title: New insights into the biogenesis of nuclear RNA polymerases?
abstract: More than 30 years of research on nuclear RNA polymerases (RNAP I, II, and III) has uncovered numerous factors that regulate the activity of these enzymes during the transcription reaction. However, very little is known about the machinery that regulates the fate of RNAPs before or after transcription. In particular, the mechanisms of biogenesis of the 3 nuclear RNAPs, which comprise both common and specific subunits, remains mostly uncharacterized and the proteins involved are yet to be discovered. Using protein affinity purification coupled to mass spectrometry (AP-MS), we recently unraveled a high-density interaction network formed by nuclear RNAP subunits from the soluble fraction of human cell extracts. Validation of the dataset using a machine learning approach trained to minimize the rate of false positives and false negatives yielded a high-confidence dataset and uncovered novel interactors that regulate the RNAP II transcription machinery, including a set of proteins we named the RNAP II-associated proteins (RPAPs). One of the RPAPs, RPAP3, is part of an 11-subunit complex we termed the RPAP3/R2TP/prefoldin-like complex. Here, we review the literature on the subunits of this complex, which points to a role in nuclear RNAP biogenesis.
authors.affiliation: Laboratory of Gene Transcription and Proteomics, Institut de recherches cliniques de Montreal, 110 avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada.
authors.forename: Philippe
authors.initials: P
authors.lastname: Cloutier
authors.forename: Benoit
authors.initials: B
authors.lastname: Coulombe
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000201:enzymology* / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000096:biosynthesis* / Q000737:chemistry / Q000235:genetics; D006801:Humans
chemical_list: D012321:DNA-Directed RNA Polymerases
references.citation: J Biol Chem. 2004 Feb 27;279(9):7576-83
references.pmid: 14662759
references.citation: J Biol Chem. 2004 Apr 2;279(14):13944-52
references.pmid: 14711828
references.citation: Microbiol Mol Biol Rev. 1999 Jun;63(2):457-78
references.pmid: 10357858
references.citation: J Biol Chem. 1997 Jan 31;272(5):2668-74
references.pmid: 9006902
references.citation: Cell. 1998 Jan 9;92(1):5-8
references.pmid: 9489694
references.citation: EMBO J. 2009 May 20;28(10):1429-41
references.pmid: 19387492
references.citation: Mol Biol Cell. 2005 Dec;16(12):5857-65
references.pmid: 16221885
references.citation: Cell. 2007 Feb 23;128(4):707-19
references.pmid: 17320508
references.citation: EMBO J. 1998 Feb 16;17(4):952-66
references.pmid: 9463374
references.citation: Cell. 2000 Nov 10;103(4):621-32
references.pmid: 11106732
references.citation: Curr Opin Genet Dev. 1995 Apr;5(2):190-6
references.pmid: 7613088
references.citation: Nat Cell Biol. 2006 Jun;8(6):631-9
references.pmid: 16699503
references.citation: Mol Cell Biol. 2001 Nov;21(22):7731-46
references.pmid: 11604509
references.citation: Oncogene. 2004 Jul 8;23(31):5316-29
references.pmid: 15107825
references.citation: Methods. 2009 Aug;48(4):381-6
references.pmid: 19450687
references.citation: Nat Cell Biol. 2003 Dec;5(12):1104-10
references.pmid: 14634666
references.citation: Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1454-9
references.pmid: 18218781
references.citation: Mol Cell Biol. 1997 Oct;17(10):5791-802
references.pmid: 9315637
references.citation: FEBS Lett. 2008 Jul 9;582(16):2365-70
references.pmid: 18538670
references.citation: Endocr Rev. 2001 Apr;22(2):153-83
references.pmid: 11294822
references.citation: Mol Cell Biol. 2004 Oct;24(19):8556-66
references.pmid: 15367675
references.citation: Mol Cell Biol. 2007 Oct;27(19):6782-93
references.pmid: 17636026
references.citation: Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4367-72
references.pmid: 15070724
references.citation: Trends Biochem Sci. 2005 May;30(5):250-5
references.pmid: 15896743
references.citation: Science. 2003 Nov 14;302(5648):1208-12
references.pmid: 14615539
references.citation: Nat Cell Biol. 2004 Feb;6(2):97-105
references.pmid: 14743216
references.citation: Oncogene. 2003 Oct 16;22(46):7247-57
references.pmid: 14562055
references.citation: J Mol Biol. 2008 Mar 7;376(5):1320-33
references.pmid: 18234224
references.citation: J Biol Chem. 1999 Jun 4;274(23):16604-10
references.pmid: 10347227
references.citation: J Biol Chem. 1998 Oct 23;273(43):27786-93
references.pmid: 9774387
references.citation: Protein Sci. 2007 Aug;16(8):1577-87
references.pmid: 17656577
references.citation: EMBO J. 2003 Oct 1;22(19):5230-40
references.pmid: 14517260
references.citation: Biochem Biophys Res Commun. 2006 Apr 7;342(2):568-72
references.pmid: 16487927
