PreprintCited by 249RNA Research and SplicingRNA regulation and diseaseRNA and protein synthesis mechanisms

The DOI matches its Crossref record; 110 of the 110 references it cites were found in a registry or an index.

The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

Open access

Shi, Yongsheng, Manley, James L.·2015·Genes & Development

DOI 10.1101/gad.261974.115PMC PMC4421977

Open this paper in CoChat — free account Open PDF

Abstract

The key RNA sequence elements and protein factors necessary for 3′ processing of polyadenylated mRNA precursors are well known. Recent studies, however, have significantly reshaped current models for the protein–RNA interactions involved in poly(A) site recognition, painting a picture more complex than previously envisioned and also providing new insights into regulation of this important step in gene expression. Here we review the recent advances in this area and provide a perspective for future studies.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1101/gad.261974.115

Cites

110 of 110 references verified0 citation errors · 0 not checkable

Statistics

Figure 1. (A) Schematic models showing distinct modules within CPSF. CPSF73, CPSF100, and Symplekin form a module (which we refer to as mCF) that contains the endonuclease activity. mCF may cooperate with different RNA-binding modules, such as mammalian polyadenylation specificity factor (mPSF) (Wdr33, CPSF30, Fip1, and CPSF160), for cleavage/polyadenylation of most mRNAs or with SLBP and U7 snRNP for the cleavage of histone mRNAs. (B, bottom panel) Domain structures of the CPSF subunits involved or implicated in RNA binding. The known or putative RNA-binding regions are marked with red solid or dotted underlines.CC BY-NC · PubMed Central

Figure 2. (A) CstF-dependent and potentially CstF-independent PAS recognition. In the CstF-independent model, CstF is shown in a dotted boundary to indicate that CstF may or may not be present in this complex. The scaffolding protein Symplekin plays a role in bridging CPSF–CstF complexes. (B) CFI–RNA interactions. (Top panel) CFI binds to UGUA motifs often found upstream of the AAUAAA hexamer. (Bottom panel) The CFI dimer may bind to two UGUA sequences at different PASs, thus looping out the proximal PASs. (C) The role of Rbbp6 in PAS recognition. The question mark denotes the fact that Rbbp6 may or may not directly interact with upstream AU-rich elements (AREs) or may rely on an unknown factor.CC BY-NC · PubMed Central

Figure 3. Context-dependent regulation of PAS recognition. Regulatory factors bound at different locations relative to the core PAS sequence have different effects on PAS recognition by the mRNA 3′ processing factors. Positive effects are indicated by an arrow, and negative effects are indicated by a vertical line.CC BY-NC · PubMed Central

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

The Spliceosome: Design Principles of a Dynamic RNP Machine
Wahl, M. C., Will, C. L., & Lührmann, R. (2009) · Cell · doi:10.1016/j.cell.2009.02.009 · Cited by 2,665
Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells
Mayr, C., & Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.06.016 · Cited by 1,613
HITS-CLIP yields genome-wide insights into brain alternative RNA processing
Licatalosi, D. D., Mele, A., Fak, J. J., Ule, J., Kayikci, M., Chi, S. W., Clark, T. A., Schweitzer, A. C., Blume, J. E., Wang, X., et al. (2008) · Nature · doi:10.1038/nature07488 · Cited by 1,352 · cited 1×
“For example, NOVA proteins, which are known splicing regulators in the brain (Jensen et al. 2000), were shown to regulate APA by binding to sites in 3′ UTRs and repress or enhance PAS usage in a position-dependent manner (Licatalosi et al. 2008).”
Background
Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites
Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A., & Burge, C. B. (2008) · Science · doi:10.1126/science.1155390 · Cited by 1,349
IFITM Proteins Mediate the Innate Immune Response to Influenza A H1N1 Virus, West Nile Virus and Dengue Virus
Brass, A., Huang, I.-C., Benita, Y., John, S., Krishnan, M. N., Feeley, E., Ryan, B., Weyer, J., van der Weyden, L., Fikrig, E., et al. (2009) · Cell · doi:10.1016/j.cell.2009.12.017 · Cited by 1,292
Integrating mRNA Processing with Transcription
Proudfoot, N. J., Furger, A., & Dye, M. J. (2002) · Cell · doi:10.1016/s0092-8674(02)00617-7 · Cited by 1,084
Context-dependent control of alternative splicing by RNA-binding proteins
Fu, X.-D., & Ares, M. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3778 · Cited by 1,044
Formation of mRNA 3′ Ends in Eukaryotes: Mechanism, Regulation, and Interrelationships with Other Steps in mRNA Synthesis
Zhao, J., Hyman, L. E., & Moore, C. L. (1999) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.63.2.405-445.1999 · Cited by 1,024
The General Transcription Machinery and General Cofactors
Thomas, M. C., & Chiang, C. (2006) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409230600648736 · Cited by 992
Large-Scale Proteomic Analysis of the Human SpliceosomePreprint
Rappsilber, J., Ryder, U., Lamond, A. I., & Mann, M. (2002) · Genome Research · doi:10.1101/gr.473902 · Cited by 945

