares features with the promoters of other tubulin-encoding genes; these include a GC-rich region between the TATA box and the transcription initiation site and multiple copies of a 10-bp sequence motif that we call the tub box. The tubB2 gene contains seven tub box motifs. Changing the GC-rich region to an AT-rich region or removing three of the seven tub box motifs did not significantly affect transcription of the chimeric gene. However, removing four or five tub box motifs prevented increased transcription following deflagellation and diminished cell cycle-regulated transcription from the tubB2 promoter.
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Davies, J. P., and A. R. Grossman. "Sequences controlling transcription of the Chlamydomonas reinhardtii beta 2-tubulin gene after deflagellation and during the cell cycle." Molecular and Cellular Biology 14, no. 8 (August 1994): 5165–74. http://dx.doi.org/10.1128/mcb.14.8.5165.
Full textAbstract:
In Chlamydomonas reinhardtii, transcripts from the beta 2-tubulin gene (tubB2), as well as those from other tubulin-encoding genes, accumulate immediately after flagellar excision as well as at a specific time in the cell cycle. Control of tubB2 transcript accumulation following deflagellation is regulated, at least partially, at the transcriptional level. We have fused the tubB2 promoter to the arylsulfatase (ars) reporter gene, introduced this construct into C. reinhardtii, and compared expression of the chimeric gene with that of the endogenous tubB2 gene. After flagellar excision, transcripts from the tubB2/ars chimeric gene accumulate with kinetics similar to those of transcripts from the endogenous tubB2 gene. The tubB2/ars transcripts also accumulate in a cell cycle-specific manner; however, chimeric transcripts are more abundant earlier in the cell cycle than the endogenous tubB2 transcripts. To elucidate transcriptional control of tubB2, we have mutated or removed sequences in the tubB2 promoter and examined the effect on transcription. The tubB2 promoter shares features with the promoters of other tubulin-encoding genes; these include a GC-rich region between the TATA box and the transcription initiation site and multiple copies of a 10-bp sequence motif that we call the tub box. The tubB2 gene contains seven tub box motifs. Changing the GC-rich region to an AT-rich region or removing three of the seven tub box motifs did not significantly affect transcription of the chimeric gene. However, removing four or five tub box motifs prevented increased transcription following deflagellation and diminished cell cycle-regulated transcription from the tubB2 promoter.
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van der Reijden, BA, M. Lombardo, HG Dauwerse, RH Giles, D. Muhlematter, MJ Bellomo, HW Wessels, GC Beverstock, GJ van Ommen, and A. Hagemeijer. "RT-PCR diagnosis of patients with acute nonlymphocytic leukemia and inv(16)(p13q22) and identification of new alternative splicing in CBFB- MYH11 transcripts." Blood 86, no. 1 (July 1, 1995): 277–82. http://dx.doi.org/10.1182/blood.v86.1.277.bloodjournal861277.
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As acute nonlymphocytic leukemia (ANLL) with inv(16) (p13q22) or t(16;16)(p13;q22) has been shown to result from the fusion of transcription factor subunit core binding factor (CBFB) to a myosin heavy chain (MYH11), we sought to design methods to detect this rearrangement using reverse transcriptase-polymerase chain reaction (RT- PCR). In all of 27 inv(16)(p13q22) and four t(16;16)(p13;q22) cases tested, a chimeric CBFB-MYH11 transcript coding for an in-frame fusion protein was detected. In a more extensive RT-PCR analysis with different primer pairs, we detected a second new chimeric CBFB-MYH11 transcript in 10 of 11 patients tested. The CBFB-MYH11 reading frame of the second transcript was maintained in one patient but not in the others. We show that the different CBFB-MYH11 transcripts in one patient arise from alternative splicing. Translation of the transcript in which the CBFB-MYH11 reading frame is not maintained leads to a slightly truncated CBFB protein.
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Chu, J. L., J. Drappa, A. Parnassa, and K. B. Elkon. "The defect in Fas mRNA expression in MRL/lpr mice is associated with insertion of the retrotransposon, ETn." Journal of Experimental Medicine 178, no. 2 (August 1, 1993): 723–30. http://dx.doi.org/10.1084/jem.178.2.723.
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Fas is a cell surface protein of the tumor necrosis factor receptor, nerve growth factor receptor, CD40 family, and is involved in the control of lymphocyte apoptosis. A mutation in the Fas gene in MRL/lpr mice results in massive lymphoproliferation (lpr) and accelerated autoimmunity. To further study the nature of this defect, Fas mRNA expression was evaluated by reverse transcriptase polymerase chain reaction as well as by Northern blotting. These studies revealed that the wild-type Fas message was produced at approximately 10-fold lower levels in the lpr compared with the ++ substrain of MRL mice. In addition to the wild-type transcript, lpr mice also synthesized chimeric transcripts containing an insertion of the early retrotransposon (ETn). Molecular cloning and nucleotide sequencing of a Fas-ETn chimeric cDNA suggested that the striking reduction in wild-type Fas mRNA levels and the presence of aberrant transcripts in MRL/lpr mice are most likely explained by the insertion of the ETn retrotransposon into an intron of the Fas gene and induction of alternative splicing involving the 5' ETn long terminal repeat.
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Cornell, Christopher T., Jo Ellen Brunner, and Bert L. Semler. "Differential Rescue of Poliovirus RNA Replication Functions by Genetically Modified RNA Polymerase Precursors." Journal of Virology 78, no. 23 (December 1, 2004): 13007–18. http://dx.doi.org/10.1128/jvi.78.23.13007-13018.2004.
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ABSTRACT We have previously described the RNA replication properties of poliovirus transcripts harboring chimeric RNA polymerase sequences representing suballelic exchanges between poliovirus type 1 (PV1) and coxsackievirus B3 (CVB3) utilizing an in vitro translation and RNA replication assay (C. Cornell, R. Perera, J. E. Brunner, and B. L. Semler, J. Virol. 78:4397-4407, 2004). We showed that three of the seven chimeras were capable of RNA replication in vitro, although replication levels were greatly reduced compared to that of wild-type transcripts. Interestingly, one of the replication-competent transcripts displayed a strand-specific RNA synthesis defect suggesting (i) a differential replication complex assembly mechanism involving 3D and/or precursor molecules (i.e., 3CD) required for negative- versus positive-strand RNA synthesis or (ii) effect(s) on the ability of the 3D polymerase to form higher-ordered structures required for positive-strand RNA synthesis. In this study, we have attempted to rescue defective RNA replication in vitro by cotranslating nonstructural proteins from a transcript encoding a large precursor polyprotein (P3) to complement 3D polymerase and/or precursor polypeptide functions altered in each of the chimeric constructs. Utilization of a wild-type P3 construct revealed that all transcripts containing chimeric PV1/CVB3 polymerase sequences can be complemented in trans for both negative- and positive-strand RNA synthesis. Furthermore, data from experiments utilizing genetically modified forms of the P3 polyprotein, containing mutations within 3C or 3D sequences, strongly suggest the existence of different protein-protein and protein-RNA interactions required for positive- versus negative-strand RNA synthesis. These results, combined with data from in vitro RNA elongation assays, indicate that the delivery of active 3D RNA polymerase to replication complexes requires a series of macromolecular interactions that rely on the presence of specific 3D amino acid sequences.
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Mukherjee, Sunanda Biswas, Rajesh Detroja, Sumit Mukherjee, and Milana Frenkel-Morgenstern. "The Landscape of Expressed Chimeric Transcripts in the Blood of Severe COVID-19 Infected Patients." Viruses 15, no. 2 (February 4, 2023): 433. http://dx.doi.org/10.3390/v15020433.
