snoRNAs associate with mRNA 3′ processing complex: New wine in old bottles

Shi, Junjie; Huang, Chunliu; Huang, Shanshan; Yao, Chengguo

doi:10.1080/15476286.2017.1416278

Cited by 19 publications

(15 citation statements)

References 29 publications

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“…Further analysis showed that U1 snRNA is the most abundant and significant non-coding RNAs (ncRNA) interacting with sequences near PASs (Figure 1(b)). Additionally, consistent with the previous finding that a subset of snoRNAs associate with mRNA 3ʹ processing complex [35,36], specific snoRNA-PAS interactions were also detected (Supplemental Table 3). Given that the interactions of U1 snRNAs with PASs were the most abundant and significant, we wished to focus on U1 in this study.…”

Section: Resultssupporting

confidence: 90%

“…We have previously shown that non-coding RNAs (ncRNAs), such as small nucleolar RNAs (snoRNAs), are associated with mRNA 3ʹ processing protein complex [35,36], which prompted us to investigate whether any ncRNA regulates mRNA 3ʹ processing through RNA-RNA interaction. To address this, we performed PAS-CLASH (PolyA site-Crosslinking, Ligation and Sequencing of Hybrid) experiment.…”

Section: Introductionmentioning

confidence: 99%

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Suboptimal RNA–RNA interaction limits U1 snRNP inhibition of canonical mRNA 3’ processing

et al. 2019

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It is increasingly appreciated that U1 snRNP transcriptomically suppresses the usage of intronic polyadenylation site (PAS) of mRNAs, an outstanding question is why frequently used PASs are not suppressed. Here we found that U1 snRNP could be transiently associated with sequences upstream of actionable PASs in human cells, and RNA-RNA interaction might contribute to the association. By focusing on individual PAS, we showed that the stable assembly of U1 snRNP near PAS might be generally required for U1 inhibition of mRNA 3ʹ processing. Therefore, actionable PASs that often lack optimal U1 snRNP docking site nearby is free from U1 inhibitory effect. Consistently, natural 5ʹ splicing site (5ʹ-SS) is moderately enriched~250 nt upstream of intronic PASs whose usage is sensitive to functional knockdown of U1 snRNA. Collectively, our results provided an insight into how U1 snRNP selectively inhibits the usage of PASs in a cellular context, and supported a prevailing model that U1 snRNP scans pre-mRNA through RNA-RNA interaction to find a stable interaction site to exercise its function in pre-mRNA processing, including repressing the usage of cryptic PASs.

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Section: Resultssupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Suboptimal RNA–RNA interaction limits U1 snRNP inhibition of canonical mRNA 3’ processing

et al. 2019

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“…Recently, direct interactions between snoRNAs and pre-mRNAs as well as further processing of snoRNAs into miRNAs and shorter RNAs have emerged as new functions of snoRNAs [[10], [11], [12], [13]]. Here we review a new, so far understudied facet of snoRNA biology: the interaction of snoRNAs, mostly C/D box snoRNAs, with viruses.…”

Section: Snornas Are a Highly Expressed Class Of Non-coding Rnasmentioning

confidence: 99%

C/D box snoRNAs in viral infections: RNA viruses use old dogs for new tricks

Stamm

Lodmell

2019

Non-coding RNA Research

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C/D box snoRNAs (SNORDs) are a highly expressed class of non-coding RNAs. Besides their well-established role in rRNA modification, C/D box snoRNAs form protein complexes devoid of fibrillarin and regulate pre-mRNA splicing and polyadenylation of numerous genes. There is an emerging body of evidence for functional interactions between RNA viruses and C/D box snoRNAs. The infectivity of some RNA viruses depends on enzymatically active fibrillarin, and many RNA viral proteins associate with nucleolin or nucleophosmin, suggesting that viruses benefit from their cytosolic accumulation. These interactions are likely reflected by morphological changes in the nucleolus, often leading to relocalization of nucleolar proteins and ncRNAs to the cytosol that are a characteristic feature of viral infections. Knock-down studies have also shown that RNA viruses need specific C/D box snoRNAs for optimal replication, suggesting that RNA viruses benefit from gene expression programs regulated by SNORDs, or that viruses have evolved “new” uses for these humble ncRNAs to advance their prospects during infection.

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“…The role of noncoding RNAs in both 3′ end processing and DDR has not been extensively studied. Recently, a small nucleolar RNA (snoRNA), normally associated with rRNA maturation, was shown to compete with CpA component Fip1 for binding to AAUAAA signal (Huang et al, ; J. Shi, Huang, Huang, & Yao, ). SNORD50A inhibits mRNA 3′ processing by blocking the Fip1‐poly(A) site interaction, and SNORD50A depletion changed APA profiles genome‐wide.…”

Section: Alternative Polyadenylationmentioning

confidence: 99%

Connections between 3′ end processing and DNA damage response: Ten years later

Murphy

Kleiman

2019

WIREs RNA

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Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady‐state levels due to turnover of the transcripts. The 3′ end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene‐specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3′ end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins‐mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3′ End Processing RNA‐Based Catalysis > Miscellaneous RNA‐Catalyzed Reactions RNA in Disease and Development > RNA in Disease

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snoRNAs associate with mRNA 3′ processing complex: New wine in old bottles

Cited by 19 publications

References 29 publications

Suboptimal RNA–RNA interaction limits U1 snRNP inhibition of canonical mRNA 3’ processing

Suboptimal RNA–RNA interaction limits U1 snRNP inhibition of canonical mRNA 3’ processing

C/D box snoRNAs in viral infections: RNA viruses use old dogs for new tricks

Connections between 3′ end processing and DNA damage response: Ten years later

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