Skipping of an alternative intron in the srsf1 3' untranslated region increases transcript stability

Akaike, Yoko; Kurokawa, Ken; Kajita, Keisuke; Kuwano, Yuki; Masuda, Kiyoshi; Nishida, Kensei; Kang, Seung Wan; Tanahashi, Takao; Rokutan, Kazuhito

doi:10.2152/jmi.58.180

Cited by 7 publications

(6 citation statements)

References 17 publications

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“…Since CDK12 and CDK13 have RS domains and associate with RNA processing and splicing factors, we tested the effects of CDK12 and CDK13 knockdowns on the processing of the SRSF1 gene, which is known to be alternatively spliced in HCT116 cells (37). SRSF1, which is upregulated in breast and lung cancers, is an oncogenic splicing factor which is targeted by MYC and mediates MYCinduced transformation (38,39).…”

Section: Resultsmentioning

confidence: 99%

“…SRSF1, which is upregulated in breast and lung cancers, is an oncogenic splicing factor which is targeted by MYC and mediates MYCinduced transformation (38,39). Akaike and colleagues reported that skipping of an alternative intron in the SRSF1 3= untranslated region (3= UTR) increases transcript stability in HCT116 cells (37). To determine if CDK12 and CDK13 affected SRSF1 alternative splicing, we measured the levels of SRSF1 isoform 1 and isoform 2, which lacks the alternative intron, by using RT-qPCR analysis of CDK12 and CDK13 knockdown cells (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Characterization of Human Cyclin-Dependent Kinase 12 (CDK12) and CDK13 Complexes in C-Terminal Domain Phosphorylation, Gene Transcription, and RNA Processing

Liang

Gào

Gilmore

et al. 2015

Molecular and Cellular Biology

166

182

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c Cyclin-dependent kinase 9 (CDK9) and CDK12 have each been demonstrated to phosphorylate the RNA polymerase II C-terminal domain (CTD) at serine 2 of the heptad repeat, both in vitro and in vivo. CDK9, as part of P-TEFb and the super elongation complex (SEC), is by far the best characterized of CDK9, CDK12, and CDK13. We employed both in vitro and in vivo assays to further investigate the molecular properties of CDK12 and its paralog CDK13. We isolated Flag-tagged CDK12 and CDK13 and found that they associate with numerous RNA processing factors. Although knockdown of CDK12, CDK13, or their cyclin partner CCNK did not affect the bulk CTD phosphorylation levels in HCT116 cells, transcriptome sequencing (RNA-seq) analysis revealed that CDK12 and CDK13 losses in HCT116 cells preferentially affect expression of DNA damage response and snoRNA genes, respectively. CDK12 and CDK13 depletion also leads to a loss of expression of RNA processing factors and to defects in RNA processing. These findings suggest that in addition to implementing CTD phosphorylation, CDK12 and CDK13 may affect RNA processing through direct physical interactions with RNA processing factors and by regulating their expression.T he largest subunit of RNA polymerase II (Pol II), Rpb1, contains a C-terminal domain (CTD) consisting of 52 heptad repeats of the YSPTSPS consensus sequence in humans (1). The CTD is phosphorylated within these repeats, including at serines 2, 5, and 7 (Ser2, Ser5, and Ser7, respectively) (2). The CTD serves as a phosphorylation-regulated platform for the recruitment of transcription factors, RNA processing factors, and chromatin modifiers, which affect mRNA synthesis, cotranscriptional processing, and histone modifications during the transcription cycle (3).The CTD undergoes a cycle of phosphorylation and dephosphorylation during the transcription cycle of initiation, elongation, and termination (4). During transcription initiation and early transcription, Ser5 of the CTD is phosphorylated by the cyclin-dependent kinase 7 (CDK7) subunit of the basal transcription factor TFIIH (2, 5). The positive transcription elongation factor, P-TEFb (comprised of CDK9 and cyclin T), regulates transcription elongation through phosphorylation of the CTD at Ser2 (6). P-TEFb also phosphorylates negative elongation factor (NELF) (7) and DRB sensitivity-inducing factor (DSIF) (8) during the transition to productive elongation.In the budding yeast Saccharomyces cerevisiae, there are two complexes for CTD Ser2 phosphorylation: the Bur1/Bur2 complex and the Ctk1/Ctk2/Ctk3 (CTDK) complex. The Bur complex implements CTD phosphorylation early in the transcription cycle, while the Ctk complex implements CTD phosphorylation during the elongation phase of RNA Pol II (9). CDK9 was long considered to be the only CTD Ser2 kinase in metazoans, but recently the Drosophila dCdk12/dCyclin K complex was shown to be the major CTD Ser2 kinase implementing Ser2 phosphorylation during the elongation stage, analogous to the S. cerevisiae Ctk1/2 complex (10). In ...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Characterization of Human Cyclin-Dependent Kinase 12 (CDK12) and CDK13 Complexes in C-Terminal Domain Phosphorylation, Gene Transcription, and RNA Processing