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The ongoing COVID-19 pandemic caused by SARS-CoV-2 infections has quickly developed into a global public health threat. COVID-19 patients show distinct clinical features, and in some cases, during the severe stage of the condition, the disease severity leads to an acute respiratory disorder. In spite of several pieces of research in this area, the molecular mechanisms behind the development of disease severity are still not clearly understood. Recent studies demonstrated that SARS-CoV-2 alters the host cell splicing and transcriptional response to overcome the host immune response that provides the virus with favorable conditions to replicate efficiently within the host cells. In several disease conditions, aberrant splicing could lead to the development of novel chimeric transcripts that could promote the functional alternations of the cell. As severe SARS-CoV-2 infection was reported to cause abnormal splicing in the infected cells, we could expect the generation and expression of novel chimeric transcripts. However, no study so far has attempted to check whether novel chimeric transcripts are expressed in severe SARS-CoV-2 infections. In this study, we analyzed several publicly available blood transcriptome datasets of severe COVID-19, mild COVID-19, other severe respiratory viral infected patients, and healthy individuals. We identified 424 severe COVID-19 -specific chimeric transcripts, 42 of which were recurrent. Further, we detected 189 chimeric transcripts common to severe COVID-19 and multiple severe respiratory viral infections. Pathway and gene enrichment analysis of the parental genes of these two subsets of chimeric transcripts reveals that these are potentially involved in immune-related processes, interferon signaling, and inflammatory responses, which signify their potential association with immune dysfunction leading to the development of disease severity. Our study provides the first detailed expression landscape of chimeric transcripts in severe COVID-19 and other severe respiratory viral infections.
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Haqshenas, G., X. Dong, H. Netter, J. Torresi, and E. J. Gowans. "A chimeric GB virus B encoding the hepatitis C virus hypervariable region 1 is infectious in vivo." Journal of General Virology 88, no. 3 (March 1, 2007): 895–902. http://dx.doi.org/10.1099/vir.0.82467-0.
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Two GB virus B (GBV-B) chimeric genomes, GBV-HVR and GBV-HVRh (with a hinge), containing the coding region of the immunodominant hypervariable region 1 (HVR1) of the E2 envelope protein of Hepatitis C virus (HCV) were constructed. Immunoblot analysis confirmed that HVR1 was anchored to the GBV-B E2 protein. To investigate the replication competence and in vivo stability of in vitro-generated chimeric RNA transcripts, two naïve marmosets were inoculated intrahepatically with the transcripts. The GBV-HVR chimeric genome was detectable for 2 weeks post-inoculation (p.i.), whereas GBV-HVRh reverted to wild type 1 week p.i. Sequencing analysis of the HVR1 and flanking regions from GBV-HVR RNA isolated from marmoset serum demonstrated that the HVR1 insert remained unaltered in the GBV-HVR chimera for 2 weeks. Inoculation of a naïve marmoset with serum collected at 1 week p.i. also resulted in viraemia and confirmed that the serum contained infectious particles. All animals cleared the infection by 3 weeks p.i. and remained negative for the remaining weeks. The chimera may prove useful for the in vivo examination of any HCV HVR1-based vaccine candidates.
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Frenkel-Morgenstern, M., V. Lacroix, I. Ezkurdia, Y. Levin, A. Gabashvili, J. Prilusky, A. del Pozo, et al. "Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts." Genome Research 22, no. 7 (May 15, 2012): 1231–42. http://dx.doi.org/10.1101/gr.130062.111.
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Linheiro, Raquel, and John Archer. "Quantification of the effects of chimerism on read mapping, differential expression and annotation following short-read de novo assembly." F1000Research 11 (January 31, 2022): 120. http://dx.doi.org/10.12688/f1000research.108489.1.
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Background: De novo assembly is often required for analysing short-read RNA sequencing data. An under-characterized aspect of the contigs produced is chimerism, the extent to which affects mapping, differential expression analysis and annotation. Despite long-read sequencing negating this issue, short-reads remain in use through on-going research and archived datasets created during the last two decades. Consequently, there is still a need to quantify chimerism and its effects. Methods: Effects on mapping were quantified by simulating reads off the Drosophila melanogaster cDNA library and mapping these to related reference sets containing increasing levels of chimerism. Next, ten read datasets were simulated and divided into two conditions where, within one, reads representing 1000 randomly selected transcripts were over-represented across replicates. Differential expression analysis was performed iteratively with increasing chimerism within the reference set. Finally, an expectation of r-squared values describing the relationship between alignment and transcript lengths for matches involving cDNA library transcripts and those within sets containing incrementing chimerism was created. Similar values calculated for contigs produced by three graph-based assemblers, relative to the cDNA library from which input reads were simulated, or sequenced (relative to the species represented), were compared. Results: At 5% and 95% chimerism within reference sets, 100% and 77% of reads still mapped, making mapping success a poor indicator of chimerism. At 5% chimerism, of the 1000 transcripts selected for over-representation, 953 were identified during differential expression analysis; at 10% 936 were identified, while at 95% it was 510. This indicates that despite mapping success, per-transcript counts are unpredictably altered. R-squared values obtained for the three assemblers suggest that between 5-15% of contigs are chimeric. Conclusions: Although not evident based on mapping, chimerism had a significant impact on differential expression analysis and megablast identification. This will have consequences for past and present experiments involving short-reads.
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Bhardwaj, Anjana, Shiyanth Thevasagayampillai, Sakuni Rankothgedera, Prisha Verma, Micah B. Castillo, Alexander C. Koh, Constance Albarracin, Preethi H. Gunaratne, and Isabelle Bedrosian. "Abstract 6077: Chimeric RNAs are abundantly expressed in precancerous breast tissue of sporadic breast cancer patients." Cancer Research 84, no. 6_Supplement (March 22, 2024): 6077. http://dx.doi.org/10.1158/1538-7445.am2024-6077.
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Abstract Background: Immuno-prevention efforts in breast cancer (BC) have been hampered by the lack of known neoantigenic targets that can be used for a cancer prevention vaccine. RNA fusions represent attractive candidates as these are more immunogenic than insertion/deletion mutations and are substantial source of neoantigens. The objective of this study was to characterize chimeric RNAs in precancerous breast tissue. Methodology: Novel RNA fusions were identified by mining the sequence reads from RNA sequencing of 25 Her2 positive, 25 hormone receptor positive (HR) and 25 triple negative (TN) breast tumors and paired histologically normal tissues by Qiagen’s CLC pipeline. Breast samples from women undergoing breast reduction surgery were used as controls to exclude normal tissue associated chimeric mRNAs from analysis. Neoantigen prediction was performed by MHCnuggets. Chimeric mRNAs were validated by PCR. Ribosomal profiling was performed to assess if fusion transcripts are engaged with ribosomes. Results: A median of 36 novel RNA fusions (range 7-877) were identified in the tumor samples. In line with high genomic instability of TNBC subtype of BC, about 1/3 of the TN tumors expressed greater than 300 RNA fusions. In order to identify RNA fusions that are relevant for BC prevention, we investigated the presence of RNA fusions in the paired histologically normal samples as compared to the index tumor. We restricted these analyses to top 20 fusion transcripts that were present across the set of 75 tumor samples and also detected in 1 or more of the TCGA samples. Interestingly, we found that more than 1/3 of the histologically normal samples express at least 1 of the top 20 RNA fusions. When compared to the corresponding tumor, we found up to 50% of the paired normal tissue expressed RNA fusions identified in the tumor, supporting a role for these chimeric mRNA as an early molecular change during breast tumorigenesis. To validate the robustness of the prediction pipeline, PCR validation was performed for the chimeric mRNA with highest prevalence, NSFP1- LRRC37A2 which confirmed the presence of the transcript in 72% (13/18) of the predicted positive patient samples. MHCnuggets pipeline predicted 15 neopeptides from intergenically spliced chimeric NSFP1 [Exon 1-13] - LRRC37A2 [Exon 2-14], ¼ of which we validated to be immunogenic by ELISA. In order to confirm that the translation of the chimeric NSFP1- LRRC37A2 transcript, we investigated their enrichment in polysome enriched fraction obtained from a BC cell line confirmed to express the fusion transcript by PCR. Enrichment of transcripts in the polysomal fraction confirmed that these transcripts are likely to be translated. Conclusions: RNA fusions are frequently present in at risk breast tissue and are the source of substantial number of neoantigens. These RNA fusion- derived neoantigens may provide novel opportunities for developing vaccines for BC prevention. Citation Format: Anjana Bhardwaj, Shiyanth Thevasagayampillai, Sakuni Rankothgedera, Prisha Verma, Micah B. Castillo, Alexander C. Koh, Constance Albarracin, Preethi H. Gunaratne, Isabelle Bedrosian. Chimeric RNAs are abundantly expressed in precancerous breast tissue of sporadic breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6077.
