Home LiteratureArticle Details
PMID: 24591651 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Review

Delineating the structural blueprint of the pre-mRNA 3'-end processing machinery.

Molecular and cellular biology ·Vol. 34 ·No. 11 ·2014-06-00 ·Pages 1894-910

Xiang K, Tong L, Manley JL

Abstract

Processing of mRNA precursors (pre-mRNAs) by polyadenylation is an essential step in gene expression. Polyadenylation consists of two steps, cleavage and poly(A) synthesis, and requires multiple cis elements in the pre-mRNA and a megadalton protein complex bearing the two essential enzymatic activities. While genetic and biochemical studies remain the major approaches in characterizing these factors, structural biology has emerged during the past decade to help understand the molecular assembly and mechanistic details of the process. With structural information about more proteins and higher-order complexes becoming available, we are coming closer to obtaining a structural blueprint of the polyadenylation machinery that explains both how this complex functions and how it is regulated and connected to other cellular processes.

MeSH Terms
Animals Cleavage And Polyadenylation Specificity Factor/chemistry,genetics Cleavage Stimulation Factor/chemistry,genetics Gene Expression Humans Poly A/genetics,metabolism Polyadenylation/genetics Protein Structure, Tertiary RNA 3' End Processing/genetics RNA Precursors/genetics,metabolism RNA, Messenger/genetics,metabolism
Chemicals
Cleavage And Polyadenylation Specificity Factor Cleavage Stimulation Factor RNA Precursors RNA, Messenger Poly A
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Xiang Kehui
Department of Biological Sciences, Columbia University, New York, New York, USA.
Tong Liang
Manley James L
References (199)
199 references, click to expand
  1. 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
  2. The FIP1 gene encodes a component of a yeast pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase.
    Cell. 1995 May 5;81(3):379-89 PMID: 7736590
  3. In silico detection of control signals: mRNA 3'-end-processing sequences in diverse species.
    Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):14055-60 PMID: 10570197
  4. 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
  5. CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3'-end processing factor, Pcf11.
    Genes Dev. 2005 Jul 1;19(13):1572-80 PMID: 15998810
  6. Locked tether formation by cooperative folding of Rna14p monkeytail and Rna15p hinge domains in the yeast CF IA complex.
    Structure. 2011 Apr 13;19(4):534-45 PMID: 21481776
  7. Molecular analyses of two poly(A) site-processing factors that determine the recognition and efficiency of cleavage of the pre-mRNA.
    Mol Cell Biol. 1991 May;11(5):2432-8 PMID: 2017162
  8. Functional interaction of BRCA1-associated BARD1 with polyadenylation factor CstF-50.
    Science. 1999 Sep 3;285(5433):1576-9 PMID: 10477523
  9. 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
  10. Crystal structure of the HEAT domain from the Pre-mRNA processing factor Symplekin.
    J Mol Biol. 2009 Sep 11;392(1):115-28 PMID: 19576221
  11. A protein of molecular weight 78,000 bound to the polyadenylate region of eukaryotic messenger RNAs.
    Proc Natl Acad Sci U S A. 1973 Mar;70(3):924-8 PMID: 4515002
  12. Structure of yeast poly(A) polymerase in complex with a peptide from Fip1, an intrinsically disordered protein.
    Biochemistry. 2008 Jul 1;47(26):6859-69 PMID: 18537269
  13. Crystal structure of the human symplekin-Ssu72-CTD phosphopeptide complex.
    Nature. 2010 Oct 7;467(7316):729-33 PMID: 20861839
  14. Purification and characterization of human cleavage factor Im involved in the 3' end processing of messenger RNA precursors.
    J Biol Chem. 1996 Mar 15;271(11):6107-13 PMID: 8626397
  15. Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease.
    Nature. 2006 Dec 14;444(7121):953-6 PMID: 17128255
  16. Transcription factor TFIID recruits factor CPSF for formation of 3' end of mRNA.
    Nature. 1997 Sep 25;389(6649):399-402 PMID: 9311784
  17. Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus.
    Nature. 2004 Sep 30;431(7008):586-90 PMID: 15457265
  18. Functional interactions between the transcription and mRNA 3' end processing machineries mediated by Ssu72 and Sub1.
    Genes Dev. 2003 Apr 15;17(8):1030-42 PMID: 12704082
  19. Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor.