Show all 108 references

Sorted by citations

Alternative polyadenylation of mRNA precursors
Tian, B., & Manley, J. L. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.116 · Cited by 1,179
Self-citation
RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms
Fay, M. M., Lyons, S. M., & Ivanov, P. V. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.05.017 · Cited by 455
The Output of Protein-Coding Genes Shifts to Circular RNAs When the Pre-mRNA Processing Machinery Is Limiting
Liang, D., Tatomer, D. C., Luo, Z., Wu, H., Yang, L. C., Chen, L., Cherry, S. R., & Wilusz, J. E. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.10.034 · Cited by 446
Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics
Nojima, T., & Proudfoot, N. J. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00447-6 · Cited by 432
m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome
Molinié, B., Wang, J., Lim, K. S., Hillebrand, R., Lu, Z., Wittenberghe, N. V., Howard, B. D., Daneshvar, K., Mullen, A. C., Dedon, P. C., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3898 · Cited by 401
The neurogenetics of alternative splicing
Vuong, C. K., Black, D. L., & Zheng, S. (2016) · Nature Reviews Neuroscience · doi:10.1038/nrn.2016.27 · Cited by 340
Codon Usage and 3′ UTR Length Determine Maternal mRNA Stability in Zebrafish
Mishima, Y., & Tomari, Y. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.02.027 · Cited by 288
Functional diversity of small nucleolar RNAs
Bratkovič, T., Božič, J., & Rogelj, B. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkz1140 · Cited by 272
Emerging Roles of Disordered Sequences in RNA-Binding Proteins
Calabretta, S., & Richard, S. (2015) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2015.08.012 · Cited by 246
The pathogenic exon 1 HTT protein is produced by incomplete splicing in Huntington’s disease patients
Neueder, A., Landles, C., Ghosh, R., Howland, D., Myers, R. H., Faull, R. L. M., Tabrizi, S. J., & Bates, G. P. (2017) · Scientific Reports · doi:10.1038/s41598-017-01510-z · Cited by 235
Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation
Zhu, Y., Wang, X., Forouzmand, E., Jeong, J., Qiao, F., Sowd, G. A., Engelman, A., Xie, X. S., Hertel, K. J., & Shi, Y. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.11.031 · Cited by 221
Self-citation
The roles of RNA processing in translating genotype to phenotype
Manning, K. S., & Cooper, T. A. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.139 · Cited by 212
Small Nucleolar RNAs Tell a Different Tale
Kufel, J., & Grzechnik, P. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.11.005 · Cited by 184
Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back
Kharel, P., Becker, G., Цветков, В. Б., & Ivanov, P. V. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1126 · Cited by 152
CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis
Hou, Y., Sun, J., Wu, B., Gao, Y., Nie, H., Nie, Z., Quan, S., Wang, Y., Cao, X., & Li, S. (2021) · Molecular Plant · doi:10.1016/j.molp.2021.01.013 · Cited by 159
Transcriptional Control by Premature Termination: A Forgotten Mechanism
Kamieniarz-Gdula, K., & Proudfoot, N. J. (2019) · Trends in Genetics · doi:10.1016/j.tig.2019.05.005 · Cited by 169
Molecular basis for the recognition of the human AAUAAA polyadenylation signal
Sun, Y., Zhang, Y., Hamilton, K., Manley, J. L., Shi, Y., Walz, T., & Tong, L. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1718723115 · Cited by 154
Self-citation
Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination
Kamieniarz-Gdula, K., Gdula, M. R., Panser, K., Nojima, T., Monks, J., Wiśniewski, J. R., Riepsaame, J., Brockdorff, N., Pauli, A., & Proudfoot, N. J. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.01.027 · Cited by 145
The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors