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Hiorns, LR, T. Min, GJ Swansbury, A. Zelent, MJ Dyer, and D. Catovsky. "Interstitial insertion of retinoic acid receptor-alpha gene in acute promyelocytic leukemia with normal chromosomes 15 and 17." Blood 83, no. 10 (May 15, 1994): 2946–51. http://dx.doi.org/10.1182/blood.v83.10.2946.2946.
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Abstract The translocation t(15;17)(q22;q21) is seen exclusively in patients with acute promyelocytic leukemia (APL) and in the promyelocytic blast crisis of chronic myeloid leukemia (CML). This translocation juxta- poses the promyelocytic leukemia (PML) gene on chromosome 15 and the retinoic acid receptor-alpha (RARA) gene on chromosome 17, resulting in the formation of a chimeric mRNA transcript. We describe a patient with the microgranular variant form of APL, with no detectable cytogenetic abnormality of either chromosomes 15 or 17, who nevertheless had juxtaposition of PML and RARA genes and expressed a chimeric transcript. Conventional cytogenetics showed the karyotype 46,XY,d- er(3)t(3;8)(p25;q12). Fluorescent in situ hybridization (FISH) with paints for chromosomes 8, 15, and 17 confirmed the presence of structurally intact chromosomes 15 and 17 and trisomy for chromosome 8q. Nevertheless, FISH using cosmid probes for PML and RARA showed their juxtaposition on one chromosome 15 homolog. Both genes were also present on their normal homologs; in addition, part of the RARA gene was still present on the remaining chromosome 17. DNA analysis by Southern blotting, performed with a variety of probes including PML, RARA and retinoic acid receptor-beta (RARB), showed a rearrangement in PML. Reverse transcriptase polymerase chain reaction (RT-PCR) confirmed the existence of hybrid transcripts of 276, 455 bp and 623 bp, from PML- RARA on the der(15) chromosome, consistent with alternate exon splicing of the long form of the transcript occurring in 50% to 60% of patients with APL. Our results show that APL patients with cytogenetically normal chromosomes 15 and 17 may, nevertheless, have involvement of both PML and RARA genes defining a subgroup of APL, t(15;17)- negative/PML-RARA-positive which is analogous to Philadelphia chromosome-negative/BCR-ABL-positive CML. In this case, the presence of chimeric transcripts suggests that treatment with all-trans RA may be warranted in APL, even in the absence of detectable cytogenetic change, showing the usefulness of RT-PCR or FISH to aid diagnosis.
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Pan, Jun, Shulin Wei, Qunnan Qiu, Xinyu Tong, Zeen Shen, Min Zhu, Xiaolong Hu, and Chengliang Gong. "A novel chimeric RNA originating from BmCPV S4 and Bombyx mori HDAC11 transcripts regulates virus proliferation." PLOS Pathogens 19, no. 12 (December 4, 2023): e1011184. http://dx.doi.org/10.1371/journal.ppat.1011184.
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Polymerases encoded by segmented negative-strand RNA viruses cleave 5’-m7G-capped host transcripts to prime viral mRNA synthesis (“cap-snatching”) to generate chimeric RNA, and trans-splicing occurs between viral and cellular transcripts. Bombyx mori cytoplasmic polyhedrosis virus (BmCPV), an RNA virus belonging to Reoviridae, is a major pathogen of silkworm (B. mori). The genome of BmCPV consists of 10 segmented double-stranded RNAs (S1-S10) from which viral RNAs encoding a protein are transcribed. In this study, chimeric silkworm-BmCPV RNAs, in which the sequence derived from the silkworm transcript could fuse with both the 5’ end and the 3’ end of viral RNA, were identified in the midgut of BmCPV-infected silkworms by RNA_seq and further confirmed by RT-PCR and Sanger sequencing. A novel chimeric RNA, HDAC11-S4 RNA 4, derived from silkworm histone deacetylase 11 (HDAC11) and the BmCPV S4 transcript encoding viral structural protein 4 (VP4), was selected for validation by in situ hybridization and Northern blotting. Interestingly, our results indicated that HDAC11-S4 RNA 4 was generated in a BmCPV RNA-dependent RNA polymerase (RdRp)-independent manner and could be translated into a truncated BmCPV VP4 with a silkworm HDAC11-derived N-terminal extension. Moreover, it was confirmed that HDAC11-S4 RNA 4 inhibited BmCPV proliferation, decreased the level of H3K9me3 and increased the level of H3K9ac. These results indicated that during infection with BmCPV, a novel mechanism, different from that described in previous reports, allows the genesis of chimeric silkworm-BmCPV RNAs with biological functions.
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Djebali, S., B. Rodríguez Martín, E. Palumbo, D. D. Pervouchine, A. Breschi, C. Davis, A. Dobin, et al. "S0103 Recurrent chimeric transcripts in human and mouse." Journal of Animal Science 94, suppl_4 (September 1, 2016): 3. http://dx.doi.org/10.2527/jas2016.94supplement43x.
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Djebali, S., B. Rodríguez Martín, E. Palumbo, D. D. Pervouchine, A. Breschi, C. Davis, A. Dobin, et al. "0414 Recurrent chimeric transcripts in human and mouse." Journal of Animal Science 94, suppl_5 (October 1, 2016): 200–201. http://dx.doi.org/10.2527/jam2016-0414.
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Frenkel-Morgenstern, Milana, Alessandro Gorohovski, Dunja Vucenovic, Lorena Maestre, and Alfonso Valencia. "ChiTaRS 2.1—an improved database of the chimeric transcripts and RNA-seq data with novel sense–antisense chimeric RNA transcripts." Nucleic Acids Research 43, no. D1 (November 20, 2014): D68—D75. http://dx.doi.org/10.1093/nar/gku1199.
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Lee, MS, KS Chang, EJ Freireich, HM Kantarjian, M. Talpaz, JM Trujillo, and SA Stass. "Detection of minimal residual bcr/abl transcripts by a modified polymerase chain reaction." Blood 72, no. 3 (September 1, 1988): 893–97. http://dx.doi.org/10.1182/blood.v72.3.893.893.
