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Journal articles on the topic 'Alternative last exon (ALE)'

Author: Grafiati

Published: 19 April 2025

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1

Lee, Seungjae, Lu Wei, Binglong Zhang, et al. "ELAV/Hu RNA binding proteins determine multiple programs of neural alternative splicing." PLOS Genetics 17, no. 4 (2021): e1009439. http://dx.doi.org/10.1371/journal.pgen.1009439.

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ELAV/Hu factors are conserved RNA binding proteins (RBPs) that play diverse roles in mRNA processing and regulation. The founding member,DrosophilaElav, was recognized as a vital neural factor 35 years ago. Nevertheless, little was known about its impacts on the transcriptome, and potential functional overlap with its paralogs. Building on our recent findings that neural-specific lengthened 3’ UTR isoforms are co-determined by ELAV/Hu factors, we address their impacts on splicing. While only a few splicing targets ofDrosophilaare known, ectopic expression of each of the three family members (E

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2

Mohamed, Aminetou Mint, Morgan Thenoz, Catherine Koering, et al. "DEK and WT1 Affect Alternative Splicing of Genes Involved in Hematopoietic Cell Lineage and Resistance to Chemotherapy in Acute Myeloid Leukemia Cells." Blood 120, no. 21 (2012): 2392. http://dx.doi.org/10.1182/blood.v120.21.2392.2392.

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Abstract Abstract 2392 In humans, the majority of all protein-coding transcripts contain introns that are removed by mRNA splicing carried out by spliceosomes. Mutations in the spliceosome machinery have recently been identified using whole-exome/genome technologies in myelodysplastic syndromes (MDS) and in acute myeloid leukemia (AML). In MDS the frequency of somatic spliceosomal mutations (SSM) range from 1–3% for U2AF1 in RARS/RCMD-RS to more than 70% for SF3B1 in ARSI. These values are significantly lower in AML whereas AML cells cumulate numerous splicing defects. Beside SSMs, one can pro

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Levallet, J., H. Mittre, B. Delarue, and S. Carreau. "Alternative splicing events in the coding region of the cytochrome P450 aromatase gene in male rat germ cells." Journal of Molecular Endocrinology 20, no. 3 (1998): 305–12. http://dx.doi.org/10.1677/jme.0.0200305.

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Expression of cytochrome P450 mRNA in rat germ cells was characterized by reverse transcription PCR with various primers located at the 3'-end of the coding region. At least two unusual isoforms (Ex10-S and INT) of P450 aromatase (P450arom) mRNA were expressed. Analysis of their sequences demonstrated that an alternative splicing event occurred first at the exon-intron boundary of the GT consensus sequence of the last coding exon, and second in the internal 5' donor inside exon 9 used as a minor cryptic splicing site. These isoforms lacked the last coding exon which contained the heme-binding

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4

Hu, Zhigang, Junting Cao, Liyan Ge, Jianqin Zhang, Huilin Zhang, and Xiaolin Liu. "Characterization and Comparative Transcriptomic Analysis of Skeletal Muscle in Pekin Duck at Different Growth Stages Using RNA-Seq." Animals 11, no. 3 (2021): 834. http://dx.doi.org/10.3390/ani11030834.

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Skeletal muscle, accounting for approximately 50% of body weight, is the largest and most important tissue. In this study, the gene expression profiles and pathways in skeletal muscle of Pekin duck were investigated and compared at embryonic day 17, 21, and 27 and postnatally at 6 months of age. An average of 49,555,936 reads in each sample was obtained from the transcriptome libraries. Over 70.0% of alternative splicing (AS) in each sample was mainly alternative 5′ first exon (transcription start site)—the first exon splicing (TSS) and alternative 3′ last exon (transcription terminal site)—th

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Vreken, Peter, René W. L. M. Niessen, Marjolein Peters, Marianne C. L. Schaap, Johanna G. M. Zuithoff-Rijntjes, and Augueste Sturk. "A Point Mutation in an Invariant Splice Acceptor Site Results in a Decreased mRNA Level in a Patient with Severe Coagulation Factor XIII Subunit A Deficiency." Thrombosis and Haemostasis 74, no. 02 (1995): 584–89. http://dx.doi.org/10.1055/s-0038-1649779.

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SummaryAmplification and sequencing of exons I-XV of the gene encoding subunit A of coagulation factor XIII (FXIII) in a patient with severe subunit A deficiency revealed a single G → A base substitution at the last position of intron E, mutating the invariant AG dinucleotide splice acceptor site to AA. Northern blot analysis of FXIII subunit A mRNA levels in peripheral mononuclear leukocytes showed that this mutation leads to an undetectable FXIII subunit A mRNA level, suggesting that the mutant transcript is either highly unstable or only spliced at low efficiency. Despite this low mRNA leve

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Bernasconi, Paolo, Barbara Rocca, Celeste Calvello, et al. "Alternative Splicing of hTERT Exon 7 in AML: Biological Fuction and Prognostic Significance." Blood 124, no. 21 (2014): 1019. http://dx.doi.org/10.1182/blood.v124.21.1019.1019.

