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Journal articles on the topic 'Chimeric transcripts'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 July 2024

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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 therapeu

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2

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

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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 b

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4

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 stud

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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.

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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 stud

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6

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 ch

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7

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.

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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 react

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8

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 chi

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9

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

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10

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 ad

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11

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, transcri

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12

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.

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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, transcri

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13

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-MYH

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14

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 MR

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15

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-com

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16

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 provide

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17

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 reverte

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18

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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19

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 mapp

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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 (T

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21

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

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22

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 tr

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23

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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25

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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26

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

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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-p

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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

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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 r

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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

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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 kinas

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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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34

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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36

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 o

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37

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 chi

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38

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

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39

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 constru

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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.

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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

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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.

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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,

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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.

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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 re

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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.

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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 (P

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44

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

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45

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.

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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

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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.

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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 m

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48

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.

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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 c

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49

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 contro

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50

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.

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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 transcript

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