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Abstract The Philadelphia (Ph1) chromosome in chronic myelogenous leukemia (CML) involves reciprocal translocation of the bcr gene and the c-abl oncogene. The fused bcr/abl gene is transcribed into two types of chimeric mRNA. By means of a combined method of S1 nuclease protection and polymerase chain reaction, we amplified sequences representative of the chimeric bcr/abl transcripts. Only 5 micrograms of total cellular RNA is needed and the chimeric bcr/abl message can be detected at a dilution of 1:100,000. We also detected residual chimeric bcr/abl transcripts in the remission samples from two Ph1-positive CML patients. This technique has the potential to identify a subpopulation of Ph1-positive CML patients in remission who are at high risk of relapse.
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Lee, MS, KS Chang, EJ Freireich, HM Kantarjian, M. Talpaz, JM Trujillo, and SA Stass. "Detection of minimal residual bcr/abl transcripts by a modified polymerase chain reaction." Blood 72, no. 3 (September 1, 1988): 893–97. http://dx.doi.org/10.1182/blood.v72.3.893.bloodjournal723893.
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The Philadelphia (Ph1) chromosome in chronic myelogenous leukemia (CML) involves reciprocal translocation of the bcr gene and the c-abl oncogene. The fused bcr/abl gene is transcribed into two types of chimeric mRNA. By means of a combined method of S1 nuclease protection and polymerase chain reaction, we amplified sequences representative of the chimeric bcr/abl transcripts. Only 5 micrograms of total cellular RNA is needed and the chimeric bcr/abl message can be detected at a dilution of 1:100,000. We also detected residual chimeric bcr/abl transcripts in the remission samples from two Ph1-positive CML patients. This technique has the potential to identify a subpopulation of Ph1-positive CML patients in remission who are at high risk of relapse.
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Magro, Gaetano, Giuseppe Broggi, Angelica Zin, Vincenzo Di Benedetto, Mariaclaudia Meli, Andrea Di Cataldo, Rita Alaggio, and Lucia Salvatorelli. "Desmoplastic Small Round Cell Tumor with “Pure” Spindle Cell Morphology and Novel EWS-WT1 Fusion Transcript: Expanding the Morphological and Molecular Spectrum of This Rare Entity." Diagnostics 11, no. 3 (March 18, 2021): 545. http://dx.doi.org/10.3390/diagnostics11030545.
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Background: Desmoplastic small round cell tumor (DSRCT) is a rare pediatric soft tissue neoplasm composed of small round tumor cells with prominent stromal desmoplasia, polyphenotypic differentiation and EWSR1-WT1 gene fusion. We, herein, present a unique case of DSRCT, exhibiting a pure spindle cell morphology, absence of desmoplastic stroma and showing a novel EWS-WT1 fusion transcript. Methods: A 12-year-old boy presented multiple intra-abdominal, confluent and mass-forming nodules that affected the entire abdominal and pelvic cavities. Results: Histologically, the nodules were composed of spindle cells with scant cytoplasm and oval nuclei arranged into short, intersecting fascicles and set in a scant, non-desmoplastic, stroma. Immunohistochemically, neoplastic cells were stained with vimentin, desmin, WT-1 (C-terminus antibodies) and EMA. Reverse-transcriptase polymerase chain reaction (RT-PCR) analysis showed the presence of an unusual chimeric transcript, composed of an in-frame junction of exon 9 of EWS to exon 7 of WT1, confirming the histological diagnosis of DSRCT. Conclusions: The present case contributes to widen the morphological spectrum of this entity; notably, the additional presence of a novel chimeric fusion transcript contributes to making the present case even more unique. Whether the detection of the above-mentioned fusion transcripts could explain the unusual morphology of the tumor remains to be established.
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Chang, Na, Jie Yi, Gaier Guo, Xinwen Liu, Yongfeng Shang, Tanjun Tong, Qinghua Cui, Ming Zhan, Myriam Gorospe, and Wengong Wang. "HuR Uses AUF1 as a Cofactor To Promote p16INK4 mRNA Decay." Molecular and Cellular Biology 30, no. 15 (May 24, 2010): 3875–86. http://dx.doi.org/10.1128/mcb.00169-10.
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ABSTRACT In this study, we show that HuR destabilizes p16INK4 mRNA. Although the knockdown of HuR or AUF1 increased p16 expression, concomitant AUF1 and HuR knockdown had a much weaker effect. The knockdown of Ago2, a component of the RNA-induced silencing complex (RISC), stabilized p16 mRNA. The knockdown of HuR diminished the association of the p16 3′ untranslated region (3′UTR) with AUF1 and vice versa. While the knockdown of HuR or AUF1 reduced the association of Ago2 with the p16 3′UTR, Ago2 knockdown had no influence on HuR or AUF1 binding to the p16 3′UTR. The use of EGFP-p16 chimeric reporter transcripts revealed that p16 mRNA decay depended on a stem-loop structure present in the p16 3′UTR, as HuR and AUF1 destabilized EGFP-derived chimeric transcripts bearing wild-type sequences but not transcripts with mutations in the stem-loop structure. In senescent and HuR-silenced IDH4 human diploid fibroblasts, the EGFP-p16 3′UTR transcript was more stable. Our results suggest that HuR destabilizes p16 mRNA by recruiting the RISC, an effect that depends on the secondary structure of the p16 3′UTR and requires AUF1 as a cofactor.
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Mätlik, Kert, Kaja Redik, and Mart Speek. "L1 Antisense Promoter Drives Tissue-Specific Transcription of Human Genes." Journal of Biomedicine and Biotechnology 2006 (2006): 1–16. http://dx.doi.org/10.1155/jbb/2006/71753.
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Transcription of transposable elements interspersed in the genome is controlled by complex interactions between their regulatory elements and host factors. However, the same regulatory elements may be occasionally used for the transcription of host genes. One such example is the human L1 retrotransposon, which contains an antisense promoter (ASP) driving transcription into adjacent genes yielding chimeric transcripts. We have characterized 49 chimeric mRNAs corresponding to sense and antisense strands of human genes. Here we show that L1 ASP is capable of functioning as an alternative promoter, giving rise to a chimeric transcript whose coding region is identical to the ORF of mRNA of the following genes:KIAA1797,CLCN5, andSLCO1A2. Furthermore, in these cases the activity of L1 ASP is tissue-specific and may expand the expression pattern of the respective gene. The activity of L1 ASP is tissue-specific also in cases where L1 ASP produces antisense RNAs complementary toCOL11A1andBOLLmRNAs. Simultaneous assessment of the activity of L1 ASPs in multiple loci revealed the presence of L1 ASP-derived transcripts in all human tissues examined. We also demonstrate that L1 ASP can act as a promoter in vivo and predict that it has a heterogeneous transcription initiation site. Our data suggest that L1 ASP-driven transcription may increase the transcriptional flexibility of several human genes.
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Lasa, Marina, Kamal R. Mahtani, Andrew Finch, Gary Brewer, Jeremy Saklatvala, and Andrew R. Clark. "Regulation of Cyclooxygenase 2 mRNA Stability by the Mitogen-Activated Protein Kinase p38 Signaling Cascade." Molecular and Cellular Biology 20, no. 12 (June 15, 2000): 4265–74. http://dx.doi.org/10.1128/mcb.20.12.4265-4274.2000.