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Abstract hTERT, a telomere specific reverse transcriptase with a crucial role in telomerase activity, prevents telomeres shortening, a pro-apototic cellular event which occurs at every round of DNA replication. Its regulation is complex as alternative spliced variants which generate the full-length hTERT transcript (+α+β) and transcripts carrying α and/or β deletions (transdominant negative isoform -α+β, inactive products +α-β and -α-β) have been reported. In AML the prognostic significance of hTERT expression is still debated, even if its over-expression has been correlated with a poor clinic

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7

Arnaud, Pauline, Margaux Cadenet, Zakaria Mougin, et al. "Early-Onset Aortic Dissection: Characterization of a New Pathogenic Splicing Variation in the MYH11 Gene with Several In-Frame Abnormal Transcripts." Human Mutation 2023 (August 14, 2023): 1–7. http://dx.doi.org/10.1155/2023/1410230.

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Rare pathogenic variants in the MYH11 gene are responsible for thoracic aortic aneurysms and dissections. They are usually heterozygous missense variants or in-frame deletions of several amino acids without alteration of the reading frame and mainly affect the coiled-coil domain of the protein. Variants leading to a premature stop codon have been described in patients with another phenotype, megacystis-microcolon-intestinal hypoperistalsis syndrome, with an autosomal recessive inheritance. The physiopathological mechanisms arising from the different genetic alterations affecting the MYH11 gene

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8

Duarte, Adriana S. S., Manoela M. Ortega, Fernando F. Costa, Carmen S. P. Lima, and Sara T. O. Saad. "PP2500 mRNA, a Splice Variant of the Multiple Ankirin Repeat Single KH Domain (Mask), Is Highly Expressed in Plasma Cells of Multiple Myeloma." Blood 106, no. 11 (2005): 5090. http://dx.doi.org/10.1182/blood.v106.11.5090.5090.

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Abstract The Ankyrin (ANK)-repeat is one of the most common protein sequence motifs, which leads itself to variation in overall domain size by simple sequence duplication or deletion. The Mask (Multiple Ankyrin Repeats Single KH domain) gene, which codifies an ANK-repeat protein, is located in chromosome 5(q31.3) and it is composed of 39 exons. It generates isoforms by alternative 3′splicing. The first splice variant (hMask) lacks the 10A exon of the Mask gene, generating a mRNA containing 34 exons. The other, Mask-BP3ARF, results from fusion of splice variant hMask, with the two last exons of

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Falkenhorst, Johanna, Rainer Hamacher, Peter Reichardt, et al. "Lower-dosing ponatinib in pre-treated GIST: Results of the POETIG phase II trial." Journal of Clinical Oncology 38, no. 15_suppl (2020): 11536. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.11536.

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11536 Background: Despite long-lasting responses to imatinib most metastatic gastrointestinal stromal tumors (GIST) eventually progress and subsequent treatments are associated with limited duration of disease control. Ponatinib is a potent KIT inhibitor with a strong activity against secondary mutations in exon 17, including the highly resistant D816 mutations of KIT. Based on the dose-depending toxicity profile we sought to evaluate the safety and activity of lower dosing (30mg) ponatinib in pretreated patients with KIT-mutant GIST. We here report safety data for the whole cohort and first e

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10

Hanke, P. D., and R. V. Storti. "The Drosophila melanogaster tropomyosin II gene produces multiple proteins by use of alternative tissue-specific promoters and alternative splicing." Molecular and Cellular Biology 8, no. 9 (1988): 3591–602. http://dx.doi.org/10.1128/mcb.8.9.3591-3602.1988.

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The structure of the Drosophila melanogaster tropomyosin II (TmII) gene has been determined by DNA sequencing of cDNA clones and the genomic DNA coding for the gene. Two overlapping transcriptional units produce at least four different tropomyosin isoforms. A combination of developmentally regulated promoters and alternative splicing produces both muscle and cytoskeletal tropomyosin isoforms. One promoter is a muscle-specific promoter and produces three different tropomyosin isoforms by alternative splicing of the last three 3' exons. The second promoter has the characteristics of a housekeepi

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Hanke, P. D., and R. V. Storti. "The Drosophila melanogaster tropomyosin II gene produces multiple proteins by use of alternative tissue-specific promoters and alternative splicing." Molecular and Cellular Biology 8, no. 9 (1988): 3591–602. http://dx.doi.org/10.1128/mcb.8.9.3591.

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The structure of the Drosophila melanogaster tropomyosin II (TmII) gene has been determined by DNA sequencing of cDNA clones and the genomic DNA coding for the gene. Two overlapping transcriptional units produce at least four different tropomyosin isoforms. A combination of developmentally regulated promoters and alternative splicing produces both muscle and cytoskeletal tropomyosin isoforms. One promoter is a muscle-specific promoter and produces three different tropomyosin isoforms by alternative splicing of the last three 3' exons. The second promoter has the characteristics of a housekeepi

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12

Martinez Gomez, Laura, Fernando Pozo, Thomas A. Walsh, Federico Abascal, and Michael L. Tress. "The clinical importance of tandem exon duplication-derived substitutions." Nucleic Acids Research 49, no. 14 (2021): 8232–46. http://dx.doi.org/10.1093/nar/gkab623.

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Abstract Most coding genes in the human genome are annotated with multiple alternative transcripts. However, clear evidence for the functional relevance of the protein isoforms produced by these alternative transcripts is often hard to find. Alternative isoforms generated from tandem exon duplication-derived substitutions are an exception. These splice events are rare, but have important functional consequences. Here, we have catalogued the 236 tandem exon duplication-derived substitutions annotated in the GENCODE human reference set. We find that more than 90% of the events have a last common

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13

Hampson, R. K., L. La Follette, and F. M. Rottman. "Alternative processing of bovine growth hormone mRNA is influenced by downstream exon sequences." Molecular and Cellular Biology 9, no. 4 (1989): 1604–10. http://dx.doi.org/10.1128/mcb.9.4.1604-1610.1989.

