Home LiteratureArticle Details
PMID: 25301780 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3' processing.

Genes & development ·Vol. 28 ·No. 21 ·2014-11-01 ·Pages 2370-80

Chan SL, Huppertz I, Yao C, Weng L, Moresco JJ, Yates JR, Ule J, Manley JL, Shi Y

Abstract

AAUAAA is the most highly conserved motif in eukaryotic mRNA polyadenylation sites and, in mammals, is specifically recognized by the multisubunit CPSF (cleavage and polyadenylation specificity factor) complex. Despite its critical functions in mRNA 3' end formation, the molecular basis for CPSF-AAUAAA interaction remains poorly defined. The CPSF subunit CPSF160 has been implicated in AAUAAA recognition, but direct evidence has been lacking. Using in vitro and in vivo assays, we unexpectedly found that CPSF subunits CPSF30 and Wdr33 directly contact AAUAAA. Importantly, the CPSF30-RNA interaction is essential for mRNA 3' processing and is primarily mediated by its zinc fingers 2 and 3, which are specifically targeted by the influenza protein NS1A to suppress host mRNA 3' processing. Our data suggest that AAUAAA recognition in mammalian mRNA 3' processing is more complex than previously thought and involves multiple protein-RNA interactions.

Keywords
cleavage and polyadenylation mRNA 3′ processing polyadenylation signal
MeSH Terms
Amino Acid Motifs Cleavage And Polyadenylation Specificity Factor/metabolism Gene Expression Profiling HEK293 Cells HeLa Cells Humans Nuclear Proteins/metabolism Polyadenylation Protein Binding Protein Structure, Tertiary RNA 3' End Processing/physiology RNA, Messenger/metabolism
Chemicals
CPSF4 protein, human Cleavage And Polyadenylation Specificity Factor Nuclear Proteins RNA, Messenger WDR33 protein, human
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Chan Serena L
Department of Microbiology and Molecular Genetics, School of Medicine, University of California at Irvine, Irvine, California 92697, USA;
Huppertz Ina
Department of Molecular Neuroscience, University College London Institute of Neurology, London WC1N 3BG, United Kingdom; Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
Yao Chengguo
Department of Microbiology and Molecular Genetics, School of Medicine, University of California at Irvine, Irvine, California 92697, USA;
Weng Lingjie
Department of Microbiology and Molecular Genetics, School of Medicine, University of California at Irvine, Irvine, California 92697, USA; Institute for Genomics and Bioinformatics, Department of Computer Science, University of California at Irvine Irvine, California 92697, USA;
Moresco James J
Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA;
Yates John R
Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA;
Ule Jernej
Department of Molecular Neuroscience, University College London Institute of Neurology, London WC1N 3BG, United Kingdom; Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
Manley James L
Department of Biological Sciences, Columbia University, New York, New York 10027, USA.
Shi Yongsheng
Department of Microbiology and Molecular Genetics, School of Medicine, University of California at Irvine, Irvine, California 92697, USA;
References (48)
48 references, click to expand
  1. Functionally significant secondary structure of the simian virus 40 late polyadenylation signal.
    Mol Cell Biol. 2000 Apr;20(8):2926-32 PMID: 10733596
  2. Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal.
    EMBO J. 2014 Apr 16;33(8):878-89 PMID: 24596251
  3. A core complex of CPSF73, CPSF100, and Symplekin may form two different cleavage factors for processing of poly(A) and histone mRNAs.
    Mol Cell. 2009 May 15;34(3):322-32 PMID: 19450530