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ABSTRACT A tetracycline-regulated reporter system was used to investigate the regulation of cyclooxygenase 2 (Cox-2) mRNA stability by the mitogen-activated protein kinase (MAPK) p38 signaling cascade. The stable β-globin mRNA was rendered unstable by insertion of the 2,500-nucleotide Cox-2 3′ untranslated region (3′ UTR). The chimeric transcript was stabilized by a constitutively active form of MAPK kinase 6, an activator of p38. This stabilization was blocked by SB203580, an inhibitor of p38, and by two different dominant negative forms of MAPK-activated protein kinase 2 (MAPKAPK-2), a kinase lying downstream of p38. Constitutively active MAPKAPK-2 was also able to stabilize chimeric β-globin–Cox-2 transcripts. The MAPKAPK-2 substrate hsp27 may be involved in stabilization, as β-globin–Cox-2 transcripts were partially stabilized by phosphomimetic mutant forms of hsp27. A short (123-nucleotide) fragment of the Cox-2 3′ UTR was necessary and sufficient for the regulation of mRNA stability by the p38 cascade and interacted with a HeLa protein immunologically related to AU-rich element/poly(U) binding factor 1.
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W. Zuccherato, Luciana, Benjamin Alleva, Marjorie A. Whiters, Claudia M. B. Carvalho, and James R. Lupski. "Chimeric transcripts resulting from complex duplications in chromosome Xq28." Human Genetics 135, no. 2 (December 14, 2015): 253–56. http://dx.doi.org/10.1007/s00439-015-1614-x.
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Lee, Ja-Rang, Yi-Deun Jung, Yun-Ji Kim, Hee-Eun Lee, HoIm Jeong, and Heui-Soo Kim. "Identification of L1ASP-derived chimeric transcripts in lung cancer." Genes & Genomics 36, no. 6 (September 5, 2014): 853–59. http://dx.doi.org/10.1007/s13258-014-0220-y.
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Frenkel-Morgenstern, Milana, and Alfonso Valencia. "Novel domain combinations in proteins encoded by chimeric transcripts." Bioinformatics 28, no. 12 (June 9, 2012): i67—i74. http://dx.doi.org/10.1093/bioinformatics/bts216.
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Olsen, Thale Kristin, Ioannis Panagopoulos, Ludmila Gorunova, Francesca Micci, Kristin Andersen, Hege Kilen Andersen, Torstein R. Meling, et al. "Novel fusion genes and chimeric transcripts in ependymal tumors." Genes, Chromosomes and Cancer 55, no. 12 (July 28, 2016): 944–53. http://dx.doi.org/10.1002/gcc.22392.
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Selleri, L., M. von Lindern, A. Hermans, D. Meijer, G. Torelli, and G. Grosveld. "Chronic myeloid leukemia may be associated with several bcr-abl transcripts including the acute lymphoid leukemia-type 7 kb transcript [see comments]." Blood 75, no. 5 (March 1, 1990): 1146–53. http://dx.doi.org/10.1182/blood.v75.5.1146.1146.
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Abstract In the majority of Philadelphia (Ph)-positive chronic myeloid leukemia (CML) patients, the c-abl gene is fused to the bcr gene, resulting in the transcription of an 8.5 kb chimeric bcr-abl mRNA, which is translated into a p210bcr-abl fusion protein. In about 50% of the Ph- positive acute lymphoid leukemias (ALL), the bcr-abl gene fusion is identical to CML, while in 50% an alternative fusion between these two genes occurs, in which the central bcr-sequences are absent. This results in transcription of a 7 kb bcr-abl mRNA, encoding a P190bcr-abl fusion protein. Cloning and sequencing of the chimeric part of bcr-abl cDNAs from two Ph-positive CML patients in chronic phase showed that in one patient, as in the Ph-positive ALL, all central bcr sequences are absent, while in the other patient, part of the bcr central sequences are deleted. Therefore, we speculate that the presence of the 7 kb chimeric ALL type mRNA in one of the patients is not sufficient to drive an acute rather than a chronic leukemic process in this case. The deletions of the central bcr-sequences described here define the minimal sequence requirement of the bcr-abl fusion gene in CML patients so far.
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Selleri, L., M. von Lindern, A. Hermans, D. Meijer, G. Torelli, and G. Grosveld. "Chronic myeloid leukemia may be associated with several bcr-abl transcripts including the acute lymphoid leukemia-type 7 kb transcript [see comments]." Blood 75, no. 5 (March 1, 1990): 1146–53. http://dx.doi.org/10.1182/blood.v75.5.1146.bloodjournal7551146.
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In the majority of Philadelphia (Ph)-positive chronic myeloid leukemia (CML) patients, the c-abl gene is fused to the bcr gene, resulting in the transcription of an 8.5 kb chimeric bcr-abl mRNA, which is translated into a p210bcr-abl fusion protein. In about 50% of the Ph- positive acute lymphoid leukemias (ALL), the bcr-abl gene fusion is identical to CML, while in 50% an alternative fusion between these two genes occurs, in which the central bcr-sequences are absent. This results in transcription of a 7 kb bcr-abl mRNA, encoding a P190bcr-abl fusion protein. Cloning and sequencing of the chimeric part of bcr-abl cDNAs from two Ph-positive CML patients in chronic phase showed that in one patient, as in the Ph-positive ALL, all central bcr sequences are absent, while in the other patient, part of the bcr central sequences are deleted. Therefore, we speculate that the presence of the 7 kb chimeric ALL type mRNA in one of the patients is not sufficient to drive an acute rather than a chronic leukemic process in this case. The deletions of the central bcr-sequences described here define the minimal sequence requirement of the bcr-abl fusion gene in CML patients so far.
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Ogawa, Hiroyasu, Hiroya Tamaki, Kazuhiro Ikegame, Toshihiro Soma, Manabu Kawakami, Akihiro Tsuboi, Eui Ho Kim, et al. "The usefulness of monitoring WT1 gene transcripts for the prediction and management of relapse following allogeneic stem cell transplantation in acute type leukemia." Blood 101, no. 5 (March 1, 2003): 1698–704. http://dx.doi.org/10.1182/blood-2002-06-1831.
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In acute-type leukemia, no method for the prediction of relapse following allogeneic stem cell transplantation based on minimal residual disease (MRD) levels is established yet. In the present study, MRD in 72 cases of allogeneic transplantation for acute myeloid leukemia, acute lymphoid leukemia, and chronic myeloid leukemia (accelerated phase or blast crisis) was monitored frequently by quantitating the transcript of WT1 gene, a “panleukemic MRD marker,” using reverse transcriptase–polymerase chain reaction. Based on the negativity of expression of chimeric genes, the background level of WT1 transcripts in bone marrow following allogeneic transplantation was significantly decreased compared with the level in healthy volunteers. The probability of relapse occurring within 40 days significantly increased step-by-step according to the increase in WT1 expression level (100% for 1.0 × 10−2-5.0 × 10−2, 44.4% for 4.0 × 10−3-1.0 × 10−2, 10.2% for 4.0 × 10−4-4.0 × 10−3, and 0.8% for < 4.0 × 10−4) when WT1 level in K562 was defined as 1.0). WT1 levels in patients having relapse increased exponentially with a constant doubling time. The doubling time of theWT1 level in patients for whom the discontinuation of immunosuppressive agents or donor leukocyte infusion was effective was significantly longer than that for patients in whom it was not (P < .05). No patients with a short doubling time of WT1 transcripts (< 13 days) responded to these immunomodulation therapies. These findings strongly suggest that the WT1 assay is very useful for the prediction and management of relapse following allogeneic stem cell transplantation regardless of the presence of chimeric gene markers.