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In a previous report, we described the presence, in pituitary tissue, of an alternatively processed species of bovine growth hormone mRNA from which the last intron (intron D) has not been removed by splicing (R. K. Hampson and F. M. Rottman, Proc. Natl. Acad. Sci. USA 84:2673-2677, 1987). Using transient expression of the bovine growth hormone gene in Cos I cells, we observed that splicing of intron D was affected by sequences within the downstream exon (exon 5). Deletion of a 115-base-pair FspI-PvuII restriction fragment in exon 5 beginning 73 base pairs downstream of the intron 4-exon 5 jun

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Hampson, R. K., L. La Follette, and F. M. Rottman. "Alternative processing of bovine growth hormone mRNA is influenced by downstream exon sequences." Molecular and Cellular Biology 9, no. 4 (1989): 1604–10. http://dx.doi.org/10.1128/mcb.9.4.1604.

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In a previous report, we described the presence, in pituitary tissue, of an alternatively processed species of bovine growth hormone mRNA from which the last intron (intron D) has not been removed by splicing (R. K. Hampson and F. M. Rottman, Proc. Natl. Acad. Sci. USA 84:2673-2677, 1987). Using transient expression of the bovine growth hormone gene in Cos I cells, we observed that splicing of intron D was affected by sequences within the downstream exon (exon 5). Deletion of a 115-base-pair FspI-PvuII restriction fragment in exon 5 beginning 73 base pairs downstream of the intron 4-exon 5 jun

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15

del Arco, Araceli. "Novel variants of human SCaMC-3, an isoform of the ATP-Mg/Pi mitochondrial carrier, generated by alternative splicing from 3′-flanking transposable elements." Biochemical Journal 389, no. 3 (2005): 647–55. http://dx.doi.org/10.1042/bj20050283.

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CaMCs (calcium-dependent mitochondrial carriers) represent a novel subfamily of metabolite carriers of mitochondria. The ATP-Mg/Pi co-transporter, functionally characterized more than 20 years ago, has been identified to be a CaMC member. There are three isoforms of the ATP-Mg/Pi carrier in mammals, SCaMC-1 (short CaMC-1), -2 and -3 (or APC-1, -3 and -2 respectively), corresponding to the genes SLC25A24, SLC25A25 and SLC25A23 respectively, as well as six N-terminal variants generated by alternative splicing for SCaMC-1 and -2 isoforms. In the present study, we describe four new variants of hum

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Ren, Kehan, Zongjun Xia, Ermin Li, Xu Han, and Peng Ji. "Rapid Degradation of mDia2 Protein during Terminal Erythropoiesis Via an In Vivo Aid System: An Alternative Approach for Loss-of-Function Studies." Blood 142, Supplement 1 (2023): 2443. http://dx.doi.org/10.1182/blood-2023-178268.

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Loss-of-function manipulations are crucial methods for studying gene functions. Despite the availability of many chemical-induced genetic manipulation techniques, there are limitations associated with these technologies. Tamoxifen-induced conditional gene expression, gene knockdown, or cell tracking represent some of the most common genetic manipulations employed in mice. However, tamoxifen-induced gene or Cre expression in bone marrow cell populations is relatively weak, affecting only a low proportion of cells. Similar observations have been made with the in vivo doxycycline-inducible system

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Libri, D., M. Goux-Pelletan, E. Brody, and M. Y. Fiszman. "Exon as well as intron sequences are cis-regulating elements for the mutually exclusive alternative splicing of the beta tropomyosin gene." Molecular and Cellular Biology 10, no. 10 (1990): 5036–46. http://dx.doi.org/10.1128/mcb.10.10.5036-5046.1990.

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The beta tropomyosin gene contains two internal exons which are spliced in a mutually exclusive manner. Exon 6B is specifically included in the mature transcripts expressed in skeletal muscle or cultured myotubes, while exon 6A is a myoblast- or smooth muscle-specific exon. The intron between them, which is never spliced in normal conditions, contains two characteristic features: first, the unusual location of the branch point at position -105 from the acceptor, and second, the presence of a very long pyrimidine stretch upstream of the skeletal muscle exon. In this study we designed a number o

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Libri, D., M. Goux-Pelletan, E. Brody, and M. Y. Fiszman. "Exon as well as intron sequences are cis-regulating elements for the mutually exclusive alternative splicing of the beta tropomyosin gene." Molecular and Cellular Biology 10, no. 10 (1990): 5036–46. http://dx.doi.org/10.1128/mcb.10.10.5036.

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The beta tropomyosin gene contains two internal exons which are spliced in a mutually exclusive manner. Exon 6B is specifically included in the mature transcripts expressed in skeletal muscle or cultured myotubes, while exon 6A is a myoblast- or smooth muscle-specific exon. The intron between them, which is never spliced in normal conditions, contains two characteristic features: first, the unusual location of the branch point at position -105 from the acceptor, and second, the presence of a very long pyrimidine stretch upstream of the skeletal muscle exon. In this study we designed a number o

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Joiner, Clinton H., Scott Crable, and Patrick G. Gallagher. "Alternative Splicing within Exon 1 of the KCl Cotransporter-3 (KCC3) Gene Results in Novel Transcripts in Erythroid Cells." Blood 108, no. 11 (2006): 1564. http://dx.doi.org/10.1182/blood.v108.11.1564.1564.