    Nucleic Acids Res. 2007;35(1):87-99 PMID: 17151076
  20. A multisubunit factor, CstF, is required for polyadenylation of mammalian pre-mRNAs.
    Genes Dev. 1990 Dec;4(12A):2112-20 PMID: 1980119
  21. Structural basis of pre-mRNA recognition by the human cleavage factor Im complex.
    Cell Res. 2011 Jul;21(7):1039-51 PMID: 21483454
  22. Emerging Views on the CTD Code.
    Genet Res Int. 2012;2012:347214 PMID: 22567385
  23. Ending the message: poly(A) signals then and now.
    Genes Dev. 2011 Sep 1;25(17):1770-82 PMID: 21896654
  24. The τCstF-64 polyadenylation protein controls genome expression in testis.
    PLoS One. 2012;7(10):e48373 PMID: 23110235
  25. Crystal structure of a dimeric archaeal cleavage and polyadenylation specificity factor.
    J Struct Biol. 2011 Jan;173(1):191-5 PMID: 20851187
  26. Stimulation of poly(A) polymerase through a direct interaction with the nuclear poly(A) binding protein allosterically regulated by RNA.
    EMBO J. 2003 Jul 15;22(14):3705-14 PMID: 12853485
  27. 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
  28. PCF11 encodes a third protein component of yeast cleavage and polyadenylation factor I.
    Mol Cell Biol. 1997 Mar;17(3):1102-9 PMID: 9032237
  29. The role of the yeast cleavage and polyadenylation factor subunit Ydh1p/Cft2p in pre-mRNA 3'-end formation.
    Nucleic Acids Res. 2003 Jul 15;31(14):3936-45 PMID: 12853609
  30. The consensus sequence YGTGTTYY located downstream from the AATAAA signal is required for efficient formation of mRNA 3' termini.
    Nucleic Acids Res. 1985 Feb 25;13(4):1347-68 PMID: 2987822
  31. RNA polymerase II is an essential mRNA polyadenylation factor.
    Nature. 1998 Sep 3;395(6697):93-6 PMID: 9738505
  32. 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
  33. Flexibility and interchangeability of polyadenylation signals in Saccharomyces cerevisiae.
    Mol Cell Biol. 1994 Jul;14(7):4633-42 PMID: 7911972
  34. Five subunits are required for reconstitution of the cleavage and polyadenylation activities of Saccharomyces cerevisiae cleavage factor I.
    Proc Natl Acad Sci U S A. 2001 May 22;98(11):6080-5 PMID: 11344258
  35. 3'-end-forming signals of yeast mRNA.
    Mol Cell Biol. 1995 Nov;15(11):5983-90 PMID: 7565751
  36. A flexible linker region in Fip1 is needed for efficient mRNA polyadenylation.
    RNA. 2011 Apr;17(4):652-64 PMID: 21282348
  37. 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
  38. Polyadenylate polymerases.
    Methods Enzymol. 1990;181:161-70 PMID: 2166211
  39. Rna15 interaction with the A-rich yeast polyadenylation signal is an essential step in mRNA 3'-end formation.
    Mol Cell Biol. 2001 Dec;21(23):8045-55 PMID: 11689695
  40. Conformation of the RNA polymerase II C-terminal domain: circular dichroism of long and short fragments.
    J Mol Biol. 2000 Mar 17;297(1):119-33 PMID: 10704311
  41. Chimeric human CstF-77/Drosophila Suppressor of forked proteins rescue suppressor of forked mutant lethality and mRNA 3' end processing in Drosophila.
    Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10593-8 PMID: 12149458
  42. Poly(A) tail length control is caused by termination of processive synthesis.
    J Biol Chem. 1995 Feb 10;270(6):2800-8 PMID: 7852352
  43. Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP.
    EMBO J. 2000 Aug 15;19(16):4193-203 PMID: 10944102
  44. Pta1, a component of yeast CF II, is required for both cleavage and poly(A) addition of mRNA precursor.
    Mol Cell Biol. 1999 Nov;19(11):7733-40 PMID: 10523662
  45. Cleavage factor II of Saccharomyces cerevisiae contains homologues to subunits of the mammalian Cleavage/ polyadenylation specificity factor and exhibits sequence-specific, ATP-dependent interaction with precursor RNA.
    J Biol Chem. 1997 Apr 18;272(16):10831-8 PMID: 9099738
  46. Structure of the Rna15 RRM-RNA complex reveals the molecular basis of GU specificity in transcriptional 3'-end processing factors.