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Alberti, S., M. Trerotola, R. Dell’ Arciprete, G. Vacca, B. Veronica, R. Cosmo, L. Rossana, R. Lattanzio, M. Piantelli, and E. Guerra. "Selective killing of human cancer cells by targeting a fusion mRNA between CYCLIN D1 and TROP2." Journal of Clinical Oncology 27, no. 15_suppl (May 20, 2009): e14569-e14569. http://dx.doi.org/10.1200/jco.2009.27.15_suppl.e14569.
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e14569 Background: Trop-2 is a calcium signal transducer and a stem cell marker. Trop-2 is widely overexpressed by human cancers and stimulates their growth. A TROP2 mRNA was isolated as post-transcriptionally joined to CYCLIN D1 transcripts, suggesting this as one of the transforming mechanisms of TROP2. Methods: In vitro cell growth assays were utilized to assess the cell growth stimulatory capacity of the chimeric mRNA. Colony assays for growth in soft agarose and tumorigenicity assays in nude mice were utilized to assess for the transforming capacity of the fusion transcript. siRNA constructs were utilized for the stably shut-down of the expression of the CYCLIN D1-TROP2 mRNA. Results: The chimeric mRNA transforms primary cells in vitro and induces aggressive tumor growth in vivo in cooperation with activated RAS. The CYCLIN D1-TROP2 mRNA is expressed by a large fraction of human ovarian, endometrial and gastro-intestinal tumors. The chimera is coexpressed with activated RAS in a subset of tumors, consistent with a cooperative transforming activity. The chimeric mRNA is a bicistronic transcript that independently translates wild type Cyclin D1 and Trop-2 proteins, i.e. it does not generate chimeric, oncogenic proteins. On the other hand, joining to the stable TROP2 mRNA leads to a higher CYCLIN D1 mRNA stability, with inappropriate persistence during the cell cycle and acquisition of transforming capacity. As essentially no normal tissues express the chimeric mRNA, we targeted it for destruction in cancer cells with stably expressed siRNA constructs. Specific targeting led to essential annnihilation of the CYCLIN D1-TROP2 mRNA, in the absence of off-target effects. Silencing of the chimeric mRNA blocked the growth of expressing breast cancer cells. Conclusions: Our findings demonstrate a novel, widespread oncogenic mechanism in human cancers, and open novel avenues for mRNA-targeted anti-cancer therapies. Acknowledgments This work was supported by the the Fondazione of the Cassa di Risparmio della Provincia di Chieti, the Association for the Application of Biotechnology in Oncology (ABO and ABO Project S.p.A., grant no. VE01D0019) and the Marie Curie Transfer of Knowledge Fellowship, contract number 014541. No significant financial relationships to disclose.
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Dalby, B., and D. M. Glover. "3′ non-translated sequences in Drosophila cyclin B transcripts direct posterior pole accumulation late in oogenesis and peri-nuclear association in syncytial embryos." Development 115, no. 4 (August 1, 1992): 989–97. http://dx.doi.org/10.1242/dev.115.4.989.
Full textAbstract:
We have characterised forms of the Drosophila cyclin B transcript that differ as a result of a splicing event which removes a nucleotide segment from the 3′ untranslated region. In oogenesis, both cyclin A RNA and a shorter form of the cyclin B transcript are seen in the cells of the germarium that are undergoing mitosis. The shorter cyclin B transcript alone is then detectable in the presumptive oocyte until stages 7–8 of oogenesis. Both cyclin A RNA and a longer form of the cyclin B RNA are then synthesised in the nurse cells during stages 9–11, to be deposited in the oocyte during stages 11–12. These transcripts become evenly distributed throughout the oocyte cytoplasm but, in addition, those of cyclin B become concentrated at the posterior pole. Examination of the distributions of RNAs transcribed from chimeric cyclin genes indicates that sequences in the 3′ untranslated region of the larger cyclin B RNA are required both for it to become concentrated at the posterior pole and to direct those transcripts in the body of the syncytial embryo to their peri-nuclear localisation. These sequences are disrupted by the splicing event which generates smaller cyclin B transcripts.
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Samani, Adrienne, Rylie M. Hightower, Andrea L. Reid, Katherine G. English, Michael A. Lopez, J. Scott Doyle, Michael J. Conklin, et al. "miR-486 is essential for muscle function and suppresses a dystrophic transcriptome." Life Science Alliance 5, no. 9 (May 5, 2022): e202101215. http://dx.doi.org/10.26508/lsa.202101215.
Full textAbstract:
miR-486 is a muscle-enriched microRNA, or “myomiR,” that has reduced expression correlated with Duchenne muscular dystrophy (DMD). To determine the function of miR-486 in normal and dystrophin-deficient muscles and elucidate miR-486 target transcripts in skeletal muscle, we characterized mir-486 knockout mice (mir-486 KO). mir-486 KO mice developed disrupted myofiber architecture, decreased myofiber size, decreased locomotor activity, increased cardiac fibrosis, and metabolic defects were exacerbated in mir-486 KO:mdx5cv (DKO) mice. To identify direct in vivo miR-486 muscle target transcripts, we integrated RNA sequencing and chimeric miRNA eCLIP sequencing to identify key transcripts and pathways that contribute towards mir-486 KO and dystrophic disease pathologies. These targets included known and novel muscle metabolic and dystrophic structural remodeling factors of muscle and skeletal muscle contractile transcript targets. Together, our studies identify miR-486 as essential for normal muscle function, a driver of pathological remodeling in dystrophin-deficient muscle, a useful biomarker for dystrophic disease progression, and highlight the use of multiple omic platforms to identify in vivo microRNA target transcripts.
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Hunger, SP, N. Galili, AJ Carroll, WM Crist, MP Link, and ML Cleary. "The t(1;19)(q23;p13) results in consistent fusion of E2A and PBX1 coding sequences in acute lymphoblastic leukemias." Blood 77, no. 4 (February 15, 1991): 687–93. http://dx.doi.org/10.1182/blood.v77.4.687.687.
Full textAbstract:
Abstract The t(1;19)(q23;p13) chromosomal translocation is observed cytogenetically in 25% of children with pre-B-cell acute lymphoblastic leukemia (ALL) and is associated with an adverse treatment outcome. The t(1;19) juxtaposes the E2A gene from chromosome 19 with the PBX1 gene on chromosome 1, leading to the production of fusion transcripts and resultant chimeric proteins that contain the transcriptional-activating motif of E2A and the DNA-binding homeodomain of PBX1. To investigate the molecular nature of E2A/PBX1 fusion in patients with t(1;19) ALL we used an RNA-based polymerase chain reaction (PCR) procedure to amplify a portion of the chimeric transcript. We detected E2A/PBX1 fusion transcripts in cells from 97% (37 of 38) of cases in which the t(1;19) had been observed cytogenetically. Molecular evidence of E2A/PBX1 fusion transcripts was also observed in a patient in whom a t(1;19) was not detected cytogenetically and in one patient with subclinical levels of minimal residual disease before overt clinical relapse. In all PCR- positive cases the junction of E2A and PBX1 coding sequences occurred at precisely the same location as demonstrated by hybridization of PCR products with a fusion site-specific detection oligonucleotide. These findings demonstrate the consistent fusion of E2A and PBX1 coding sequences resulting from t(1;19) and suggest that site-specific fusion of E2A and PBX1 is an important pathogenic event in t(1;19) ALL.