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Abstract The KCl Cotransporter (KCC) is a key component of the volume regulation system of human reticulocytes, and its excessive activity in sickle cells contributes to cellular dehydration and therefore to sickling pathology. Three of the four KCC genes, including KCC3, are expressed in erythroid cells (Exp.Hematol.2005;33:624), but their relative contribution to KCC fluxes and volume regulation in red cells remains unknown. Heterogenity of the 5′ ends of the KCC3 mRNA transcripts has been described by Mount and colleagues (Mercado et al. Am J Physiol289:F1246, 2005), including two untransla

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Tien, Jerry F., Alborz Mazloomian, S. W. Grace Cheng, et al. "CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion." Nucleic Acids Research 45, no. 11 (2017): 6698–716. http://dx.doi.org/10.1093/nar/gkx187.

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Costas, María Jesús, Ana Couto, Alicia Cabezas, Rosa María Pinto, João Meireles Ribeiro, and José Carlos Cameselle. "Alternative Splicing of the Last TKFC Intron Yields Transcripts Differentially Expressed in Human Tissues That Code In Vitro for a Protein Devoid of Triokinase and FMN Cyclase Activity." Biomolecules 14, no. 10 (2024): 1288. http://dx.doi.org/10.3390/biom14101288.

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The 18-exon human TKFC gene codes for dual-activity triokinase and FMN cyclase (TKFC) in an ORF, spanning from exon 2 to exon 18. In addition to TKFC-coding transcripts (classified as tkfc type by their intron-17 splice), databases contain evidence for alternative TKFC transcripts, but none of them has been expressed, studied, and reported in the literature. A novel full-ORF transcript was cloned from brain cDNA and sequenced (accession no. DQ344550). It results from an alternative 3′ splice-site in intron 17. The cloned cDNA contains an ORF also spanning from exon 2 to exon 18 of the TKFC gen

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Sogawa, Chiharu, Kei Kumagai, Norio Sogawa, Katsuya Morita, Toshihiro Dohi, and Shigeo Kitayama. "C-terminal region regulates the functional expression of human noradrenaline transporter splice variants." Biochemical Journal 401, no. 1 (2006): 185–95. http://dx.doi.org/10.1042/bj20060495.

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The NET [noradrenaline (norepinephrine) transporter], an Na+/Cl−-dependent neurotransmitter transporter, has several isoforms produced by alternative splicing in the C-terminal region, each differing in expression and function. We characterized the two major isoforms of human NET, hNET1, which has seven C-terminal amino acids encoded by exon 15, and hNET2, which has 18 amino acids encoded by exon 16, by site-directed mutagenesis in combination with NE (noradrenaline) uptake assays and cell surface biotinylation. Mutants lacking one third or more of the 24 amino acids encoded by exon 14 exhibit

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Hu, Zhigang, Junting Cao, Jianqin Zhang, Liyan Ge, Huilin Zhang, and Xiaolin Liu. "Skeletal Muscle Transcriptome Analysis of Hanzhong Ma Duck at Different Growth Stages Using RNA-Seq." Biomolecules 11, no. 2 (2021): 315. http://dx.doi.org/10.3390/biom11020315.

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As one of the most important poultry worldwide, ducks (Anas platyrhynchos) are raised mainly for meat and egg products, and muscle development in ducks is important for meat production. Therefore, an investigation of gene expression in duck skeletal muscle would significantly contribute to our understanding of muscle development. In this study, twenty-four cDNA libraries were constructed from breast and leg muscles of Hanzhong Ma ducks at day 17, 21, 27 of the embryo and postnatal at 6-month-old. High-throughput sequencing and bioinformatics were used to determine the abundances and characteri

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Crable, Scott, Clinton H. Joiner, and Patrick G. Gallagher. "A GC Box Element Is Critical for Transcriptional Regulation of the K-Cl Cotransporter Isoform KCC3a in Hematopoetic Cells." Blood 110, no. 11 (2007): 1712. http://dx.doi.org/10.1182/blood.v110.11.1712.1712.

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Abstract The KCl Cotransporter (KCC) is a key component of the volume regulation system of human reticulocytes, and its excessive activity in sickle cells contributes to cellular dehydration and therefore to sickling pathology. Three of the four KCC genes, are expressed in erythroid cells (Crable et al. Exp. Hematol.2005;33:624). Although the relative contribution of the three KCC isoforms to KCC fluxes and volume regulation in red cells remains unknown, KCC3 appears to be the dominant transcript in late erythroid cells. Heterogenity of the 5′ ends of the KCC3 mRNA transcripts has been describ

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Carrion, Shane A., Jennifer J. Michal, and Zhihua Jiang. "Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases." Genes 14, no. 11 (2023): 2051. http://dx.doi.org/10.3390/genes14112051.

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Manipulation using alternative exon splicing (AES), alternative transcription start (ATS), and alternative polyadenylation (APA) sites are key to transcript diversity underlying health and disease. All three are pervasive in organisms, present in at least 50% of human protein-coding genes. In fact, ATS and APA site use has the highest impact on protein identity, with their ability to alter which first and last exons are utilized as well as impacting stability and translation efficiency. These RNA variants have been shown to be highly specific, both in tissue type and stage, with demonstrated i

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Essand, M., S. Vikman, J. Grawé, et al. "Identification and characterization of a novel splicing variant of vesicular monoamine transporter 1." Journal of Molecular Endocrinology 35, no. 3 (2005): 489–501. http://dx.doi.org/10.1677/jme.1.01875.

