New insights into the biogenesis of nuclear RNA polymerases?
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.
Cloutier
Philippe
P
Laboratory of Gene Transcription and Proteomics, Institut de recherches cliniques de Montreal, 110 avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada.
Coulombe
Benoit
B
D000818:Animals; D002467:Cell Nucleus / Q000201:enzymology* / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000096:biosynthesis* / Q000737:chemistry / Q000235:genetics; D006801:Humans
D012321:DNA-Directed RNA Polymerases
J Biol Chem. 2004 Feb 27;279(9):7576-83
14662759
J Biol Chem. 2004 Apr 2;279(14):13944-52
14711828
Microbiol Mol Biol Rev. 1999 Jun;63(2):457-78
10357858
J Biol Chem. 1997 Jan 31;272(5):2668-74
9006902
Cell. 1998 Jan 9;92(1):5-8
9489694
EMBO J. 2009 May 20;28(10):1429-41
19387492
Mol Biol Cell. 2005 Dec;16(12):5857-65
16221885
Cell. 2007 Feb 23;128(4):707-19
17320508
EMBO J. 1998 Feb 16;17(4):952-66
9463374
Cell. 2000 Nov 10;103(4):621-32
11106732
Curr Opin Genet Dev. 1995 Apr;5(2):190-6
7613088
Nat Cell Biol. 2006 Jun;8(6):631-9
16699503
Mol Cell Biol. 2001 Nov;21(22):7731-46
11604509
Oncogene. 2004 Jul 8;23(31):5316-29
15107825
Methods. 2009 Aug;48(4):381-6
19450687
Nat Cell Biol. 2003 Dec;5(12):1104-10
14634666
Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1454-9
18218781
Mol Cell Biol. 1997 Oct;17(10):5791-802
9315637
FEBS Lett. 2008 Jul 9;582(16):2365-70
18538670
Endocr Rev. 2001 Apr;22(2):153-83
11294822
Mol Cell Biol. 2004 Oct;24(19):8556-66
15367675
Mol Cell Biol. 2007 Oct;27(19):6782-93
17636026
Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4367-72
15070724
Trends Biochem Sci. 2005 May;30(5):250-5
15896743
Science. 2003 Nov 14;302(5648):1208-12
14615539
Nat Cell Biol. 2004 Feb;6(2):97-105
14743216
Oncogene. 2003 Oct 16;22(46):7247-57
14562055
J Mol Biol. 2008 Mar 7;376(5):1320-33
18234224
J Biol Chem. 1999 Jun 4;274(23):16604-10
10347227
J Biol Chem. 1998 Oct 23;273(43):27786-93
9774387
Protein Sci. 2007 Aug;16(8):1577-87
17656577
EMBO J. 2003 Oct 1;22(19):5230-40
14517260
Biochem Biophys Res Commun. 2006 Apr 7;342(2):568-72
16487927
Mol Cell. 2007 Oct 12;28(1):28-40
17936702
Curr Opin Genet Dev. 1999 Apr;9(2):148-51
10322131
Microbiol Mol Biol Rev. 1998 Jun;62(2):465-503
9618449
J Biol Chem. 1999 Dec 17;274(51):36035-8
10593883
Proc Natl Acad Sci U S A. 1997 Jan 7;94(1):15-22
8990153
Genomics. 2002 Jan;79(1):124-36
11827465
J Mol Biol. 2007 Feb 9;366(1):179-92
17157868
J Mol Biol. 2005 Feb 18;346(2):437-55
15670595
Proc Natl Acad Sci U S A. 1998 Dec 22;95(26):15281-6
9860960
J Cell Biochem. 2009 Apr 1;106(5):920-8
19180575
Genes Dev. 1996 Nov 1;10(21):2657-83
8946909
Nature. 1997 Apr 10;386(6625):569-77
9121580
BMC Mol Biol. 2008 Apr 15;9:36
18412953
J Cell Biol. 2008 Feb 11;180(3):563-78
18268103
Nature. 2000 Sep 28;407(6803):471-5
11028991
Hum Mol Genet. 1999 Dec;8(13):2557-66
10556305
In Vitro Cell Dev Biol Anim. 2007 Mar-Apr;43(3-4):139-46
17554592
Am J Respir Cell Mol Biol. 2004 Apr;30(4):428-34
14630615
FEBS J. 2007 Aug;274(15):3960-71
17635584
RNA. 2000 Jun;6(6):861-79
10864044
Nature. 2001 Mar 1;410(6824):37-40
11242034
Mol Biol Cell. 2002 Feb;13(2):670-82
11854421
J Cell Biol. 2007 Jul 16;178(2):231-44
17620405
Mol Endocrinol. 2007 Dec;21(12):2864-76
17761951
Cell. 1988 Feb 12;52(3):311-20
3345562
Mol Cell. 2007 Jul 20;27(2):262-74
17643375
Genes Dev. 2006 Jun 1;20(11):1458-69
16751183
J Cell Biol. 2008 Feb 11;180(3):579-95
18268104
Cell. 1998 May 29;93(5):863-73
9630229
Genomics. 1999 Mar 15;56(3):340-3
10087202
J Biol Chem. 1996 Mar 8;271(10):5361-8
8621389
J Proteome Res. 2007 May;6(5):1963-73
17348703
FEBS J. 2005 Sep;272(17):4450-63
16128814
Cell. 1994 Apr 8;77(1):5-8
8156597
EMBO J. 1999 Jan 4;18(1):75-84
9878052
Eukaryot Cell. 2008 Jun;7(6):938-48
18408053
Nat Immunol. 2001 Jul;2(7):620-4
11429546
Mol Cell. 2009 Apr 24;34(2):168-78
19394294
Development. 2006 Feb;133(4):621-9
16436622
Diabetes. 2002 Apr;51(4):910-4
11916906
Development. 1996 Oct;122(10):3133-40
8898226
Traffic. 2006 Apr;7(4):465-73
16536744
Science. 2003 Dec 5;302(5651):1727-36
14605208
Cell. 2008 Mar 21;132(6):945-57
18358808
J Biol Chem. 1997 May 30;272(22):14489-96
9162092
Prog Nucleic Acid Res Mol Biol. 1997;56:327-46
9187058
Cell. 2005 Mar 11;120(5):715-27
15766533
Trends Biochem Sci. 2005 May;30(5):235-9
15896740
Cell. 2000 Apr 14;101(2):199-210
10786835
FEBS Lett. 2005 Feb 7;579(4):909-15
15680973
J Biol Chem. 1999 Aug 6;274(32):22437-44
10428817
Mol Cell Biol. 1998 Dec;18(12):7546-55
9819440
Mol Gen Genet. 1998 Jan;257(2):103-12
9491068
Mol Cell. 2003 Nov;12(5):1287-300
14636585
Cell Res. 2003 Apr;13(2):111-20
12737519
J Cell Biol. 1997 Jan 13;136(1):19-28
9008700
J Biol Chem. 2004 Mar 26;279(13):12804-11
14676191