Antosz, W., Pfab, A., Ehrnsberger, H. F., Holzinger, P., Köllen, K., Mortensen, S. A., Bruckmann, A., Schubert, T. E. O., Längst, G., Griesenbeck, J., et al. (2017) · The Plant Cell · doi:10.1105/tpc.16.00735 · Cited by 147
Translation initiation by cap‐dependent ribosome recruitment: Recent insights and open questions
Shirokikh, N. E., & Preiß, T. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1473 · Cited by 142
The Untranslated Regions of mRNAs in Cancer
Schuster, S. L., & Hsieh, A. C. (2019) · Trends in cancer · doi:10.1016/j.trecan.2019.02.011 · Cited by 145
A Polyadenylation-Dependent 3′ End Maturation Pathway Is Required for the Synthesis of the Human Telomerase RNA
Nguyen, D., St-Sauveur, V. G., Bergeron, D., Dupuis‐Sandoval, F., Scott, M. S., & Bachand, F. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.11.003 · Cited by 125
Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex
Clerici, M., Faini, M., Muckenfuss, L. M., Aebersold, R. H., & Jínek, M. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-017-0020-6 · Cited by 119
U1 snRNP telescripting regulates a size–function-stratified human genome
Oh, J., Di, C., Venters, C. C., Guo, J., Arai, C., So, B. R., Pinto, A. M., Zhang, Z., Wan, L., Younis, I., et al. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3473 · Cited by 118
Alternative Splicing as a Regulator of Early Plant Development
Szakonyi, D., & Duque, P. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.01174 · Cited by 117
A Complex of U1 snRNP with Cleavage and Polyadenylation Factors Controls Telescripting, Regulating mRNA Transcription in Human Cells
So, B. R., Di, C., Cai, Z., Venters, C. C., Guo, J., Oh, J., Arai, C., & Dreyfuss, G. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.08.007 · Cited by 120
The Chemical Biology of Human Metallo-β-Lactamase Fold Proteins
Pettinati, I., Brem, J., Lee, S. Y., McHugh, P. J., & Schofield, C. J. (2016) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2015.12.007 · Cited by 114
A snoRNA modulates mRNA 3′ end processing and regulates the expression of a subset of mRNAs
Huang, C., Shi, J., Guo, Y., Huang, W., Huang, S., Ming, S., Wu, X., Zhang, R., Ding, J., Zhao, W., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx651 · Cited by 113
Self-citation
Rules and tools to predict the splicing effects of exonic and intronic mutations
Ohno, K., Takeda, J., & Masuda, A. (2017) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1451 · Cited by 110
A compendium of conserved cleavage and polyadenylation events in mammalian genesPreprint
Wang, R., Zheng, D., Yehia, G., & Tian, B. (2018) · Genome Research · doi:10.1101/gr.237826.118 · Cited by 108
Regulation of Intronic Polyadenylation by PCF11 Impacts mRNA Expression of Long Genes
Wang, R., Zheng, D., Lü, W., Ding, Q., & Tian, B. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.02.049 · Cited by 103
Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27
Wang, X., Hennig, T., Whisnant, A. W., Erhard, F., Prusty, B. K., Friedel, C. C., Forouzmand, E., Hu, W. K., Erber, L. N., Chen, Y., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-14109-x · Cited by 99
Self-citation
Activation of the Endonuclease that Defines mRNA 3′ Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex
Hill, C. H., Boreikaitė, V., Kumar, A., Casañal, A., Kubík, P., Degliesposti, G., Maslen, S., Mariani, A., von Loeffelholz, O., Girbig, M., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2018.12.023 · Cited by 96
Alternative Polyadenylation: a new frontier in post transcriptional regulation
Ren, F., Zhang, N., Zhang, L., Miller, E. W., & Pu, J. J. (2020) · Biomarker Research · doi:10.1186/s40364-020-00249-6 · Cited by 92
Structural insights into the assembly and polyA signal recognition mechanism of the human CPSF complex
Clerici, M., Faini, M., Aebersold, R. H., & Jínek, M. (2017) · eLife · doi:10.7554/elife.33111 · Cited by 87
Transcription and splicing: A two‐way street