    Nucleic Acids Res. 2010 May;38(9):3119-32 PMID: 20097654
  47. Updating the RNA polymerase CTD code: adding gene-specific layers.
    Trends Genet. 2012 Jul;28(7):333-41 PMID: 22622228
  48. Human Pcf11 enhances degradation of RNA polymerase II-associated nascent RNA and transcriptional termination.
    Nucleic Acids Res. 2008 Feb;36(3):905-14 PMID: 18086705
  49. The BARD1-CstF-50 interaction links mRNA 3' end formation to DNA damage and tumor suppression.
    Cell. 2001 Mar 9;104(5):743-53 PMID: 11257228
  50. Complex protein interactions within the human polyadenylation machinery identify a novel component.
    Mol Cell Biol. 2000 Mar;20(5):1515-25 PMID: 10669729
  51. Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing.
    Proc Natl Acad Sci U S A. 2010 Jun 1;107(22):10062-7 PMID: 20479262
  52. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold.
    EMBO J. 1982;1(8):945-51 PMID: 6329717
  53. Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3'-end maturation.
    EMBO Rep. 2008 Oct;9(10):1013-8 PMID: 18688255
  54. Four factors are required for 3'-end cleavage of pre-mRNAs.
    Genes Dev. 1989 Nov;3(11):1711-24 PMID: 2558045
  55. Distinct roles of two Yth1p domains in 3'-end cleavage and polyadenylation of yeast pre-mRNAs.
    EMBO J. 2000 Jul 17;19(14):3778-87 PMID: 10899131
  56. Primary structure and expression of bovine poly(A) polymerase.
    Nature. 1991 Sep 19;353(6341):229-34 PMID: 1896071
  57. The major yeast poly(A)-binding protein is associated with cleavage factor IA and functions in premessenger RNA 3'-end formation.
    Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7897-902 PMID: 9223284
  58. Crystal structure of murine CstF-77: dimeric association and implications for polyadenylation of mRNA precursors.
    Mol Cell. 2007 Mar 23;25(6):863-75 PMID: 17386263
  59. Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development.
    Proc Natl Acad Sci U S A. 2009 Apr 28;106(17):7028-33 PMID: 19372383
  60. Characterization of cleavage and polyadenylation specificity factor and cloning of its 100-kilodalton subunit.
    Mol Cell Biol. 1994 Dec;14(12):8183-90 PMID: 7969155
  61. 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
  62. Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors.
    Nature. 2004 Jul 8;430(6996):223-6 PMID: 15241417
  63. Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation.
    RNA. 2005 Oct;11(10):1485-93 PMID: 16131587
  64. Patterns of variant polyadenylation signal usage in human genes.
    Genome Res. 2000 Jul;10(7):1001-10 PMID: 10899149
  65. Reconstitution of CF IA from overexpressed subunits reveals stoichiometry and provides insights into molecular topology.
    Biochemistry. 2011 Nov 29;50(47):10203-14 PMID: 22026644
  66. X-ray crystallographic and steady state fluorescence characterization of the protein dynamics of yeast polyadenylate polymerase.
    J Mol Biol. 2007 Mar 9;366(5):1401-15 PMID: 17223131
  67. 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
  68. Comparison of ARM and HEAT protein repeats.
    J Mol Biol. 2001 May 25;309(1):1-18 PMID: 11491282
  69. Recognition of GU-rich polyadenylation regulatory elements by human CstF-64 protein.
    EMBO J. 2003 Jun 2;22(11):2821-30 PMID: 12773396
  70. Functional interaction of yeast pre-mRNA 3' end processing factors with RNA polymerase II.
    Mol Cell. 2002 May;9(5):1101-11 PMID: 12049745
  71. Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3' processing.
    RNA. 2013 Dec;19(12):1781-90 PMID: 24149845
  72. Structural basis for suppression of a host antiviral response by influenza A virus.
    Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):13093-8 PMID: 18725644
  73. Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases.
    EMBO J. 1996 May 15;15(10):2593-603 PMID: 8665867
  74. Mechanism and regulation of mRNA polyadenylation.
    Genes Dev. 1997 Nov 1;11(21):2755-66 PMID: 9353246
  75. RNA polymerase II CTD phosphopeptides compete with RNA for the interaction with Pcf11.
    RNA. 2006 Apr;12(4):555-60 PMID: 16497660
  76. 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
  77. The crystal structure of human cleavage and polyadenylation specific factor-5 reveals a dimeric Nudix protein with a conserved catalytic site.
