The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Transcriptome-wide analyses of CstF64–RNA interactions in global regulation of mRNA alternative polyadenylation
Open accessAbstract
Cleavage stimulation factor 64 kDa (CstF64) is an essential pre-mRNA 3′ processing factor and an important regulator of alternative polyadenylation (APA). Here we characterized CstF64–RNA interactions in vivo at the transcriptome level and investigated the role of CstF64 in global APA regulation through individual nucleotide resolution UV crosslinking and immunoprecipitation sequencing and direct RNA sequencing analyses. We observed highly specific CstF64–RNA interactions at poly(A) sites (PASs), and we provide evidence that such interactions are widely variable in affinity and may be differentially required for PAS recognition. Depletion of CstF64 by RNAi has a relatively small effect on the global APA profile, but codepletion of the CstF64 paralog CstF64τ leads to greater APA changes, most of which are characterized by the increased relative use of distal PASs. Finally, we found that CstF64 binds to thousands of dormant intronic PASs that are suppressed, at least in part, by U1 small nuclear ribonucleoproteins. Taken together, our findings provide insight into the mechanisms of PAS recognition and identify CstF64 as an important global regulator of APA.
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iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
König, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M., & Ule, J. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1838 · Cited by 1,126
Mechanism and regulation of mRNA polyadenylation
Colgan, D. F., & Manley, J. L. (1997) · Genes & Development · doi:10.1101/gad.11.21.2755 · Cited by 784
Mechanisms and Consequences of Alternative Polyadenylation
Di Giammartino, D. C., Nishida, K., & Manley, J. L. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.017 · Cited by 737
U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation
Kaida, D., Berg, M. G., Younis, I., Kasim, M., Singh, L. N., Wan, L., & Dreyfuss, G. (2010) · Nature · doi:10.1038/nature09479 · Cited by 638
Flavell, S. W., Kim, T.-K., Gray, J. M., Harmin, D. A., Hemberg, M., Hong, E. J., Markenscoff-Papadimitriou, E., Bear, D. M., & Greenberg, M. E. (2008) · Neuron · doi:10.1016/j.neuron.2008.11.029 · Cited by 440
Ji, Z., & Tian, B. (2009) · PLoS ONE · doi:10.1371/journal.pone.0008419 · Cited by 264
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Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing
Nojima, T., Gomes, T., Grosso, A. R. F., Kimura, H., Dye, M. J., Dhir, S., Carmo-Fonseca, M., & Proudfoot, N. J. (2015) · Cell · doi:10.1016/j.cell.2015.03.027 · Cited by 562
Dynamic landscape and evolution of m6A methylation in human
Zhang, H., Shi, X., Huang, T., Zhao, X., Chen, W., Gu, N., & Zhang, R. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa347 · Cited by 359
Alternative mRNA transcription, processing, and translation: insights from RNA sequencing
de Klerk, E., & ‘t Hoen, P. A. C. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.01.001 · Cited by 350
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Metadata
- Authors
- Yao, C., Biesinger, J., Wan, J., Weng, L., Xing, Y., Xie, X., & Shi, Y.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2012-10-29
- Volume
- 109
- Issue
- 46
- Pages
- 18773-18778
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2045709965
- Cited by
- 208
- References
- 6
- FWCI
- 6.16
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Yao, C., Biesinger, J., Wan, J., Weng, L., Xing, Y., Xie, X., & Shi, Y. (2012). Transcriptome-wide analyses of CstF64–RNA interactions in global regulation of mRNA alternative polyadenylation. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1211101109
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