Tellier, M., Maudlin, I., & Murphy, S. (2020) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1593 · Cited by 88
Alternative cleavage and polyadenylation in spermatogenesis connects chromatin regulation with post-transcriptional control
Li, W., Park, J. Y., Zheng, D., Hoque, M., Yehia, G., & Tian, B. (2016) · BMC Biology · doi:10.1186/s12915-016-0229-6 · Cited by 90
Structural Insights into the Human Pre-mRNA 3′-End Processing Machinery
Zhang, Y., Sun, Y., Shi, Y., Walz, T., & Tong, L. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.11.005 · Cited by 78
Self-citation
PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation
Yang, Y., Li, W., Hoque, M., Hou, L., Shen, S., Tian, B., & Dynlacht, B. D. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005794 · Cited by 79
U1 snRNP Telescripting: Suppression of Premature Transcription Termination in Introns as a New Layer of Gene RegulationPreprint
Venters, C. C., Oh, J., Di, C., So, B. R., & Dreyfuss, G. (2019) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a032235 · Cited by 75
RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases
Battaglia, S., Lidschreiber, M., Baejen, C., Torkler, P., Vos, S. M., & Cramer, P. (2017) · eLife · doi:10.7554/elife.25637 · Cited by 75
Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long-Term Potentiation
Fontes, M. M., Güvenek, A., Kawaguchi, R., Zheng, D., Huang, A., Ho, V. M., Chen, P. B., Liu, X., O’Dell, T. J., Coppola, G., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-17407-w · Cited by 69
Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinomaPreprint
Venkat, S., Tisdale, A. A., Schwarz, J. R., Alahmari, A. A., Maurer, H. C., Olive, K. P., Eng, K. H., & Feigin, M. E. (2020) · Genome Research · doi:10.1101/gr.257550.119 · Cited by 72
Recent molecular insights into canonical pre-mRNA 3’-end processing
Sun, Y., Hamilton, K., & Tong, L. (2020) · Transcription · doi:10.1080/21541264.2020.1777047 · Cited by 76
Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation
Zhou, Z., Dang, Y., Zhou, M., Yuan, H., & Liu, Y. (2018) · eLife · doi:10.7554/elife.33569 · Cited by 71
Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster
Liu, X., Freitas, J., Zheng, D., Oliveira, M. S., Hoque, M., Martins, T., Henriques, T., Tian, B., & Moreira, A. (2017) · RNA · doi:10.1261/rna.062661.117 · Cited by 67
The landscape of alternative polyadenylation in single cells of the developing mouse embryo
Agarwal, V., Lopez-Darwin, S. L., Kelley, D. R., & Shendure, J. (2021) · Nature Communications · doi:10.1038/s41467-021-25388-8 · Cited by 66
Transcriptome Analyses of FY Mutants Reveal Its Role in mRNA Alternative Polyadenylation
Yu, Z., Lin, J., & Li, Q. Q. (2019) · The Plant Cell · doi:10.1105/tpc.18.00545 · Cited by 67
CDK11 in TREX/THOC Regulates HIV mRNA 3′ End Processing
Pak, V., Eifler, T., Jäger, S., Krogan, N. J., Fujinaga, K., & Peterlin, B. M. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.10.012 · Cited by 66
The m6A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants
Pontier, D., Picart, C., Baidouri, M. E., Roudier, F., Xu, T., Lahmy, S., Llauro, C., Azevedo, J., Laudié, M., Attina, A., et al. (2019) · Life Science Alliance · doi:10.26508/lsa.201900393 · Cited by 66
Widespread transcript shortening through alternative polyadenylation in secretory cell differentiation
Cheng, L. C., Zheng, D., Baljinnyam, E., Sun, F., Ogami, K., Yeung, P. L., Hoque, M., Lu, C.-W., Manley, J. L., & Tian, B. (2020) · Nature Communications · doi:10.1038/s41467-020-16959-2 · Cited by 61
Self-citation
Alternative polyadenylation by sequential activation of distal and proximal PolyA sites
Tang, P., Yang, Y., Li, G., Huang, L., Wen, M., Ruan, W., Guo, X., Zhang, C., Zuo, X., Luo, D., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-021-00709-z · Cited by 65
Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis