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Vesicular monoamine transporter 1 (VMAT1) is an integral protein in the membrane of secretory vesicles of neuroendocrine and endocrine cells that allows the transport of biogenic monoamines, such as serotonin, from the cytoplasm into the secretory vesicles. The full-length VMAT1 transcript is produced from 16 exons. We have identified and characterized an alternatively spliced form of VMAT1 that lacks exon 15, the next to last exon of VMAT1. The new form was therefore denoted VMAT1Δ15. Exon 15 does not contain an even multiple of three nucleotides. As a consequence, there is a shift of reading

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Sumanasekera, Chiranthani, David S. Watt, and Stefan Stamm. "Substances that can change alternative splice-site selection." Biochemical Society Transactions 36, no. 3 (2008): 483–90. http://dx.doi.org/10.1042/bst0360483.

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Alternative pre-mRNA splicing is an important element in eukaryotic gene expression, as most of the protein-coding genes use this process to generate multiple protein isoforms from a single gene. An increasing number of human diseases are now recognized to be caused by the selection of ‘wrong’ alternative exons. Research during the last few years identified a number of low–molecular-mass chemical substances that can change alternative exon usage. Most of these substances act by either blocking histone deacetylases or by interfering with the phosphorylation of splicing factors. How the remainin

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Duthie, S. M., P. L. Taylor, and K. A. Eidne. "Characterization of the mouse thyrotrophin-releasing hormone receptor gene: an exon corresponds to a deletion in the rat cDNA." Journal of Molecular Endocrinology 11, no. 2 (1993): 141–49. http://dx.doi.org/10.1677/jme.0.0110141.

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ABSTRACT The cloning and characterization of the mouse TRH receptor (TRH-R) gene revealed an untranslated exon (exon 1), a single intron and an upstream dinucleotide repeat sequence (d(TG)16.d(AG)21) in the 5′ untranslated region (UTR). The coding region was contained almost entirely on a second exon (exon 2), with the final amino acid and stop codon at the COOH terminus of the gene encoded by a third exon (exon 3) flanked by two introns. The 3′ UTR was contained on the remainder of exon 3 and on the final exon (exon 4). Exon 3 (228 bp) corresponds exactly to a 228 bp deletion that exists in t

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Santoro, Alessandra, Lea Dagnino, Cecilia Agueli, et al. "Altered mRNA Expression of Pax-5 Is a Common Event in Acute Lymphoblastic Leukemia." Blood 112, no. 11 (2008): 1189. http://dx.doi.org/10.1182/blood.v112.11.1189.1189.

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Abstract Introduction. Pax-5 gene codifies for a transcription factor central to B-cell differentiation and function, expressed during the early stage of differentiation and alternatively spliced during B-cell development. In addition to the full-length isoform (Pax-5a), isoforms arising from the inclusion or exclusion of exons 2, 7, 8, and/or 9, and lacking the DNA-binding and the transactivating domains, have been described. These isoforms and their levels of expression increase during B-cell maturation. In particular, Pax-5b isoform (deleted of exon 2), resulting in protein with partial DNA

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Catarsi, Paolo, Vittorio Rosti, Vittorio Abbonante, et al. "JAK2 exon 14 Skipping in Patients with Primary Myelofibrosis (PMF),." Blood 118, no. 21 (2011): 3844. http://dx.doi.org/10.1182/blood.v118.21.3844.3844.

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Abstract Abstract 3844 In recent years the diagnosis and treatment of patients with myeloproliferative disorders has focused on the JAK2 gene. Recently, an alternative splicing of JAK2 transcript lacking the entire exon 14 (88bp), has been described (Ma et al. (2010) PLoS ONE, 5, e12165). This mRNA has a stop codon in exon 15 and is translated into a truncated protein that has a deletion within the JH2 pseudokinase domain and complete deletion of the kinase domain (JH1). The alternative transcript was detected in plasma of patients with myeloproliferative neoplasms (MPNs) (58% of patients posi

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Herbrechter, Robin, Nadine Hube, Raoul Buchholz, and Andreas Reiner. "Splicing and editing of ionotropic glutamate receptors: a comprehensive analysis based on human RNA-Seq data." Cellular and Molecular Life Sciences 78, no. 14 (2021): 5605–30. http://dx.doi.org/10.1007/s00018-021-03865-z.

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AbstractIonotropic glutamate receptors (iGluRs) play key roles for signaling in the central nervous system. Alternative splicing and RNA editing are well-known mechanisms to increase iGluR diversity and to provide context-dependent regulation. Earlier work on isoform identification has focused on the analysis of cloned transcripts, mostly from rodents. We here set out to obtain a systematic overview of iGluR splicing and editing in human brain based on RNA-Seq data. Using data from two large-scale transcriptome studies, we established a workflow for the de novo identification and quantificatio

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Mamala, A., and W. Sciężor. "Evaluation of the Effect of Selected Alloying Elements on the Mechanical and Electrical Aluminium Properties." Archives of Metallurgy and Materials 59, no. 1 (2014): 413–17. http://dx.doi.org/10.2478/amm-2014-0069.