    Proteins. 2008 Dec;73(4):1047-52 PMID: 18767156
  78. Hexameric architecture of CstF supported by CstF-50 homodimerization domain structure.
    RNA. 2011 Mar;17(3):412-8 PMID: 21233223
  79. mRNA 3' end processing and more--multiple functions of mammalian cleavage factor I-68.
    Wiley Interdiscip Rev RNA. 2011 Jan-Feb;2(1):79-91 PMID: 21956970
  80. Key features of the interaction between Pcf11 CID and RNA polymerase II CTD.
    Nat Struct Mol Biol. 2005 Feb;12(2):144-51 PMID: 15665873
  81. A mechanism for the regulation of pre-mRNA 3' processing by human cleavage factor Im.
    Mol Cell. 2003 Dec;12(6):1467-76 PMID: 14690600
  82. Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae.
    Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):445-50 PMID: 11149954
  83. Structural and biochemical analysis of the assembly and function of the yeast pre-mRNA 3' end processing complex CF I.
    Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21342-7 PMID: 23236150
  84. The Role of the poly(A) sequence in mammalian messenger RNA.
    CRC Crit Rev Biochem. 1981;10(1):1-38 PMID: 6111419
  85. Symplekin, a novel type of tight junction plaque protein.
    J Cell Biol. 1996 Aug;134(4):1003-18 PMID: 8769423
  86. Fip1 regulates the activity of Poly(A) polymerase through multiple interactions.
    Mol Cell Biol. 2001 Mar;21(6):2026-37 PMID: 11238938
  87. An interaction between U2AF 65 and CF I(m) links the splicing and 3' end processing machineries.
    EMBO J. 2006 Oct 18;25(20):4854-64 PMID: 17024186
  88. A multisubunit 3' end processing factor from yeast containing poly(A) polymerase and homologues of the subunits of mammalian cleavage and polyadenylation specificity factor.
    EMBO J. 1997 Aug 1;16(15):4727-37 PMID: 9303317
  89. PSI-BLAST searches using hidden markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein.
    Nucleic Acids Res. 2000 Sep 15;28(18):3570-80 PMID: 10982878
  90. The CTD code of RNA polymerase II: a structural view.
    Wiley Interdiscip Rev RNA. 2013 Jan-Feb;4(1):1-16 PMID: 23042580
  91. Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription.
    Biochim Biophys Acta. 2013 Jan;1829(1):55-62 PMID: 22982363
  92. Assembly of a processive messenger RNA polyadenylation complex.
    EMBO J. 1993 Feb;12(2):585-94 PMID: 8440247
  93. An Arabidopsis Fip1 homolog interacts with RNA and provides conceptual links with a number of other polyadenylation factor subunits.
    J Biol Chem. 2006 Jan 6;281(1):176-86 PMID: 16282318
  94. The hinge domain of the cleavage stimulation factor protein CstF-64 is essential for CstF-77 interaction, nuclear localization, and polyadenylation.
    J Biol Chem. 2010 Jan 1;285(1):695-704 PMID: 19887456
  95. Protein factors in pre-mRNA 3'-end processing.
    Cell Mol Life Sci. 2008 Apr;65(7-8):1099-122 PMID: 18158581
  96. Isolation of genomic and cDNA clones encoding bovine poly(A) binding protein II.
    Nucleic Acids Res. 1995 Oct 25;23(20):4034-41 PMID: 7479061
  97. WD40 proteins propel cellular networks.
    Trends Biochem Sci. 2010 Oct;35(10):565-74 PMID: 20451393
  98. novel modifications on C-terminal domain of RNA polymerase II can fine-tune the phosphatase activity of Ssu72.
    ACS Chem Biol. 2013 Sep 20;8(9):2042-52 PMID: 23844594
  99. An essential role for Clp1 in assembly of polyadenylation complex CF IA and Pol II transcription termination.
    Nucleic Acids Res. 2012 Feb;40(3):1226-39 PMID: 21993300
  100. A human polyadenylation factor is a G protein beta-subunit homologue.
    J Biol Chem. 1992 Nov 25;267(33):23471-4 PMID: 1358884
  101. cis-Proline-mediated Ser(P)5 dephosphorylation by the RNA polymerase II C-terminal domain phosphatase Ssu72.