Thomas, Q. A., Ard, R., Liu, J., Li, B., Wang, J., Pelechano, V., & Marquardt, S. (2020) · Nature Communications · doi:10.1038/s41467-020-16390-7 · Cited by 63
Structure of the catalytic core of the Integrator complex
Pfleiderer, M. M., & Galej, W. P. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.01.005 · Cited by 63
The mRNA Export Receptor NXF1 Coordinates Transcriptional Dynamics, Alternative Polyadenylation, and mRNA Export
Chen, S., Wang, R., Zheng, D., Zhang, H., Chang, X., Wang, K., Li, W., Fan, J., Tian, B., & Cheng, H. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.01.026 · Cited by 59
Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition
Schlundt, A., Tants, J., & Sattler, M. (2017) · Methods · doi:10.1016/j.ymeth.2017.03.015 · Cited by 59
The Nrd1-like protein Seb1 coordinates cotranscriptional 3′ end processing and polyadenylation site selectionPreprint
Lemay, J., Marguerat, S., Larochelle, M., Liu, X., van Nues, R. W., Hunyadkürti, J., Hoque, M., Tian, B., Granneman, S., Bähler, J., et al. (2016) · Genes & Development · doi:10.1101/gad.280222.116 · Cited by 58
ALYREF links 3′‐end processing to nuclear export of non‐polyadenylated mRNAs
Fan, J., Wang, K., Du, X., Wang, J., Chen, S., Wang, Y., Shi, M. Y., Zhang, L., Wu, X., Zheng, D., et al. (2019) · The EMBO Journal · doi:10.15252/embj.201899910 · Cited by 56
The G-Quadruplex-Specific RNA Helicase DHX36 Regulates p53 Pre-mRNA 3′-End Processing Following UV-Induced DNA Damage
Newman, M., Sfaxi, R., Saha, A., Monchaud, D., Teulade‐Fichou, M., & Vagner, S. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.11.033 · Cited by 56
The Integrator Complex in Transcription and Development
Mendoza-Figueroa, M. S., Tatomer, D. C., & Wilusz, J. E. (2020) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2020.07.004 · Cited by 54
Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombePreprint
Liu, X., Hoque, M., Larochelle, M., Lemay, J., Yurko, N., Manley, J. L., Bachand, F., & Tian, B. (2017) · Genome Research · doi:10.1101/gr.222331.117 · Cited by 53
Self-citation
Reconstitution of mammalian cleavage factor II involved in 3′ processing of mRNA precursors
Schafer, P. H., Tüting, C., Schönemann, L., Kühn, U., Treiber, T., Treiber, N., Ihling, C. H., Graber, A., Keller, W., Meister, G., et al. (2018) · RNA · doi:10.1261/rna.068056.118 · Cited by 54
Cleavage and polyadenylation specificity factor 30: An RNA-binding zinc-finger protein with an unexpected 2Fe–2S cluster
Shimberg, G. D., Michalek, J. L., Oluyadi, A. A., Rodrigues, A. V., Zucconi, B. E., Neu, H. M., Ghosh, S., Sureschandra, K., Wilson, G. M., Stemmler, T. L., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1517620113 · Cited by 54
Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast
Larochelle, M., Robert, M.-A., Hébert, J.-N., Liu, X., Matteau, D., Rodrigue, S., Tian, B., Jacques, P., & Bachand, F. (2018) · Nature Communications · doi:10.1038/s41467-018-06546-x · Cited by 53
Competitive regulation of alternative splicing and alternative polyadenylation by hnRNP H and CstF64 determines acetylcholinesterase isoforms
Nazim, M., Masuda, A., Rahman, M. A., Nasrin, F., Takeda, J., Ohe, K., Ohkawara, B., Ito, M., & Ohno, K. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw823 · Cited by 53
Plant 3’ Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression
Bernardes, W. S., & Menossi, M. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.01252 · Cited by 53
The polyadenylation factor FIP1 is important for plant development and root responses to abiotic stresses
Téllez‐Robledo, B., Manzano, C., Saéz, Á., Navarro‐Neila, S., Silva‐Navas, J., de Lorenzo, L., González‐García, M. P., Toribio, R., Hunt, A. G., Baigorri, R., et al. (2019) · The Plant Journal · doi:10.1111/tpj.14416 · Cited by 51
The Ins and Outs of Messenger RNA Electroporation for Physical Gene Delivery in Immune Cell-Based Therapy