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Abstract Modern industry expects aluminum products with new, unusual, and well-defined functional properties. Last years we are able to notice constant development of aluminium alloys. In food industry, power engineering, electrical engineering and building engineering, flat rolled products of 1XXX series aluminium alloys are used.8XXX series alloys registered in Aluminium Association during last 20 years may be used as an alternative. These alloys have very good thermal and electrical conductivity and perfect technological formability. Moreover, these materials are able to obtain by aluminium

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Gee, Sherry, Jonathan Villalobos, Miki Yamamoto, et al. "Stage-Specific Switches in Alternative Pre-mRNA Splicing during Late Erythropoiesis Are Conserved from Mouse to Human." Blood 112, no. 11 (2008): 531. http://dx.doi.org/10.1182/blood.v112.11.531.531.

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Abstract Spatial and temporal regulation of alternative pre-mRNA splicing determines which exons are incorporated into mature mRNA, modulating mRNA coding capacity to ensure synthesis of appropriate protein isoforms throughout normal differentiation and development. During erythropoiesis, a stage-specific switch in pre-mRNA splicing activates incorporation of protein 4.1R exon 16, thereby increasing 4.1R affinity for spectrin and actin and mechanically strengthening red blood cell membranes. We are exploring the hypothesis that stage-specific changes in pre-mRNA splicing regulate expression of

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Shen, Yulei, Baosheng Ge, Himabindu Ramachandrareddy, Timothy McKeithan, and Wing-Chung Chan. "Alternative Splicing Generates a BCL6 Isoform Encoding a Compact Repressor." Blood 108, no. 11 (2006): 2383. http://dx.doi.org/10.1182/blood.v108.11.2383.2383.

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Abstract BCL6 encodes a BTB/POZ zinc finger (ZF) transcriptional repressor which is essential for normal germinal center (GC) reactions. Its dysregulated expression contributes to the pathogenesis of B cell non-Hodgkin lymphoma (NHL). The BCL6 gene consists of ten exons, BCL6 translation start site is located in exon 3, and the six-ZF DNA binding domain is encoded by exons 7 to 10. BCL6S, was cloned from the cDNA of a BCL-6 positive cell line, DHL-16. DNA sequencing showed that BCL6S was a normal splicing isoform that excludes the entire exon 7 of the BCL6 gene and encodes a 650 amino acid (aa

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Razavian, Niema, and Vivian Cheung. "SRSF1 Is a Mediator of Radiation-Induced Alternative Splicing in B-Lymphocytes." Blood 128, no. 22 (2016): 1341. http://dx.doi.org/10.1182/blood.v128.22.1341.1341.

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Abstract Ionizing radiation is used in the treatment of Hodgkin and non-Hodgkin lymphomas (Spetch et al. 2014; Illidge et al. 2014). Despite its effectiveness, radiation is a "blunt" therapy that damages indiscriminately both cancer and normal cells, and can result in secondary malignancies (Dores et al. 2002). To better understand cellular response to radiation, we examined alternative splicing, and its regulation, in irradiated human cells. To accomplish this, we exposed cultured B-lymphocytes from 10 individuals to 10 Gy of ionizing radiation, and performed RNA sequencing before, and two an

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Tabata, Hidemi, Momoko Kobayashi, Junko H. Ikeda, Nobuhiro Nakao, Toru R. Saito, and Minoru Tanaka. "Characterization of multiple first exons in murine prolactin receptor gene and the effect of prolactin on their expression in the choroid plexus." Journal of Molecular Endocrinology 48, no. 2 (2012): 169–76. http://dx.doi.org/10.1530/jme-11-0122.

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Prolactin (Prl) receptor (Prlr) gene is expressed in various brain regions, with the highest level present in the choroid plexus, a site for receptor-mediated PRL transport from the blood to cerebrospinal fluid. We investigated the regulatory mechanism ofPrlrgene expression by PRL in the murine choroid plexus. We first examined the organization of the alternative first exons in murinePrlrgene. In addition to the three known first exons, mE11, mE12, and mE13, two first exons, mE14and mE15, were newly identified by cDNA cloning. Each first exon variant ofPrlrmRNA exhibited tissue-specific or gen

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Kuwahara, Mitsuhiro, Sumiko Kurachi, and Kotoku Kurachi. "Molecular Mechanism of Prothrombin G20210A Variant: Critical New Role of Exon Splicing Enhancer in Poly (A) Tailing." Blood 104, no. 11 (2004): 1944. http://dx.doi.org/10.1182/blood.v104.11.1944.1944.

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Abstract Although prothrombin G20210A variant was first found in 1996 as a genetic risk factor of thrombosis, the underlying molecular mechanism for elevation of circulatory prothrombin levels due to the variant has remained elusive. The position 20210 is at the poly (A) tailing site, and several research groups reported different, contradictive possibilities including enhancement in poly (A) tailing, change in RNA stability or no difference in prothrombin mRNA level between G (wild type) and A (variant) at position 20210. Such confusions appear to be due to no reliable assay model availabilit

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Renosi, Florian, Ambre Giguelay, Jean Francis Berry, et al. "Blastic Plasmacytoid Dendritic Cell Neoplasm Are Not Characterized By Two Distinct Subgroups, but By a Transcriptomic and Phenotypic Gradient." Blood 144, Supplement 1 (2024): 6106. https://doi.org/10.1182/blood-2024-206941.