Liang

Gào

Gilmore

et al. 2015

Molecular and Cellular Biology

166

182

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“…Furthermore, there is an alternative intron in SRSF1 in between two highly conserved elements in its 3′UTR. Skipping of this alternative intron appears to increase transcript stability, perhaps by removing a microRNA binding site [23]. …”

Section: Regulation Of the Expression Of The Oncogenic Splice Factmentioning

confidence: 99%

Aberrant Alternative Splicing Is Another Hallmark of Cancer

Ladomery

2013

International Journal of Cell Biology

159

132

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The vast majority of human genes are alternatively spliced. Not surprisingly, aberrant alternative splicing is increasingly linked to cancer. Splice isoforms often encode proteins that have distinct and even antagonistic properties. The abnormal expression of splice factors and splice factor kinases in cancer changes the alternative splicing of critically important pre-mRNAs. Aberrant alternative splicing should be added to the growing list of cancer hallmarks.

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“…Conversely, such events can result in the generation of premature termination codons, which trigger mRNA degradation by the nonsense-mediated decay (NMD) pathway [6]. Moreover, alternative splicing events that occur within cis -acting elements in untranslated regions can lead to pronounced effects on mRNA stability [7] and translation [8]. Thus, accurate and efficient splicing is a critical feature of the regulation of gene expression and is thought to be one of the major sources for functional diversity in complex organisms.…”

Section: Introductionmentioning

confidence: 99%

RBM5 Is a Male Germ Cell Splicing Factor and Is Required for Spermatid Differentiation and Male Fertility

et al. 2013

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Alternative splicing of precursor messenger RNA (pre-mRNA) is common in mammalian cells and enables the production of multiple gene products from a single gene, thus increasing transcriptome and proteome diversity. Disturbance of splicing regulation is associated with many human diseases; however, key splicing factors that control tissue-specific alternative splicing remain largely undefined. In an unbiased genetic screen for essential male fertility genes in the mouse, we identified the RNA binding protein RBM5 (RNA binding motif 5) as an essential regulator of haploid male germ cell pre-mRNA splicing and fertility. Mice carrying a missense mutation (R263P) in the second RNA recognition motif (RRM) of RBM5 exhibited spermatid differentiation arrest, germ cell sloughing and apoptosis, which ultimately led to azoospermia (no sperm in the ejaculate) and male sterility. Molecular modelling suggested that the R263P mutation resulted in compromised mRNA binding. Within the adult mouse testis, RBM5 localises to somatic and germ cells including spermatogonia, spermatocytes and round spermatids. Through the use of RNA pull down coupled with microarrays, we identified 11 round spermatid-expressed mRNAs as putative RBM5 targets. Importantly, the R263P mutation affected pre-mRNA splicing and resulted in a shift in the isoform ratios, or the production of novel spliced transcripts, of most targets. Microarray analysis of isolated round spermatids suggests that altered splicing of RBM5 target pre-mRNAs affected expression of genes in several pathways, including those implicated in germ cell adhesion, spermatid head shaping, and acrosome and tail formation. In summary, our findings reveal a critical role for RBM5 as a pre-mRNA splicing regulator in round spermatids and male fertility. Our findings also suggest that the second RRM of RBM5 is pivotal for appropriate pre-mRNA splicing.

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Skipping of an alternative intron in the srsf1 3' untranslated region increases transcript stability

Cited by 7 publications

References 17 publications

Characterization of Human Cyclin-Dependent Kinase 12 (CDK12) and CDK13 Complexes in C-Terminal Domain Phosphorylation, Gene Transcription, and RNA Processing

Characterization of Human Cyclin-Dependent Kinase 12 (CDK12) and CDK13 Complexes in C-Terminal Domain Phosphorylation, Gene Transcription, and RNA Processing

Aberrant Alternative Splicing Is Another Hallmark of Cancer

RBM5 Is a Male Germ Cell Splicing Factor and Is Required for Spermatid Differentiation and Male Fertility

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