Campillo-Davó, D., Laere, M. D., Roex, G., Versteven, M., Flumens, D., Berneman, Z. N., Tendeloo, V. F. V., Anguille, S., & Lion, E. (2021) · Pharmaceutics · doi:10.3390/pharmaceutics13030396 · Cited by 50
RNA Binding Protein CELF2 Regulates Signal-Induced Alternative Polyadenylation by Competing with Enhancers of the Polyadenylation Machinery
Chatrikhi, R., Mallory, M. J., Gazzara, M. R., Agosto, L. M., Zhu, W. S., Litterman, A. J., Ansel, K. M., & Lynch, K. W. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.08.022 · Cited by 47
mRNA Editing, Processing and Quality Control in Caenorhabditis elegans
Arribere, J. A., Kuroyanagi, H., & Hundley, H. A. (2020) · Genetics · doi:10.1534/genetics.119.301807 · Cited by 46
Codon usage bias regulates gene expression and protein conformation in yeast expression system P. pastoris
Xu, Y., Liu, K., Han, Y., Xing, Y., Zhang, Y., Yang, Q., & Zhou, M. (2021) · Microbial Cell Factories · doi:10.1186/s12934-021-01580-9 · Cited by 48
Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential
Vlaming, H., Mimoso, C. A., Field, A. R., Martin, B. J. E., & Adelman, K. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00785-9 · Cited by 46
LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival
Goering, R., Engel, K. L., Gillen, A. E., Fong, N., Bentley, D. L., & Taliaferro, J. M. (2021) · BMC Genomics · doi:10.1186/s12864-021-07781-1 · Cited by 45
The three as: Alternative splicing, alternative polyadenylation and their impact on apoptosis in immune function
Blake, D., & Lynch, K. W. (2021) · Immunological Reviews · doi:10.1111/imr.13018 · Cited by 49
CPF Recruitment to Non-canonical Transcription Termination Sites Triggers Heterochromatin Assembly and Gene Silencing
Vo, T. V., Dhakshnamoorthy, J., Larkin, M., Zofall, M., Thillainadesan, G., Balachandran, V., Holla, S., Wheeler, D. L., & Grewal, S. I. S. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.05.107 · Cited by 47
Alternative polyadenylation factors link cell cycle to migration
Mitra, M., Johnson, E. L., Swamy, V. S., Nersesian, L., Corney, D. C., Robinson, D. G., Taylor, D. G., Ambrus, A., Jelínek, D., Wang, W., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1551-9 · Cited by 42
The reciprocal regulation between splicing and 3′‐end processing
Kaida, D. (2016) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1348 · Cited by 47
Distinct regulation of alternative polyadenylation and gene expression by nuclear poly(A) polymerases
Li, W., Li, W., Laishram, R. S., Hoque, M., Ji, Z., Tian, B., & Anderson, R. A. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx560 · Cited by 45
A conserved RNA degradation complex required for spreading and epigenetic inheritance of heterochromatin
Shipkovenska, G. G., Durango, A., Kalocsay, M., Gygi, S. P., & Moazed, D. (2020) · eLife · doi:10.7554/elife.54341 · Cited by 42
Alternative polyadenylation: An enigma of transcript length variation in health and disease
Mohanan, N. K., Shaji, F., Koshre, G. R., & Laishram, R. S. (2021) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1692 · Cited by 43
FUS ‐mediated regulation of alternative RNA processing in neurons: insights from global transcriptome analysis
Masuda, A., Takeda, J., & Ohno, K. (2016) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1338 · Cited by 42
RNA regulatory processes in RNA virus biology
Cross, S. T., Michalski, D., Miller, M. R., & Wilusz, J. (2019) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1536 · Cited by 40
Two distinct transcription termination modes dictated by promotersPreprint
Miki, T., Carl, S. H., & Großhans, H. (2017) · Genes & Development · doi:10.1101/gad.301093.117 · Cited by 40
Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA‐seq data
Güvenek, A., & Tian, B. (2018) · Quantitative Biology · doi:10.1007/s40484-018-0148-3 · Cited by 38