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Background: Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN) is a rare haematological malignancy characterized by NF-κB activation (Sapienza et al., 2014), but also BCL2 overexpression (Montero et al., 2017), UV exposure damages (Griffin et al., 2023), neural signatures (Sapienza et al., 2021) and fatty acid metabolism (Ceroi et al., 2016). However, BPDCN is heterogenous: recent studies showed two subgroups, based on immune response involving CD11b/CD177 (Summerer et al., 2021) or on pure pDC/conventional DC-enriched signatures (Künster et al., 2022). Künster et al. also showed NF-κB signa

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Hooper, J. E., M. Pérez-Alonso, J. R. Bermingham, et al. "Comparative studies of Drosophila Antennapedia genes." Genetics 132, no. 2 (1992): 453–69. http://dx.doi.org/10.1093/genetics/132.2.453.

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Abstract The Antennapedia (Antp) homeotic gene of Drosophila melanogaster controls cell fates and pattern formation in the epidermis, nervous system and mesoderm of thoracic segments. Its expression is controlled at the levels of transcription, alternative RNA splicing, polyadenylation and translation. Two nested Antp transcription units extend over 103 kb and produce sixteen different transcripts. We have compared the Antp genes of Drosophila virilis, Drosophila subobscura and D. melanogaster to determine which structural features are conserved and therefore may be important to the gene's fun

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Hou, Yue, Huan Huang, Wenqiao Hu, Hongde Liu, and Xiao Sun. "Histone modifications influence skipped exons inclusion." Journal of Bioinformatics and Computational Biology 15, no. 01 (2017): 1750003. http://dx.doi.org/10.1142/s0219720017500032.

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Alternative splicing (AS), by which individual genes can produce multiple mRNA, associates with genomic complexity, disease, and development. Histone modifications show important roles in both transcription initiation and mRNA splicing. Here, we intended to find the link between AS and histone modifications in flanking regions through analyzing publicly available data in two human cell lines, GM12878 and K562 cell lines. According to exon inclusion levels, exons were classified into three types, included skipped exons, excluded skipped exons and expressed constitutive exons. We revealed that t

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Bishop, David F., Xiaoye Schneider-Yin, Sonia Clavero, Han-Wook Yoo, Elisabeth I. Minder, and Robert J. Desnick. "Congenital erythropoietic porphyria: a novel uroporphyrinogen III synthase branchpoint mutation reveals underlying wild-type alternatively spliced transcripts." Blood 115, no. 5 (2010): 1062–69. http://dx.doi.org/10.1182/blood-2009-04-218016.

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Abstract Splicing mutations account for approximately 10% of lesions causing genetic diseases, but few branchpoint sequence (BPS) lesions have been reported. In 3 families with autosomal recessive congenital erythropoietic porphyria (CEP) resulting from uroporphyrinogen III synthase (URO-synthase) deficiency, sequencing the promoter, all 10 exons and the intron/exon boundaries did not detect a mutation. Northern analyses of lymphoblast mRNAs from 2 patients and reverse-transcribed polymerase chain reaction (RT-PCR) of lymphoblast mRNAs from all 3 patients revealed multiple longer transcripts i

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Chandradas, Sajiv, Jonathan G. Tardos, Ke Jiang, and Vladimir Bogdanov. "Post-Transcriptional Regulation of Tissue Factor Expression in Human Monocytic Cells: Identification of Novel Exonic Splicing Enhancers for the Spliceosomal Protein SRp40 and Intronic Elements Critical for Exon 5 Definition." Blood 112, no. 11 (2008): 1031. http://dx.doi.org/10.1182/blood.v112.11.1031.1031.

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Abstract Background. Circulating monocytes play a critical role in the pathophysiology of many thrombotic disorders. These cells are known to exhibit complex post-transcriptional regulation of Tissue Factor (TF), the principal trigger of coagulation, which they express in two forms – full length TF(flTF), a highly thrombogenic integral membrane protein, and alternatively spliced TF (asTF), a secreted hypomorphic TF form. Biosynthesis of these two forms is achieved by inclusion or, alternatively, exclusion of TF exon 5 during pre-mRNA processing. Little is known about molecular mechanisms contr

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Laudadio, Jennifer, Michael W. N. Deininger, Michael J. Mauro, Brian J. Druker, and Richard D. Press. "An Intron-Derived Insertion/Truncation Mutation in the BCR-ABL Kinase Domain in Three CML Patients Undergoing Kinase Inhibitor Therapy." Blood 110, no. 11 (2007): 1953. http://dx.doi.org/10.1182/blood.v110.11.1953.1953.

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Abstract Although targeted inhibition of BCR-ABL with imatinib is an effective therapy for patients with chronic myeloid leukemia, a minority acquire mutations in the kinase domain (KD) that cause imatinib resistance. The spectrum of KD mutations thus far discovered, although quite heterogeneous, includes almost exclusively single nucleotide substitutions in key amino acids regulating drug binding or BCR-ABL function. Here, we describe a KD insertion/truncation mutation in 3 CML patients undergoing kinase inhibitor therapy. Two of these patients were being treated with imatinib (for 12 and 17

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DODE, Leonard, Frank WUYTACK, Patrick F. J. KOOLS, et al. "cDNA cloning, expression and chromosomal localization of the human sarco/endoplasmic reticulum Ca2+-ATPase 3 gene." Biochemical Journal 318, no. 2 (1996): 689–99. http://dx.doi.org/10.1042/bj3180689.