    J Biol Chem. 2011 Feb 18;286(7):5717-26 PMID: 21159777
  102. The HAT helix, a repetitive motif implicated in RNA processing.
    Trends Biochem Sci. 1998 Jan;23(1):15-6 PMID: 9478129
  103. Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery.
    Nature. 2006 Oct 5;443(7111):590-3 PMID: 16964240
  104. Interactions of CstF-64, CstF-77, and symplekin: implications on localisation and function.
    Mol Biol Cell. 2011 Jan 1;22(1):91-104 PMID: 21119002
  105. Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis.
    Nucleic Acids Res. 2001 Apr 15;29(8):1690-4 PMID: 11292841
  106. Structural biology of poly(A) site definition.
    Wiley Interdiscip Rev RNA. 2011 Sep-Oct;2(5):732-47 PMID: 21823232
  107. An ordered pathway of assembly of components required for polyadenylation site recognition and processing.
    Genes Dev. 1989 Dec;3(12B):2180-90 PMID: 2628166
  108. Pre-mRNA processing reaches back to transcription and ahead to translation.
    Cell. 2009 Feb 20;136(4):688-700 PMID: 19239889
  109. Structure of yeast poly(A) polymerase alone and in complex with 3'-dATP.
    Science. 2000 Aug 25;289(5483):1346-9 PMID: 10958780
  110. Symplekin, a constitutive protein of karyo- and cytoplasmic particles involved in mRNA biogenesis in Xenopus laevis oocytes.
    Mol Biol Cell. 2002 May;13(5):1665-76 PMID: 12006661
  111. Biochemical and structural insights into substrate binding and catalytic mechanism of mammalian poly(A) polymerase.
    J Mol Biol. 2004 Aug 20;341(4):911-25 PMID: 15328606
  112. A polyadenylation factor subunit is the human homologue of the Drosophila suppressor of forked protein.
    Nature. 1994 Dec 1;372(6505):471-4 PMID: 7984242
  113. The C-terminal domains of vertebrate CstF-64 and its yeast orthologue Rna15 form a new structure critical for mRNA 3'-end processing.
    J Biol Chem. 2007 Jan 19;282(3):2101-15 PMID: 17116658
  114. Structure and function of poly(A) binding proteins.
    Biochim Biophys Acta. 2004 May 25;1678(2-3):67-84 PMID: 15157733
  115. A novel poly(A)-binding protein acts as a specificity factor in the second phase of messenger RNA polyadenylation.
    Cell. 1991 Aug 23;66(4):759-68 PMID: 1878970
  116. The RNA binding domains of the nuclear poly(A)-binding protein.
    J Biol Chem. 2003 May 9;278(19):16916-25 PMID: 12637556
  117. 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
  118. 3' end mRNA processing: molecular mechanisms and implications for health and disease.
    EMBO J. 2008 Feb 6;27(3):482-98 PMID: 18256699
  119. The Nudix hydrolase superfamily.
    Cell Mol Life Sci. 2006 Jan;63(2):123-43 PMID: 16378245
  120. Definition of essential sequences and functional equivalence of elements downstream of the adenovirus E2A and the early simian virus 40 polyadenylation sites.
    Mol Cell Biol. 1985 Nov;5(11):2975-83 PMID: 3018490
  121. The poly(A)-dependent transcriptional pause is mediated by CPSF acting on the body of the polymerase.
    Nat Struct Mol Biol. 2007 Jul;14(7):662-9 PMID: 17572685
  122. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription.
    Nature. 1997 Jan 23;385(6614):357-61 PMID: 9002523
  123. The Saccharomyces cerevisiae RNA-binding protein Rbp29 functions in cytoplasmic mRNA metabolism.
    J Biol Chem. 2000 Jul 21;275(29):21817-26 PMID: 10764794
  124. Sumoylation regulates multiple aspects of mammalian poly(A) polymerase function.
    Genes Dev. 2008 Feb 15;22(4):499-511 PMID: 18281463
  125. The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites.
    Cell. 2012 Apr 27;149(3):538-53 PMID: 22502866
  126. Alternative cleavage and polyadenylation: the long and short of it.
    Trends Biochem Sci. 2013 Jun;38(6):312-20 PMID: 23632313
  127. Evidence that polyadenylation factor CPSF-73 is the mRNA 3' processing endonuclease.
    RNA. 2004 Apr;10(4):565-73 PMID: 15037765
  128. Sequence and position requirements for uridylate-rich downstream elements of polyadenylation signals.
    Nucleic Acids Res. 1994 Jul 11;22(13):2525-31 PMID: 7518915
  129. A CPSF-73 homologue is required for cell cycle progression but not cell growth and interacts with a protein having features of CPSF-100.