  4. Gemin5-snRNA interaction reveals an RNA binding function for WD repeat domains.
    Nat Struct Mol Biol. 2009 May;16(5):486-91 PMID: 19377484
  5. Targeted disruption of an essential vertebrate gene: ASF/SF2 is required for cell viability.
    Genes Dev. 1996 Oct 15;10(20):2588-99 PMID: 8895660
  6. Purification of the cleavage and polyadenylation factor involved in the 3'-processing of messenger RNA precursors.
    J Biol Chem. 1991 Oct 15;266(29):19768-76 PMID: 1918081
  7. Recent advances in understanding the structure and function of general transcription factor TFIID.
    Cell Mol Life Sci. 2009 Jul;66(13):2123-34 PMID: 19308322
  8. Separation and characterization of a poly(A) polymerase and a cleavage/specificity factor required for pre-mRNA polyadenylation.
    Cell. 1988 Mar 11;52(5):731-42 PMID: 2830992
  9. Inactivation of the pre-mRNA cleavage and polyadenylation factor Pfs2 in fission yeast causes lethal cell cycle defects.
    Mol Cell Biol. 2005 Mar;25(6):2288-96 PMID: 15743824
  10. Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase.
    EMBO J. 2004 Feb 11;23(3):616-26 PMID: 14749727
  11. iCLIP: protein-RNA interactions at nucleotide resolution.
    Methods. 2014 Feb;65(3):274-87 PMID: 24184352
  12. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins.
    Cell. 2012 Jun 8;149(6):1393-406 PMID: 22658674
  13. Mechanisms and consequences of alternative polyadenylation.
    Mol Cell. 2011 Sep 16;43(6):853-66 PMID: 21925375
  14. The human Prp8 protein is a component of both U2- and U12-dependent spliceosomes.
    RNA. 1999 Jul;5(7):893-908 PMID: 10411133
  15. Influenza virus NS1 protein interacts with the cellular 30 kDa subunit of CPSF and inhibits 3'end formation of cellular pre-mRNAs.
    Mol Cell. 1998 Jun;1(7):991-1000 PMID: 9651582
  16. The 30-kD subunit of mammalian cleavage and polyadenylation specificity factor and its yeast homolog are RNA-binding zinc finger proteins.
    Genes Dev. 1997 Jul 1;11(13):1703-16 PMID: 9224719
  17. Ending the message: poly(A) signals then and now.
    Genes Dev. 2011 Sep 1;25(17):1770-82 PMID: 21896654
  18. The CPSF30 binding site on the NS1A protein of influenza A virus is a potential antiviral target.
    J Virol. 2006 Apr;80(8):3957-65 PMID: 16571812
  19. The 160-kD subunit of human cleavage-polyadenylation specificity factor coordinates pre-mRNA 3'-end formation.
    Genes Dev. 1995 Nov 1;9(21):2672-83 PMID: 7590244
  20. Point mutations in AAUAAA and the poly (A) addition site: effects on the accuracy and efficiency of cleavage and polyadenylation in vitro.
    Nucleic Acids Res. 1990 Oct 11;18(19):5799-805 PMID: 2170946
  21. Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length.
    Cell Rep. 2012 Jun 28;1(6):753-63 PMID: 22813749
  22. The RNA-binding protein repertoire of embryonic stem cells.
    Nat Struct Mol Biol. 2013 Sep;20(9):1122-30 PMID: 23912277
  23. CPSF recognition of an HIV-1 mRNA 3'-processing enhancer: multiple sequence contacts involved in poly(A) site definition.
    Genes Dev. 1995 Jan 1;9(1):72-83 PMID: 7828853
  24. Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis.
    Microbiol Mol Biol Rev. 1999 Jun;63(2):405-45 PMID: 10357856
  25. Delineating the structural blueprint of the pre-mRNA 3'-end processing machinery.
    Mol Cell Biol. 2014 Jun;34(11):1894-910 PMID: 24591651
  26. Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33.
    Genes Dev. 2014 Nov 1;28(21):2381-93 PMID: 25301781
  27. Nuclear pre-mRNA 3'-end processing regulates synapse and axon development in C. elegans.
    Development. 2010 Jul;137(13):2237-50 PMID: 20530551
