Spliceostatin A interaction with SF3B limits U1 snRNP availability and causes premature cleavage and polyadenylation

Yoshimoto, Rei; Chhipi-Shrestha, Jagat K.; Schneider‐Poetsch, Tilman; Furuno, Masaaki; Burroughs, A. Maxwell; Noma, Shohei; Suzuki, Harukazu; Hayashizaki, Yoshihide; Mayeda, Akila; Nakagawa, Shinichi; Kaida, Daisuke; Iwasaki, Shigeo; Yoshida, Minoru

doi:10.1016/j.chembiol.2021.03.002

Cited by 11 publications

(13 citation statements)

References 46 publications

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“…By calculating the export efficiency of the U1-AMO-induced PCPAed products (cytoplasm/total reads ratio), we found that >80% of them could be exported to the cytoplasm using a cutoff value of 0.2 (Figure 6A; Supplemental Table 5). This number is in line with current reports that most of the reported intronic polyadenylated products could be exported to the cytoplasm (29,57).…”

Section: Resultssupporting

confidence: 92%

“…Altogether, consistent with other reports (29,57), we concluded that most of these intronic PCPAed products could be exported to the cytoplasm and have the potential to be translated.…”

Section: Pcpaed Products Could Be Exported To the Cytoplasm And Trans...supporting

confidence: 92%

“…Fourth, although we have provided data that U1 AMO disrupts U1 snRNP structure and affects transcription elongation, which emerges an important factor in regulation of alternative polyadenylation (APA) (58-59), we still do not know how U1 protects against intronic PAS usage, and whether it associates with U1's role in splicing needs to be further investigated, given the intimate links between 3' processing, splicing and transcription regulation (37,57,60,61).…”

Section: Discussionmentioning

confidence: 99%

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U1 AMO (antisense morpholino oligo) disrupts U1 snRNP structure to promote intronic premature cleavage and polyadenylation (PCPA)

Feng

Lin

Deng

et al. 2023

Preprint

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Functional depletion of U1 snRNP with a 25 nt U1 AMO (antisense morpholino oligonucleotides) may lead to intronic premature cleavage and polyadenylation (PCPA) of thousands of genes, a phenomenon known as U1 snRNP telescripting; however, the underlying mechanism remains elusive. In this study, we demonstrated that U1 AMO could disrupt U1 snRNP structure both in vitro and in vivo, thereby affecting U1 snRNP/RNAP polymerase II (RNAPII) interaction. We further showed that U1 AMO treatment might promote RNAPII disassociation with pre-mRNA in an RNA pull-down assay. By performing ChIP-seq for phosphorylation of Ser2 (Ser2P) and Ser5 (Ser5P) of the C-terminal domain (CTD) of RNA polymerase II (RNAPII), we showed that transcription elongation was disturbed upon U1 AMO treatment, with a particular high Ser2P signal at intronic cryptic polyadenylation sites (PASs). In addition, we showed that core 3' processing factors CPSF/CstF are involved in the processing of intronic cryptic PAS. Their recruitment accumulated toward cryptic PASs upon U1 AMO treatment, as indicated by ChIP-seq and iCLIP-seq analysis. Furthermore, we showed that most of these PCPAed transcripts could be exported to cytoplasm and have the potential to be translated. Conclusively, our data provide more insight into U1 snRNP telescripting, and suggest a common theme that modulation of transcription elongation may be an important mode for the regulation of mRNA polyadenylation.

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Section: Resultssupporting

confidence: 92%

“…Altogether, consistent with other reports (29,57), we concluded that most of these intronic PCPAed products could be exported to the cytoplasm and have the potential to be translated.…”

Section: Pcpaed Products Could Be Exported To the Cytoplasm And Trans...supporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

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U1 AMO (antisense morpholino oligo) disrupts U1 snRNP structure to promote intronic premature cleavage and polyadenylation (PCPA)

Feng

Lin

Deng

et al. 2023

Preprint

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“…In support of this idea, inhibition of SF3B1 with PlaB or SSA promotes premature termination of pol II (18,19), which relies on mRNA CPA (18,19), indicating that SF3B1 inhibition does not promote a loss of mRNA CPA factors from chromatin and therefore transcriptional readthrough, contrary to Isoginkgetin and Madrasin. Another important aspect that will require further investigation is the effect of these small molecule inhibitors on pol II elongation rate, which is known to affect pre-mRNA splicing and mRNA CPA (2)(3)(4)6,15,62).…”

Section: Discussionmentioning

confidence: 89%

“…In addition, the pol II elongation rate, which can be modified by cellular stresses or by mutating pol II, can affect the inclusion or the exclusion of some exons from the final mRNA in yeasts, mammals, and plants (2)(3)(4)6,(13)(14)(15)(16)(17). It also works the other way round as inhibition of pre-mRNA splicing by Spliceostatin A (SSA) or Pladienolide B (PlaB), two small molecule inhibitors of the U2 snRNP protein SF3B1, affect pol II transcription (5,7,18,19), pol II CTD phosphorylation (5), and recruitment of the key transcription elongation kinase, P-TEFb (7), which is composed of cyclin-dependent kinase (CDK)9 and cyclin T1. Interestingly, P-TEFb has also been found to be recruited to chromatin by the splicing factors SFPQ (20) and SRSF2 (21,22).…”

Section: Introductionmentioning

confidence: 99%

Isoginkgetin and Madrasin are poor splicing inhibitors

Tellier

Ansa

Murphy

2023

Preprint

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The production of eukaryotic mRNA requires transcription by RNA polymerase (pol) II and co-transcriptional processing, including capping, splicing, and cleavage and polyadenylation (CPA). Pol II can positively affect co-transcriptional processing through interaction of factors with its carboxyl terminal domain (CTD), comprising 52 repeats of the heptapeptide Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Small molecule inhibitors of the splicing factor SF3B1 cause loss of the transcription elongation factor P-TEFb from protein-coding gene templates and major transcription defects, indicating that splicing can, in turn, positively affect transcription. To understand better the relationship between pre-mRNA splicing and pol II transcription, we have investigated the effect of two other splicing inhibitors, Madrasin and Isoginkgetin, on transcription. We found that Madrasin rapidly inhibits pre-mRNA splicing, whereas Isoginkgetin affects transcription before any detectable effect on pre-mRNA splicing. Interestingly, we found that both of these small molecules promote general downregulation of transcription and global transcriptional readthrough, including on intronless and histone genes. Both small molecules affect the association of the mRNA CPA complex with chromatin, likely explaining the transcription termination defect. However, splicing inhibition is not necessarily associated with transcriptional readthrough as small molecule inhibitors of SF3B1 or knockdown of splicing factors do not cause a global transcription termination defect.

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SAP30BP interacts with RBM17/SPF45 to promote splicing in a subset of human short introns

Fukumura,

Sperotto,

Seuß

et al. 2023

Cell Reports

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Spliceostatin A interaction with SF3B limits U1 snRNP availability and causes premature cleavage and polyadenylation

Cited by 11 publications

References 46 publications

U1 AMO (antisense morpholino oligo) disrupts U1 snRNP structure to promote intronic premature cleavage and polyadenylation (PCPA)

U1 AMO (antisense morpholino oligo) disrupts U1 snRNP structure to promote intronic premature cleavage and polyadenylation (PCPA)

Isoginkgetin and Madrasin are poor splicing inhibitors

SAP30BP interacts with RBM17/SPF45 to promote splicing in a subset of human short introns

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