    Mol Cell Biol. 2005 Feb;25(4):1489-500 PMID: 15684398
  130. Cell-cycle related regulation of poly(A) polymerase by phosphorylation.
    Nature. 1996 Nov 21;384(6606):282-5 PMID: 8918882
  131. 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
  132. Evolutionarily conserved interaction between CstF-64 and PC4 links transcription, polyadenylation, and termination.
    Mol Cell. 2001 May;7(5):1013-23 PMID: 11389848
  133. Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d.
    Nat Struct Mol Biol. 2004 Mar;11(3):257-64 PMID: 14981510
  134. Functional dissection of the zinc finger and flanking domains of the Yth1 cleavage/polyadenylation factor.
    Nucleic Acids Res. 2003 Mar 15;31(6):1744-52 PMID: 12626716
  135. Crystal structure of a human cleavage factor CFI(m)25/CFI(m)68/RNA complex provides an insight into poly(A) site recognition and RNA looping.
    Structure. 2011 Mar 9;19(3):368-77 PMID: 21295486
  136. Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail.
    Nat Rev Genet. 2008 Nov;9(11):843-54 PMID: 18927579
  137. The essential N terminus of the Pta1 scaffold protein is required for snoRNA transcription termination and Ssu72 function but is dispensable for pre-mRNA 3'-end processing.
    Mol Cell Biol. 2009 Apr;29(8):2296-307 PMID: 19188448
  138. Cloning and expression of the essential gene for poly(A) polymerase from S. cerevisiae.
    Nature. 1991 Dec 12;354(6353):496-8 PMID: 1840648
  139. Characterization of the multisubunit cleavage-polyadenylation specificity factor from calf thymus.
    J Biol Chem. 1992 Jul 25;267(21):14804-11 PMID: 1634525
  140. Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex.
    Cell. 2008 Dec 26;135(7):1213-23 PMID: 19109893
  141. Crystal structure of the 25 kDa subunit of human cleavage factor Im.
    Nucleic Acids Res. 2008 Jun;36(10):3474-83 PMID: 18445629
  142. A multicomponent complex is required for the AAUAAA-dependent cross-linking of a 64-kilodalton protein to polyadenylation substrates.
    Mol Cell Biol. 1990 Mar;10(3):1244-8 PMID: 2304466
  143. Pre-mRNA 3'-end processing complex assembly and function.
    Wiley Interdiscip Rev RNA. 2011 May-Jun;2(3):321-35 PMID: 21957020
  144. RNA recognition by the human polyadenylation factor CstF.
    Mol Cell Biol. 1997 Jul;17(7):3907-14 PMID: 9199325
  145. Kin28, the TFIIH-associated carboxy-terminal domain kinase, facilitates the recruitment of mRNA processing machinery to RNA polymerase II.
    Mol Cell Biol. 2000 Jan;20(1):104-12 PMID: 10594013
  146. Multiple histone deacetylases and the CREB-binding protein regulate pre-mRNA 3'-end processing.
    J Biol Chem. 2007 Feb 16;282(7):4470-4478 PMID: 17172643
  147. Purification and characterization of a mammalian polyadenylate polymerase involved in the 3' end processing of messenger RNA precursors.
    J Biol Chem. 1991 Feb 15;266(5):3131-9 PMID: 1993684
  148. Novel protein-protein contacts facilitate mRNA 3'-processing signal recognition by Rna15 and Hrp1.
    J Mol Biol. 2010 Aug 20;401(3):334-49 PMID: 20600122
  149. Updating the CTD Story: From Tail to Epic.
    Genet Res Int. 2011;2011:623718 PMID: 22567360
  150. Independent functions of yeast Pcf11p in pre-mRNA 3' end processing and in transcription termination.
    EMBO J. 2003 May 1;22(9):2167-77 PMID: 12727883
  151. 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
  152. Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii.
    Proteins. 2010 Aug 1;78(10):2395-8 PMID: 20544974
  153. Crystal structure and possible dimerization of the single RRM of human PABPN1.
    Proteins. 2008 May 15;71(3):1539-45 PMID: 18275081
  154. Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells.