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Hunger, SP, N. Galili, AJ Carroll, WM Crist, MP Link, and ML Cleary. "The t(1;19)(q23;p13) results in consistent fusion of E2A and PBX1 coding sequences in acute lymphoblastic leukemias." Blood 77, no. 4 (February 15, 1991): 687–93. http://dx.doi.org/10.1182/blood.v77.4.687.bloodjournal774687.
Full textAbstract:
The t(1;19)(q23;p13) chromosomal translocation is observed cytogenetically in 25% of children with pre-B-cell acute lymphoblastic leukemia (ALL) and is associated with an adverse treatment outcome. The t(1;19) juxtaposes the E2A gene from chromosome 19 with the PBX1 gene on chromosome 1, leading to the production of fusion transcripts and resultant chimeric proteins that contain the transcriptional-activating motif of E2A and the DNA-binding homeodomain of PBX1. To investigate the molecular nature of E2A/PBX1 fusion in patients with t(1;19) ALL we used an RNA-based polymerase chain reaction (PCR) procedure to amplify a portion of the chimeric transcript. We detected E2A/PBX1 fusion transcripts in cells from 97% (37 of 38) of cases in which the t(1;19) had been observed cytogenetically. Molecular evidence of E2A/PBX1 fusion transcripts was also observed in a patient in whom a t(1;19) was not detected cytogenetically and in one patient with subclinical levels of minimal residual disease before overt clinical relapse. In all PCR- positive cases the junction of E2A and PBX1 coding sequences occurred at precisely the same location as demonstrated by hybridization of PCR products with a fusion site-specific detection oligonucleotide. These findings demonstrate the consistent fusion of E2A and PBX1 coding sequences resulting from t(1;19) and suggest that site-specific fusion of E2A and PBX1 is an important pathogenic event in t(1;19) ALL.
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Fazio, Grazia, Clelia Tiziana Storlazzi, Marco Severgnini, Valeria Cazzaniga, Luciana Impera, Giulia Daniele, Ilaria Iacobucci, et al. "Novel Chimeric Transcripts Involving PAX5 in B-Cell Precursor ALL." Blood 122, no. 21 (November 15, 2013): 1367. http://dx.doi.org/10.1182/blood.v122.21.1367.1367.
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Abstract PAX5, located on 9p13, belongs to the PAX gene family and encodes for a transcription factor essential for B lymphoid cell commitment. It functions both as a transcriptional activator and repressor of different target genes involved in lineages development. PAX5 has been recently reported to be target of aberrancies (including point mutation, deletions, and gene fusions), in approximately 30% of pediatric patients affected by BCP-ALL, the most frequent leukemia subset in children. Translocations are estimated to occur at an incidence of 2-3%, with a variety of partner genes, encoding for transcription factors (TEL, PML, FOXP1), kinases (JAK2), structural proteins (ELN, POM121) or molecules of unknown function (C20orf112, AUTS2). We performed a FISH-based study on an Italian cohort of BCP-ALL patients having 9p13 chromosomal rearrangement (as a hallmark of PAX5 rearrangement), and we identified novel PAX5 partner genes. Two pediatric patients were harboring a t(7;9)(q11.2;p13.2) with a PAX5/AUTS2 fusion transcript, thus confirming its recurrent alteration in pediatric B-ALL. Three novel partner genes of PAX5 were identified by FISH. SOX5 was found as a PAX5 partner in a pediatric patient harboring a dic(9;12)(p13;p13) chromosome. A further patient, showing a t(9;12)(p13;q34) translocation, revealed PAX5 as fused to a novel transcript isoform of CHFR, a gene widely expressed in a library of normal tissues. A third partner was identified in an adult B-ALL case, which showed a deletion within the short arm of chromosome 9, leading to the fusion of PAX5 to MLLT3. A fourth PAX-rearranged case, involving POM121C (different from the already described POM121) as fused to PAX5 in a t(7;9)(q11;p13) translocation, was identified by a RNAseq approach on BCP-ALL cases without known prognostic features. The breakpoint on chromosome 7q11 is similar to the one associated with PAX5/AUTS2. An accurate FISH analysis was performed on bone marrow cells of all cases to dissect the genomic breakpoints and the structure of the rearrangements. The fusion genes were cloned by 5’ and/or 3’ RACE PCR, confirmed by sequencing and verified by RT-PCR with specific primers on the source material. PAX5-translocated cases were further characterized by genome-wide Single Nucleotide Polymorphism array. Interestingly, Copy Number Variation analysis showed that a limited number of cooperative genetic lesions were present in addition to the translocation event, thus suggesting a primary role of the PAX rearrangement in leukemogenesis. We therefore hypothesize that PAX5 alterations may represent single genetic aberration events in a simple background, rather than being part of a complex scenario of cooperating genetic lesions involved in leukemogenesis. A common pathway for all PAX5 genomic lesions still need to be elucidated. Disclosures: No relevant conflicts of interest to declare.
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Sridhar, Aksheetha, Ankita S. More, Amruta R. Jadhav, Komal Patil, Anuj Mavlankar, Vaishnavi M. Dixit, and Sharmila A. Bapat. "Pattern recognition in the landscape of seemingly random chimeric transcripts." Computational and Structural Biotechnology Journal 21 (2023): 5153–64. http://dx.doi.org/10.1016/j.csbj.2023.10.028.
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Bishop, Kate N., Rebecca K. Holmes, and Michael H. Malim. "Antiviral Potency of APOBEC Proteins Does Not Correlate with Cytidine Deamination." Journal of Virology 80, no. 17 (September 1, 2006): 8450–58. http://dx.doi.org/10.1128/jvi.00839-06.
Full textAbstract:
ABSTRACT The human cytidine deaminases APOBEC3G (hA3G) and APOBEC3F (hA3F) are intracellular antiretroviral factors that can hypermutate nascent reverse transcripts and inhibit the replication of human immunodeficiency virus type 1 (HIV-1). Both enzymes have two cytidine deaminase motifs, although only the C-terminal motif is catalytic. Current models of APOBEC protein function imply editing is the principal mechanism of antiviral activity. In particular, hA3G is a more potent inhibitor of HIV-1 infectivity than hA3F and also induces a greater frequency of mutations in HIV-1 cDNA. We used hA3G/hA3F chimeric proteins to investigate whether cytidine deaminase potential reflects antiviral potency. We show here that the origin of the C-terminal deaminase motif is sufficient to determine the degree of mutation induced in a bacterial assay that measures mutations in chromosomal DNA. In contrast, this was not the case in the context of HIV-1 infection where the N-terminal deaminase motif also modulated the editing capabilities of the chimeras. Surprisingly, although three of the chimeric proteins induced levels of mutation that approximated those of parental hA3F, they displayed lower levels of antiviral activity. Most importantly, real-time PCR experiments revealed that the quantity of reverse transcripts detected in target cells, rather than the mutational burden carried by such DNAs, corresponded closely with viral infectivity. In other words, the antiviral phenotype of APOBEC proteins correlates with their ability to prevent the accumulation of reverse transcripts and not with the induction of hypermutation.
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Privitera, E., MP Kamps, Y. Hayashi, T. Inaba, LH Shapiro, SC Raimondi, F. Behm, L. Hendershot, AJ Carroll, and D. Baltimore. "Different molecular consequences of the 1;19 chromosomal translocation in childhood B-cell precursor acute lymphoblastic leukemia." Blood 79, no. 7 (April 1, 1992): 1781–88. http://dx.doi.org/10.1182/blood.v79.7.1781.1781.