  28. Activation of HIV-1 pre-mRNA 3' processing in vitro requires both an upstream element and TAR.
    EMBO J. 1992 Dec;11(12):4419-28 PMID: 1425577
  29. The U1 snRNP protein U1C recognizes the 5' splice site in the absence of base pairing.
    Nature. 2002 Sep 5;419(6902):86-90 PMID: 12214237
  30. Mechanism and regulation of mRNA polyadenylation.
    Genes Dev. 1997 Nov 1;11(21):2755-66 PMID: 9353246
  31. Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination.
    EMBO J. 2002 Aug 1;21(15):4125-35 PMID: 12145212
  32. Protein factors in pre-mRNA 3'-end processing.
    Cell Mol Life Sci. 2008 Apr;65(7-8):1099-122 PMID: 18158581
  33. Alternative polyadenylation: new insights from global analyses.
    RNA. 2012 Dec;18(12):2105-17 PMID: 23097429
  34. WD40 proteins propel cellular networks.
    Trends Biochem Sci. 2010 Oct;35(10):565-74 PMID: 20451393
  35. The WD-repeat protein pfs2p bridges two essential factors within the yeast pre-mRNA 3'-end-processing complex.
    EMBO J. 2000 Jan 4;19(1):37-47 PMID: 10619842
  36. 3' end mRNA processing: molecular mechanisms and implications for health and disease.
    EMBO J. 2008 Feb 6;27(3):482-98 PMID: 18256699
  37. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.
    Cell. 2010 Apr 2;141(1):129-41 PMID: 20371350
  38. Molecular mechanisms of eukaryotic pre-mRNA 3' end processing regulation.
    Nucleic Acids Res. 2010 May;38(9):2757-74 PMID: 20044349
  39. Alternative cleavage and polyadenylation: the long and short of it.
    Trends Biochem Sci. 2013 Jun;38(6):312-20 PMID: 23632313
  40. Characterization of the multisubunit cleavage-polyadenylation specificity factor from calf thymus.
    J Biol Chem. 1992 Jul 25;267(21):14804-11 PMID: 1634525
  41. Pre-mRNA 3'-end processing complex assembly and function.
    Wiley Interdiscip Rev RNA. 2011 May-Jun;2(3):321-35 PMID: 21957020
  42. FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition.
    Cell. 2003 Jun 13;113(6):777-87 PMID: 12809608
  43. Molecular architecture of the human pre-mRNA 3' processing complex.
    Mol Cell. 2009 Feb 13;33(3):365-76 PMID: 19217410
  44. 3' cleavage and polyadenylation of mRNA precursors in vitro requires a poly(A) polymerase, a cleavage factor, and a snRNP.
    Cell. 1988 Sep 9;54(6):875-89 PMID: 2842067
  45. Cleavage and polyadenylation factor CPF specifically interacts with the pre-mRNA 3' processing signal AAUAAA.
    EMBO J. 1991 Dec;10(13):4241-9 PMID: 1756731
  46. Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation.
    Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):18773-8 PMID: 23112178
  47. Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis.
    Plant Cell. 2012 Nov;24(11):4376-88 PMID: 23136375
  48. Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit.
    Plant Physiol. 2006 Apr;140(4):1507-21 PMID: 16500995
Article Info
Journal
Genes & development
Abbr.
Genes Dev
ISSN
1549-5477
DOI
10.1101/gad.250993.114
Published
2014-11-01
Epub
2014-00-09
Pages
2370-80
Language
English
Region
United States
NLM ID
8711660
PMCID
PMC4215182
Subset
IM
Grants
NIGMS NIH HHS · P41 GM103533 · United States
NCRR NIH HHS · 5P41RR011823 · United States
NIGMS NIH HHS · R01 GM090056 · United States
NIGMS NIH HHS · GM090056 · United States
HSRD VA · CDP 12-186 · United States
NIGMS NIH HHS · GM28983 · United States
NIGMS NIH HHS · 8 P41 GM103533 · United States
Wellcome Trust · 089701 · United Kingdom
NIGMS NIH HHS · R01 GM028983 · United States
NCRR NIH HHS · P41 RR011823 · United States
Medical Research Council · MC_U105185858 · United Kingdom
External Links
PubMed source DOI: 10.1101/gad.250993.114 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2