    Cell. 2009 Aug 21;138(4):673-84 PMID: 19703394
  155. Distinct sequence motifs within the 68-kDa subunit of cleavage factor Im mediate RNA binding, protein-protein interactions, and subcellular localization.
    J Biol Chem. 2004 Aug 20;279(34):35788-97 PMID: 15169763
  156. Molecular architecture of the human pre-mRNA 3' processing complex.
    Mol Cell. 2009 Feb 13;33(3):365-76 PMID: 19217410
  157. The hunt for the 3' endonuclease.
    Wiley Interdiscip Rev RNA. 2010 Sep-Oct;1(2):325-40 PMID: 21935893
  158. The P-loop domain of yeast Clp1 mediates interactions between CF IA and CPF factors in pre-mRNA 3' end formation.
    PLoS One. 2011;6(12):e29139 PMID: 22216186
  159. Structure and activity of a novel archaeal β-CASP protein with N-terminal KH domains.
    Structure. 2011 May 11;19(5):622-32 PMID: 21565697
  160. The nuclear poly(A) binding protein, PABP2, forms an oligomeric particle covering the length of the poly(A) tail.
    J Mol Biol. 2000 Mar 31;297(3):569-83 PMID: 10731412
  161. The 64-kilodalton subunit of the CstF polyadenylation factor binds to pre-mRNAs downstream of the cleavage site and influences cleavage site location.
    Mol Cell Biol. 1994 Oct;14(10):6647-54 PMID: 7935383
  162. The role of the Brr5/Ysh1 C-terminal domain and its homolog Syc1 in mRNA 3'-end processing in Saccharomyces cerevisiae.
    RNA. 2006 Mar;12(3):435-45 PMID: 16431986
  163. Poly(A) tail length is controlled by the nuclear poly(A)-binding protein regulating the interaction between poly(A) polymerase and the cleavage and polyadenylation specificity factor.
    J Biol Chem. 2009 Aug 21;284(34):22803-14 PMID: 19509282
  164. The structure of the CstF-77 homodimer provides insights into CstF assembly.
    Nucleic Acids Res. 2007;35(13):4515-22 PMID: 17584787
  165. Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family.
    Nucleic Acids Res. 2002 Aug 15;30(16):3592-601 PMID: 12177301
  166. Recognition of polyadenylation sites in yeast pre-mRNAs by cleavage and polyadenylation factor.
    EMBO J. 2001 Jun 15;20(12):3197-209 PMID: 11406596
  167. Extended disordered proteins: targeting function with less scaffold.
    Trends Biochem Sci. 2003 Feb;28(2):81-5 PMID: 12575995
  168. Crystal structure of the Rna14-Rna15 complex.
    RNA. 2012 Jun;18(6):1154-62 PMID: 22513198
  169. Position-dependent sequence elements downstream of AAUAAA are required for efficient rabbit beta-globin mRNA 3' end formation.
    Cell. 1987 May 8;49(3):399-406 PMID: 3568131
  170. Human RNA 5'-kinase (hClp1) can function as a tRNA splicing enzyme in vivo.
    RNA. 2008 Sep;14(9):1737-45 PMID: 18648070
  171. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution.
    Science. 2001 Jun 8;292(5523):1863-76 PMID: 11313498
  172. Rna14-Rna15 assembly mediates the RNA-binding capability of Saccharomyces cerevisiae cleavage factor IA.
    Nucleic Acids Res. 2004 Jun 23;32(11):3364-75 PMID: 15215336
  173. The RNA polymerase II CTD coordinates transcription and RNA processing.
    Genes Dev. 2012 Oct 1;26(19):2119-37 PMID: 23028141
  174. Nucleases of the metallo-beta-lactamase family and their role in DNA and RNA metabolism.
    Crit Rev Biochem Mol Biol. 2007 Mar-Apr;42(2):67-93 PMID: 17453916
  175. Association of polyadenylation cleavage factor I with U1 snRNP.
    RNA. 2003 Nov;9(11):1400-9 PMID: 14561889
  176. Human pre-mRNA cleavage factor Im is related to spliceosomal SR proteins and can be reconstituted in vitro from recombinant subunits.
    Mol Cell. 1998 Jan;1(2):243-53 PMID: 9659921
  177. Accurate cleavage and polyadenylation of exogenous RNA substrate.
    Cell. 1985 Jul;41(3):845-55 PMID: 2408761
  178. Structural insights into the dual activity of RNase J.
    Nat Struct Mol Biol. 2008 Feb;15(2):206-12 PMID: 18204464
  179. Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis.
    Structure. 2007 Sep;15(9):1117-31 PMID: 17850751
  180. Human pre-mRNA cleavage factor II(m) contains homologs of yeast proteins and bridges two other cleavage factors.
    EMBO J. 2000 Nov 1;19(21):5895-904 PMID: 11060040
  181. The interaction of Pcf11 and Clp1 is needed for mRNA 3'-end formation and is modulated by amino acids in the ATP-binding site.
    Nucleic Acids Res. 2012 Feb;40(3):1214-25 PMID: 21993299
  182. Mechanisms and consequences of alternative polyadenylation.
    Mol Cell. 2011 Sep 16;43(6):853-66 PMID: 21925375
  183. PARP1 represses PAP and inhibits polyadenylation during heat shock.
    Mol Cell. 2013 Jan 10;49(1):7-17 PMID: 23219533
  184. Knock-down of 25 kDa subunit of cleavage factor Im in Hela cells alters alternative polyadenylation within 3'-UTRs.
    Nucleic Acids Res. 2006;34(21):6264-71 PMID: 17098938
  185. MEARA sequence repeat of human CstF-64 polyadenylation factor is helical in solution. A spectroscopic and calorimetric study.
    Biochemistry. 1999 Sep 28;38(39):12869-75 PMID: 10504257
  186. Sequence similarity between the 73-kilodalton protein of mammalian CPSF and a subunit of yeast polyadenylation factor I.
    Science. 1996 Nov 29;274(5292):1514-7 PMID: 8929409
  187. Two distinct forms of the 64,000 Mr protein of the cleavage stimulation factor are expressed in mouse male germ cells.
    Proc Natl Acad Sci U S A. 1999 Jun 8;96(12):6763-8 PMID: 10359786
  188. 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
  189. A 64 kd nuclear protein binds to RNA segments that include the AAUAAA polyadenylation motif.
    Cell. 1988 Jan 29;52(2):221-8 PMID: 2830023
  190. A novel WD40 repeat protein, WDC146, highly expressed during spermatogenesis in a stage-specific manner.
    Biochem Biophys Res Commun. 2001 Jan 26;280(3):656-63 PMID: 11162572
  191. Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition.
    Genes Dev. 2005 Jun 1;19(11):1315-27 PMID: 15937220
  192. The human 64-kDa polyadenylylation factor contains a ribonucleoprotein-type RNA binding domain and unusual auxiliary motifs.
    Proc Natl Acad Sci U S A. 1992 Feb 15;89(4):1403-7 PMID: 1741396
  193. 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
  194. Novel interactions at the essential N-terminus of poly(A) polymerase that could regulate poly(A) addition in Saccharomyces cerevisiae.
    FEBS Lett. 2012 Apr 24;586(8):1173-8 PMID: 22575652
  195. The human RNA kinase hClp1 is active on 3' transfer RNA exons and short interfering RNAs.
    Nature. 2007 May 10;447(7141):222-6 PMID: 17495927
  196. Complex alternative RNA processing generates an unexpected diversity of poly(A) polymerase isoforms.
    Mol Cell Biol. 1996 May;16(5):2378-86 PMID: 8628305
  197. Large-scale proteomic analysis of the human spliceosome.
    Genome Res. 2002 Aug;12(8):1231-45 PMID: 12176931
  198. The structure of human cleavage factor I(m) hints at functions beyond UGUA-specific RNA binding: a role in alternative polyadenylation and a potential link to 5' capping and splicing.
    RNA Biol. 2011 Sep-Oct;8(5):748-53 PMID: 21881408
  199. Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites.
    Science. 2008 Jun 20;320(5883):1643-7 PMID: 18566288
Article Info
Journal
Molecular and cellular biology
Abbr.
Mol Cell Biol
ISSN
1098-5549
Published
2014-06-00
Epub
2014-00-03
Pages
1894-910
Language
English
Region
United States
NLM ID
8109087
PMCID
PMC4019069
Subset
IM
Grants
NIGMS NIH HHS · R01 GM028983 · United States
NIGMS NIH HHS · R01 GM077175 · United States
NIGMS NIH HHS · GM077175 · United States
NIGMS NIH HHS · GM28983 · United States
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