Full textAbstract:
Abstract The prognostically important 1;19 chromosomal translocation can alter the E2A gene on chromosome 19p13 in childhood B-cell precursor acute lymphoblastic leukemia (ALL), leading to formation of a fusion gene (E2A-PBX1) that encodes a hybrid transcription factor with oncogenic potential. It is not known whether this molecular alteration is a uniform consequence of the t(1;19) or is restricted to translocation events within specific immunologic subtypes of the disease. Therefore, we studied leukemic cells from 25 cases of B-cell precursor ALL, with or without evidence of cytoplasmic Ig mu heavy chains (cIg); 17 cases had the t(1;19) by cytogenetic analysis. Leukemic cell DNA samples were analyzed by Southern blotting to detect alterations within the E2A genomic locus; a polymerase chain reaction assay was used to identify expression of chimeric E2A-pbx1 transcripts in leukemic cell RNA; and immunoblotting with anti-Pbx1 antibodies was used to detect hybrid E2A- Pbx1 proteins. Of 11 cases of cIg+ ALL with the t(1;19), 10 had E2A- pbx1 chimeric transcripts with identical junctions and a characteristic set of E2A-Pbx1 hybrid proteins. Each of these cases had E2A gene rearrangements, including the one in which fusion transcripts were not detected. By contrast, none of the six cases of t(1;19)-positive, cIg- ALL had evidence of rearranged E2A genomic restriction fragments, detectable E2A-pbx1 chimeric transcripts, or hybrid E2A-Pbx1 proteins. Typical chimeric E2A-pbx1 transcripts and proteins were detected in one of eight cIg+ leukemias in which the t(1;19) was not identified by cytogenetic analysis, emphasizing the increased sensitivity of molecular analysis for detection of this abnormality. We conclude that the molecular breakpoints in cases of cIg- B-cell precursor ALL with the t(1;19) differ from those in cIg+ cases with this translocation. Leukemias that express hybrid oncoproteins such as E2A-Pbx1 or Bcr-Abl have had a poor prognosis in most studies. Thus, molecular techniques to detect fusion genes and their aberrant products should allow more timely and appropriate treatment of these aggressive subtypes of the disease.
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Privitera, E., MP Kamps, Y. Hayashi, T. Inaba, LH Shapiro, SC Raimondi, F. Behm, L. Hendershot, AJ Carroll, and D. Baltimore. "Different molecular consequences of the 1;19 chromosomal translocation in childhood B-cell precursor acute lymphoblastic leukemia." Blood 79, no. 7 (April 1, 1992): 1781–88. http://dx.doi.org/10.1182/blood.v79.7.1781.bloodjournal7971781.
Full textAbstract:
The prognostically important 1;19 chromosomal translocation can alter the E2A gene on chromosome 19p13 in childhood B-cell precursor acute lymphoblastic leukemia (ALL), leading to formation of a fusion gene (E2A-PBX1) that encodes a hybrid transcription factor with oncogenic potential. It is not known whether this molecular alteration is a uniform consequence of the t(1;19) or is restricted to translocation events within specific immunologic subtypes of the disease. Therefore, we studied leukemic cells from 25 cases of B-cell precursor ALL, with or without evidence of cytoplasmic Ig mu heavy chains (cIg); 17 cases had the t(1;19) by cytogenetic analysis. Leukemic cell DNA samples were analyzed by Southern blotting to detect alterations within the E2A genomic locus; a polymerase chain reaction assay was used to identify expression of chimeric E2A-pbx1 transcripts in leukemic cell RNA; and immunoblotting with anti-Pbx1 antibodies was used to detect hybrid E2A- Pbx1 proteins. Of 11 cases of cIg+ ALL with the t(1;19), 10 had E2A- pbx1 chimeric transcripts with identical junctions and a characteristic set of E2A-Pbx1 hybrid proteins. Each of these cases had E2A gene rearrangements, including the one in which fusion transcripts were not detected. By contrast, none of the six cases of t(1;19)-positive, cIg- ALL had evidence of rearranged E2A genomic restriction fragments, detectable E2A-pbx1 chimeric transcripts, or hybrid E2A-Pbx1 proteins. Typical chimeric E2A-pbx1 transcripts and proteins were detected in one of eight cIg+ leukemias in which the t(1;19) was not identified by cytogenetic analysis, emphasizing the increased sensitivity of molecular analysis for detection of this abnormality. We conclude that the molecular breakpoints in cases of cIg- B-cell precursor ALL with the t(1;19) differ from those in cIg+ cases with this translocation. Leukemias that express hybrid oncoproteins such as E2A-Pbx1 or Bcr-Abl have had a poor prognosis in most studies. Thus, molecular techniques to detect fusion genes and their aberrant products should allow more timely and appropriate treatment of these aggressive subtypes of the disease.
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Moz, Yulia, Justin Silver, and Tally Naveh-Many. "Characterization of cis-acting element in renal NaPi-2 cotransporter mRNA that determines mRNA stability." American Journal of Physiology-Renal Physiology 284, no. 4 (April 1, 2003): F663—F670. http://dx.doi.org/10.1152/ajprenal.00332.2002.
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Hypophosphatemia leads to an increase in Na+-Pi cotransporter (NaPi-2) mRNA levels. This increase is posttranscriptional and correlates with a more stable transcript mediated by the terminal 698 nt of the NaPi-2 mRNA. A 71-nt binding element was identified with renal proteins from rats fed control and low-Pi (−Pi) diet. The binding of −Pi renal proteins to this transcript was increased compared with control proteins. The functionality of the ciselement was demonstrated by an in vitro degradation assay. −Pi renal proteins stabilized transcripts that included the cis element compared with control renal extracts. The full-length NaPi-2 transcript, but not control transcripts, was stabilized by −Pi extracts. Insertion of the binding element into green fluorescent protein (GFP) as a reporter gene decreased chimeric GFP mRNA levels in transfection experiments. Our results suggest that the protein-binding region of the NaPi-2 mRNA functions as a cis-acting instability element. In hypophosphatemia there is increased binding to the cis-acting element and subsequent stabilization of NaPi-2 mRNA.
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Marienfeld, J. R., and K. J. Newton. "The maize NCS2 abnormal growth mutant has a chimeric nad4-nad7 mitochondrial gene and is associated with reduced complex I function." Genetics 138, no. 3 (November 1, 1994): 855–63. http://dx.doi.org/10.1093/genetics/138.3.855.
Full textAbstract:
Abstract The molecular basis of the maternally inherited, heteroplasmic NCS2 mutant of maize was investigated. Analysis of the NCS2 mtDNA showed that it closely resembles the progenitor cmsT mitochondrial genome, except that the mutant genome contains a fused nad4-nad7 gene and is deleted for the small fourth exon of nad4. The rearrangement has occurred at a 16-bp repeat present in the third intron of the nad4 gene and in the second intron of the nad7 gene. Transcripts containing exon 4 of the nad4 gene are greatly reduced in mtRNA preparations from heteroplasmic NCS2 plants; larger transcripts are associated with the first three nad4 exons. Identical 5' ends of the nad4 transcripts have been mapped 396 and 247 bp upstream of the start codon in mtRNAs from both NCS2 and related non-NCS plants. The putative transcription termination signal of nad4 is deleted in mutant DNA, resulting in the production of the unique longer transcripts. The complex transcript pattern associated with nad7 is also altered in the mutant. Both nad4 and nad7 encode subunits of complex I (NADH dehydrogenase) of the mitochondrial electron transfer chain. Oxygen uptake experiments show that the functioning of complex I is specifically reduced in mitochondria isolated from NCS2 mutant plants.