NAA10 polyadenylation signal variants cause syndromic microphthalmia
Johnston, J. J., Williamson, K. A., Chou, C. M., Sapp, J. C., Ansari, M., Chapman, H. M., Cooper, D. N., Dabir, T. A., Dudley, J. N., Holt, R. J., et al. (2019) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2018-105836 · Cited by 37
Target Identification of an Antimalarial Oxaborole Identifies AN13762 as an Alternative Chemotype for Targeting CPSF3 in Apicomplexan Parasites
Bellini, V., Swale, C., Brenier‐Pinchart, M., Pézier, T., Georgeault, S., Laurent, F., Hakimi, M., & Bougdour, A. (2020) · iScience · doi:10.1016/j.isci.2020.101871 · Cited by 39
Prenatal maternal stress and offspring aggressive behavior: Intergenerational and transgenerational inheritance
Mbiydzenyuy, N. E., Hemmings, S. M. J., & Qulu, L. (2022) · Frontiers in Behavioral Neuroscience · doi:10.3389/fnbeh.2022.977416 · Cited by 44
Processing and transcriptome expansion at the mRNA 3′ end in health and disease: finding the right end
Ogorodnikov, A., Kargapolova, Y., & Danckwardt, S. (2016) · Pflügers Archiv - European Journal of Physiology · doi:10.1007/s00424-016-1828-3 · Cited by 39
TENT5 cytoplasmic noncanonical poly(A) polymerases regulate the innate immune response in animals
Liudkovska, V., Krawczyk, P. S., Brouze, A., Gumińska, N., Węgierski, T., Cysewski, D., Mackiewicz, Z., Ewbank, J. J., Drabikowski, K., Mroczek, S., et al. (2022) · Science Advances · doi:10.1126/sciadv.add9468 · Cited by 36
The PAF1 complex promotes 3′ processing of pervasive transcripts
Liu, X., Guo, Z., Han, J., Peng, B., Zhang, B., Li, H., Hu, X., David, C. J., & Chen, M. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110519 · Cited by 36
Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons
Cole, B. S., Tapescu, I., Allon, S. J., Mallory, M. J., Qiu, J., Lake, R. J., Fan, H.-Y., Fu, X., & Lynch, K. W. (2015) · RNA · doi:10.1261/rna.052969.115 · Cited by 34
Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation
Wang, X., Liu, L., Whisnant, A. W., Hennig, T., Djaković, L., Haque, N., Bach, C., Sandri-Goldin, R. M., Erhard, F., Friedel, C. C., et al. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009263 · Cited by 35
Self-citation
On the Cutting Edge: Regulation and Therapeutic Potential of the mRNA 3′ End Nuclease
Liu, H., & Moore, C. L. (2021) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2021.04.003 · Cited by 33
Rapid and Scalable Profiling of Nascent RNA with fastGRO
Barbieri, E., Hill, C., Quesnel-Vallières, M., Zucco, A. J., Barash, Y., & Gardini, A. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108373 · Cited by 33
Roles of Sumoylation in mRNA Processing and Metabolism
Richard, P., Vethantham, V., & Manley, J. L. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-50044-7_2 · Cited by 32
Self-citation
A conserved role for the ALS-linked splicing factor SFPQ in repression of pathogenic cryptic last exons
Gordon, P. M., Hamid, F., Makeyev, E. V., & Houart, C. (2021) · Nature Communications · doi:10.1038/s41467-021-22098-z · Cited by 29
Elevated pre-mRNA 3′ end processing activity in cancer cells renders vulnerability to inhibition of cleavage and polyadenylation
Cui, Y., Wang, L., Ding, Q., Shin, J., Cassel, J. A., Liu, Q., Salvino, J. M., & Tian, B. (2023) · Nature Communications · doi:10.1038/s41467-023-39793-8 · Cited by 31
Characterization of mRNA polyadenylation in the apicomplexa
Stevens, A. T., Howe, D. K., & Hunt, A. G. (2018) · PLoS ONE · doi:10.1371/journal.pone.0203317 · Cited by 29
A Genome-wide Study of “Non-3UTR” Polyadenylation Sites in Arabidopsis thaliana
Guo, C., Spinelli, M., Liu, M., Li, Q. Q., & Liang, C. (2016) · Scientific Reports · doi:10.1038/srep28060 · Cited by 29
SnoRNAs: Exploring Their Implication in Human Diseases
Chauhan, W., Sudharshan, S. J., Kafle, S., & Zennadi, R. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25137202 · Cited by 30