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cDNA and genomic clones encoding human sarco/endoplasmic reticulum Ca2+-ATPase 3 (SERCA3) were isolated. The composite nucleotide sequence of the 4.6 kb cDNA, as well as the partial structure of 25 kb of genomic DNA encoding all but the 5´ region of the gene, was determined. The nucleotide sequence coding for the last six amino acids of the pump and the 3´-untranslated region were identified within the sequence of the last exon. Northern blot hybridization analysis using cDNA probes derived from this exon detected a 4.8 kb transcript in several human tissues. Using a cDNA probe derived from th

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Post, T. W., M. A. Arce, M. K. Liszewski, E. S. Thompson, J. P. Atkinson, and D. M. Lublin. "Structure of the gene for human complement protein decay accelerating factor." Journal of Immunology 144, no. 2 (1990): 740–44. http://dx.doi.org/10.4049/jimmunol.144.2.740.

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Abstract Decay accelerating factor (DAF) is a glycophospholipid-anchored membrane protein that is part of the regulators of complement activation (RCA) gene family located on human chromosome 1, band q32. These proteins, beginning at their amino terminus, consist largely of multiple copies of an approximately 60 amino acid short consensus repeat (SCR). A DAF cDNA clone was used to identify overlapping bacteriophage genomic clones. The human DAF gene spans approximately 40 kb and consists of 11 exons. The length of these exons and introns varies considerably, with the exons ranging from 21 to 9

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Van de Wetering, M., J. Castrop, V. Korinek, and H. Clevers. "Extensive alternative splicing and dual promoter usage generate Tcf-1 protein isoforms with differential transcription control properties." Molecular and Cellular Biology 16, no. 3 (1996): 745–52. http://dx.doi.org/10.1128/mcb.16.3.745.

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Previously, we reported the isolation of cDNA clones representing four alternative splice forms of TCF-1, a T-cell-specific transcription factor. In the present study, Western blotting (immunoblotting) yielded a multitude of TCF-1 proteins ranging from 25-55 kDa, a pattern not simply explained from the known splice alternatives. Subsequent cDNA cloning, PCR amplification, and analysis by rapid amplification of 5' cDNA ends revealed (i) the presence of an alternative upstream promoter, which extended the known N terminus by 116 amino acids, (ii) the presence of four alternative exons, and (iii)

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Risitano, Antonio M., Elisa Seneca, Ludovica Marando, et al. "Subcutaneous Alemtuzumab Is a Safe and Effective Treatment for Global or Single-Lineage Immune-Mediated Marrow Failures: a Survey from the EBMT-WPSAA." Blood 112, no. 11 (2008): 1042. http://dx.doi.org/10.1182/blood.v112.11.1042.1042.

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Abstract Acquired marrow failure syndromes may globally affect all hematopoietic lineages, as in aplastic anemia (AA), or may selectively involve single lineages, as in pure red cell (PRCA) or in pure white cell aplasias (PWCA). Because of their common cellular immune-mediated pathophysiology, standard treatment for these conditions includes immunosuppression (IS), which may differ according to the specific disease. We investigated an experimental IS regimen based on the anti-CD52 antibody alemtuzumab (MabCampath®, ALE); the study included a phase II/III prospective trial, as well as a collect

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Maggi, Jordi, James V. M. Hanson, Lisa Kurmann, et al. "Retinal Dystrophy Associated with Homozygous Variants in NRL." Genes 15, no. 12 (2024): 1594. https://doi.org/10.3390/genes15121594.

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Background/Objectives: Neural retina leucine zipper (NRL) is a transcription factor involved in the differentiation of rod photoreceptors. Pathogenic variants in the gene encoding NRL have been associated with autosomal dominant retinitis pigmentosa and autosomal recessive clumped pigmentary retinal degeneration. Only a dozen unrelated families affected by recessive NRL-related retinal dystrophy have been described. The purpose of this study was to expand the genotypic spectrum of this disease by reporting clinical and genetic findings of two unrelated families. Methods: Index patients affecte

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Wang, Hui-Qin, Tian He, Xiao-Feng Yu, and Ya-Nan Huo. "A novel pathogenic splicing mutation of RPGR in a Chinese family with X-linked retinitis pigmentosa verified by minigene splicing assay." International Journal of Ophthalmology 16, no. 10 (2023): 1595–600. http://dx.doi.org/10.18240/ijo.2023.10.06.

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AIM: To report a novel splicing mutation in the RPGR gene (encoding retinitis pigmentosa GTPase regulator) in a three-generation Chinese family with X-linked retinitis pigmentosa (XLRP). METHODS: Comprehensive ophthalmic examinations including best corrected visual acuity, fundus photography, vision field, and pattern-visual evoked potential were performed to identify the disease phenotype of a six-year-old boy from the family (proband). Genomic DNA was extracted from peripheral blood of five available members of the pedigree. Whole-exome sequencing (WES), Sanger sequencing, and pSPL3-based ex

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Sag, Erdal, Fuat Akal, Erdal Atalay, et al. "Anti-IL1 treatment in colchicine-resistant paediatric FMF patients: real life data from the HELIOS registry." Rheumatology 59, no. 11 (2020): 3324–29. http://dx.doi.org/10.1093/rheumatology/keaa121.

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Abstract Objectives FMF is a prototype of autoinflammatory diseases associated with excess IL1 production. Anti-IL1 treatments are the first-line alternatives in colchicine-resistant/intolerant FMF patients. We aimed to investigate the efficacy and safety of anti-IL1 treatment in paediatric FMF patients in our local [Hacettepe univErsity eLectronIc research fOrmS (HELIOS)] registry. Methods HELIOS is a web-based biologic drug registry for paediatric rheumatology patients. We have analysed the clinical features, disease activity parameters, treatment responses and safety outcomes in FMF patient

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