references.citation: Mol Cell. 2007 Oct 12;28(1):28-40
references.pmid: 17936702
references.citation: Curr Opin Genet Dev. 1999 Apr;9(2):148-51
references.pmid: 10322131
references.citation: Microbiol Mol Biol Rev. 1998 Jun;62(2):465-503
references.pmid: 9618449
references.citation: J Biol Chem. 1999 Dec 17;274(51):36035-8
references.pmid: 10593883
references.citation: Proc Natl Acad Sci U S A. 1997 Jan 7;94(1):15-22
references.pmid: 8990153
references.citation: Genomics. 2002 Jan;79(1):124-36
references.pmid: 11827465
references.citation: J Mol Biol. 2007 Feb 9;366(1):179-92
references.pmid: 17157868
references.citation: J Mol Biol. 2005 Feb 18;346(2):437-55
references.pmid: 15670595
references.citation: Proc Natl Acad Sci U S A. 1998 Dec 22;95(26):15281-6
references.pmid: 9860960
references.citation: J Cell Biochem. 2009 Apr 1;106(5):920-8
references.pmid: 19180575
references.citation: Genes Dev. 1996 Nov 1;10(21):2657-83
references.pmid: 8946909
references.citation: Nature. 1997 Apr 10;386(6625):569-77
references.pmid: 9121580
references.citation: BMC Mol Biol. 2008 Apr 15;9:36
references.pmid: 18412953
references.citation: J Cell Biol. 2008 Feb 11;180(3):563-78
references.pmid: 18268103
references.citation: Nature. 2000 Sep 28;407(6803):471-5
references.pmid: 11028991
references.citation: Hum Mol Genet. 1999 Dec;8(13):2557-66
references.pmid: 10556305
references.citation: In Vitro Cell Dev Biol Anim. 2007 Mar-Apr;43(3-4):139-46
references.pmid: 17554592
references.citation: Am J Respir Cell Mol Biol. 2004 Apr;30(4):428-34
references.pmid: 14630615
references.citation: FEBS J. 2007 Aug;274(15):3960-71
references.pmid: 17635584
references.citation: RNA. 2000 Jun;6(6):861-79
references.pmid: 10864044
references.citation: Nature. 2001 Mar 1;410(6824):37-40
references.pmid: 11242034
references.citation: Mol Biol Cell. 2002 Feb;13(2):670-82
references.pmid: 11854421
references.citation: J Cell Biol. 2007 Jul 16;178(2):231-44
references.pmid: 17620405
references.citation: Mol Endocrinol. 2007 Dec;21(12):2864-76
references.pmid: 17761951
references.citation: Cell. 1988 Feb 12;52(3):311-20
references.pmid: 3345562
references.citation: Mol Cell. 2007 Jul 20;27(2):262-74
references.pmid: 17643375
references.citation: Genes Dev. 2006 Jun 1;20(11):1458-69
references.pmid: 16751183
references.citation: J Cell Biol. 2008 Feb 11;180(3):579-95
references.pmid: 18268104
references.citation: Cell. 1998 May 29;93(5):863-73
references.pmid: 9630229
references.citation: Genomics. 1999 Mar 15;56(3):340-3
references.pmid: 10087202
references.citation: J Biol Chem. 1996 Mar 8;271(10):5361-8
references.pmid: 8621389
references.citation: J Proteome Res. 2007 May;6(5):1963-73
references.pmid: 17348703
references.citation: FEBS J. 2005 Sep;272(17):4450-63
references.pmid: 16128814
references.citation: Cell. 1994 Apr 8;77(1):5-8
references.pmid: 8156597
references.citation: EMBO J. 1999 Jan 4;18(1):75-84
references.pmid: 9878052
references.citation: Eukaryot Cell. 2008 Jun;7(6):938-48
references.pmid: 18408053
references.citation: Nat Immunol. 2001 Jul;2(7):620-4
references.pmid: 11429546
references.citation: Mol Cell. 2009 Apr 24;34(2):168-78
references.pmid: 19394294
references.citation: Development. 2006 Feb;133(4):621-9
references.pmid: 16436622
references.citation: Diabetes. 2002 Apr;51(4):910-4
references.pmid: 11916906
references.citation: Development. 1996 Oct;122(10):3133-40
references.pmid: 8898226
references.citation: Traffic. 2006 Apr;7(4):465-73
references.pmid: 16536744
references.citation: Science. 2003 Dec 5;302(5651):1727-36
references.pmid: 14605208
references.citation: Cell. 2008 Mar 21;132(6):945-57
references.pmid: 18358808
references.citation: J Biol Chem. 1997 May 30;272(22):14489-96
references.pmid: 9162092
references.citation: Prog Nucleic Acid Res Mol Biol. 1997;56:327-46
references.pmid: 9187058
references.citation: Cell. 2005 Mar 11;120(5):715-27
references.pmid: 15766533
references.citation: Trends Biochem Sci. 2005 May;30(5):235-9
references.pmid: 15896740
references.citation: Cell. 2000 Apr 14;101(2):199-210
references.pmid: 10786835
references.citation: FEBS Lett. 2005 Feb 7;579(4):909-15
references.pmid: 15680973
references.citation: J Biol Chem. 1999 Aug 6;274(32):22437-44
references.pmid: 10428817
references.citation: Mol Cell Biol. 1998 Dec;18(12):7546-55
references.pmid: 9819440
references.citation: Mol Gen Genet. 1998 Jan;257(2):103-12
references.pmid: 9491068
references.citation: Mol Cell. 2003 Nov;12(5):1287-300
references.pmid: 14636585
references.citation: Cell Res. 2003 Apr;13(2):111-20
references.pmid: 12737519
references.citation: J Cell Biol. 1997 Jan 13;136(1):19-28
references.pmid: 9008700
references.citation: J Biol Chem. 2004 Mar 26;279(13):12804-11
references.pmid: 14676191