Authors: Shi, Y., & Manley, J. L.
Affiliations: University of California, Irvine (US)
Columbia University (US)
Corresponding author: Shi, Yongsheng
Manley, James L.
ORCID: Shi, Yongsheng
Manley, James L.
Venue: Genes & Development
Publisher: Cold Spring Harbor Laboratory
Published: 2015-05-01
Volume: 29
Issue: 9
Pages: 889-897
ISSN: 0890-9369 (ISSN-L)
1549-5477
DOI: 10.1101/gad.261974.115
PMC: PMC4421977
OpenAlex: W2056608604
Cited by: 249
References: 108
Citations by year: 2026: 5 · 2025: 19 · 2024: 12 · 2023: 19 · 2022: 22 · 2021: 34 · 2020: 29 · 2019: 30 · 2018: 22 · 2017: 27 · 2016: 26 · 2015: 4
Type: posted content
Language: en
Open access: hybrid
doi.org
Licence: cc-by-nc
Locations: Genes & Development (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
eScholarship (California Digital Library) (submittedVersion, cc-by)
eScholarship (California Digital Library) (submittedVersion, cc-by-nc)
Funders: National Institutes of Health (GM090056, CA177651)
American Cancer Society (RSG-12-186)
NIH (GM28983)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords: mRNA polyadenylation, RNA-protein interactions, polyadenylation factors, 3' end processing, mRNA precursors, gene expression regulation, polyadenylation signal
MeSH terms: Gene Expression Regulation, Protein Binding, RNA Precursors, RNA, Messenger, Conserved Sequence, Amino Acid Motifs, Polyadenylation, Cleavage And Polyadenylation Specificity Factor

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

Abstract

Overview

Integrity signals

Figures

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks