U1 snRNP telescripting regulates a size–function-stratified human genome

Oh, Jung Min; Di, Chao; Venters, Christopher C.; Guo, Jiannan; Arai, Chie; So, Byung Ran; Pinto, Anna Maria; Zhang, Zhenxi; Wan, Lili; Younis, Ihab; Dreyfuss, Gideon

doi:10.1038/nsmb.3473

Cited by 100 publications

(152 citation statements)

References 42 publications

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“…Similarly, the combinatorial effects of U1 inhibition and Exosc3 depletion were observed in the first intron but not in the fourth intron (Figure 2G). Unlike Exosc3 depletion, U1 inhibition led to about 2 fold increase in PAS-linked unique cleavage sites in the 4th intron, consistent with the idea that U1 suppresses the use of nearby PAS sites throughout the gene (Berg et al, 2012; Kaida et al, 2010; Oh et al, 2017). …”

Section: Resultssupporting

confidence: 79%

“…This transition could be pictured as a checkpoint where transcription is coupled to the necessary elongation factors that probably include the RNA splicing machinery. A recent report demonstrated that suppression of premature cleavage and polyadenylation by U1 snRNP, called U1 telescripting, is selectively required for long-distance transcription elongation in introns of large genes (Oh et al, 2017). Thus, U1 snRNP telescripting may have pleiotropic roles in transcriptional elongation: regulation of the +1 stable nucleosome-associated elongation checkpoint and subsequent prevention of Pol II termination in downstream large introns.…”

Section: Discussionmentioning

confidence: 99%

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Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP

et al. 2018

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Summary Regulation of RNA polymerase II (Pol II) elongation is a critical step in gene regulation. Here, we report that U1 snRNP recognition and transcription pausing at stable nucleosomes are linked through premature polyadenylation signal (PAS) termination. By generating RNA exosome conditional deletion mouse embryonic stem cells, we identified a large class of polyadenylated short transcripts in the sense direction destabilized by the RNA exosome. These PAS termination events are enriched at the first few stable nucleosomes flanking CpG islands and suppressed by U1 snRNP. Thus, promoter-proximal Pol II pausing consists of two processes: TSS-proximal and +1 stable nucleosome pausing, with PAS termination coinciding with the latter. While pausing factors NELF/DSIF only function in the former step, flavopiridol-sensitive mechanism(s) and Myc modulate both steps. We propose that premature PAS termination near the nucleosome-associated pause site represents a common transcriptional elongation checkpoint regulated by U1 snRNP recognition, nucleosome stability, and Myc activity.

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Section: Resultssupporting

confidence: 79%

Section: Discussionmentioning

confidence: 99%

Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP

et al. 2018

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“…Second, partial defects in complex formation might be expected to result in partial termination defects instead of the very strong effect caused by exclusive H73A expression. Moreover, recent results show that polyadenylation factors, exemplified by CstF64, assemble on inactive intronic PASs, but this is insufficient to cause termination unless cleavage is activated by U1 snRNA inhibition (Oh et al 2017). Finally, the widespread requirement for Xrn2 in efficient termination is most readily explained by PAS cleavage preceding its action.…”

Section: Discussionmentioning

confidence: 99%

Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity

et al. 2018

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Termination is a ubiquitous phase in every transcription cycle but is incompletely understood and a subject of debate. We used gene editing as a new approach to address its mechanism through engineered conditional depletion of the 5 ′ → 3 ′ exonuclease Xrn2 or the polyadenylation signal (PAS) endonuclease CPSF73 (cleavage and polyadenylation specificity factor 73). The ability to rapidly control Xrn2 reveals a clear and general role for it in cotranscriptional degradation of 3 ′ flanking region RNA and transcriptional termination. This defect is characterized genome-wide at high resolution using mammalian native elongating transcript sequencing (mNET-seq). An Xrn2 effect on termination requires prior RNA cleavage, and we provide evidence for this by showing that catalytically inactive CPSF73 cannot restore termination to cells lacking functional CPSF73. Notably, Xrn2 plays no significant role in either Histone or small nuclear RNA (snRNA) gene termination even though both RNA classes undergo 3 ′ end cleavage. In sum, efficient termination on most protein-coding genes involves CPSF73-mediated RNA cleavage and cotranscriptional degradation of polymerase-associated RNA by Xrn2. However, as CPSF73 loss caused more extensive readthrough transcription than Xrn2 elimination, it likely plays a more underpinning role in termination.

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“…Depletion of U1 snRNP creates a stress on the splicing machinery as well as on other co-transcriptional events dependent upon the availability of U1 snRNP [121]. A diverse set of SMN transcripts is generated upon depletion of U1 snRNP by an ASO that sequesters the 5′ end of endogenous U1 snRNA [49].…”

Section: Alternative Splicing Of Other Smn Exonsmentioning

confidence: 99%

Mechanism of Splicing Regulation of Spinal Muscular Atrophy Genes

Singh

2018

Advances in Neurobiology

112

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Spinal muscular atrophy (SMA) is one of the major genetic disorders associated with infant mortality. More than 90% cases of SMA result from deletions or mutations of Survival Motor Neuron 1 (SMN1) gene. SMN2, a nearly identical copy of SMN1, does not compensate for the loss of SMN1 due to predominant skipping of exon 7. However, correction of SMN2 exon 7 splicing has proven to confer therapeutic benefits in SMA patients. The only approved drug for SMA is an antisense oligonucleotide (Spinraza™/Nusinersen), which corrects SMN2 exon 7 splicing by blocking intronic splicing silencer N1 (ISS-N1) located immediately downstream of exon 7. ISS-N1 is a complex regulatory element encompassing overlapping negative motifs and sequestering a cryptic splice site. More than 40 protein factors have been implicated in the regulation of SMN exon 7 splicing. There is evidence to support that multiple exons of SMN are alternatively spliced during oxidative stress, which is associated with a growing number of pathological conditions. Here, we provide the most up to date account of the mechanism of splicing regulation of the SMN genes.

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U1 snRNP telescripting regulates a size–function-stratified human genome

Cited by 100 publications

References 42 publications

Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP

Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP

Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity

Mechanism of Splicing Regulation of Spinal Muscular Atrophy Genes

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