Pervasive transcription constitutes a new level of eukaryotic genome regulation.
During the past few years, it has become increasingly evident that the expression of eukaryotic genomes is far more complex than had been previously noted. The idea that the transcriptome is derived exclusively from protein-coding genes and some specific non-coding RNAs--such as snRNAs, snoRNAs, tRNAs or rRNAs--has been swept away by numerous studies indicating that RNA polymerase II can be found at almost any genomic location. Pervasive transcription is widespread and, far from being a futile process, has a crucial role in controlling gene expression and genomic plasticity. Here, we review recent findings that point to cryptic transcription as a fundamental component of the regulation of eukaryotic genomes.
Berretta
Julia
J
Centre de Génétique Moléculaire-Centre National de la Recherche Scientifique, Université of Pierre et Marie Curie, 91198 Gif-sur-Yvette, Paris 6, France.
Morillon
Antonin
A
D000818:Animals; D005057:Eukaryotic Cells / Q000378:metabolism*; D005786:Gene Expression Regulation; D016678:Genome; D006801:Humans; D034622:RNA Interference; D022661:RNA, Untranslated; D014158:Transcription, Genetic
D022661:RNA, Untranslated
Science. 2005 Sep 2;309(5740):1564-6
16141073
EMBO J. 2007 Dec 12;26(24):4996-5006
18007593
Curr Opin Cell Biol. 2009 Jun;21(3):359-66
19477626
Mol Cell. 2008 Oct 24;32(2):232-46
18951091
Nature. 2008 Jun 26;453(7199):1239-43
18488015
Nature. 2007 Feb 8;445(7128):666-70
17237763
Mol Cell. 2006 Dec 8;24(5):735-746
17157256
Science. 2008 Dec 19;322(5909):1849-51
19056940
Genes Dev. 2005 Mar 15;19(6):697-708
15741315
Science. 2008 Dec 19;322(5909):1855-7
19056939
Science. 2007 May 4;316(5825):744-7
17446352
Nature. 2008 Nov 6;456(7218):130-4
18820678
PLoS Biol. 2005 Jun;3(6):e189
15828860
Cell. 2009 Feb 20;136(4):642-55
19239886
Science. 2008 Dec 12;322(5908):1717-20
18988810
Cell. 2005 Nov 18;123(4):581-92
16286007
Genes Dev. 2009 Jul 1;23(13):1534-45
19571181
Nat Genet. 2008 Aug;40(8):977-86
18641648
PLoS Biol. 2008 Dec 23;6(12):2817-30
19108609
Mol Biol Cell. 2006 Sep;17(9):3848-59
16807355
Annu Rev Genet. 2008;42:733-72
18729722
Science. 2007 Jun 8;316(5830):1484-8
17510325
Nat Rev Genet. 2007 Jun;8(6):413-23
17486121
Nature. 2009 Feb 19;457(7232):1033-7
19169243
Mol Cell. 2008 Sep 26;31(6):785-99
18922463
Mol Cell. 2006 Sep 15;23(6):853-64
16973437
Science. 2004 Oct 22;306(5696):655-60
15499012
Nat Cell Biol. 2008 Feb;10(2):228-36
18157120
Nat Genet. 2009 May;41(5):572-8
19377478
Nature. 2009 Feb 19;457(7232):1038-42
19169244
Science. 2008 Dec 19;322(5909):1845-8
19056941
Genes Dev. 2008 Mar 1;22(5):615-26
18316478
Science. 2004 Dec 24;306(5705):2242-6
15539566
Mol Cell. 2006 Sep 15;23(6):841-51
16973436
Mol Cell. 2008 Jul 25;31(2):201-11
18657503
Science. 2005 Sep 2;309(5740):1559-63
16141072
Cell. 2007 Jun 29;129(7):1311-23
17604720
PLoS Genet. 2008 Dec;4(12):e1000299
19096707
Cell. 2007 Mar 23;128(6):1089-103
17346786
Cell. 2005 Jun 3;121(5):713-24
15935758
Nat Genet. 2006 Jun;38(6):626-35
16645617
Science. 2008 Jun 6;320(5881):1344-9
18451266
Nat Genet. 2006 Jan;38(1):124-9
16369532
Science. 2003 Aug 22;301(5636):1096-9
12934008
Nature. 2005 Aug 11;436(7052):876-80
15988478
Mol Cell Biol. 2007 Jan;27(1):92-101
17074811
Nature. 2007 Dec 13;450(7172):1031-5
18075583
EMBO J. 1997 Dec 1;16(23):7184-95
9384595
EMBO J. 2009 Jun 17;28(12):1697-707
19407817
Nature. 2008 Jul 3;454(7200):126-30
18509338
Mol Cell. 2008 Nov 21;32(4):465-77
19026778
Science. 2008 Dec 19;322(5909):1851-4
19056938
Cell. 2007 Nov 16;131(4):706-17
18022365
Science. 2007 Nov 2;318(5851):798-801
17916692
Proc Natl Acad Sci U S A. 2007 May 8;104(19):8011-6
17470801
Mol Cell. 2008 Feb 15;29(3):313-23
18280237
Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5320-5
16569694
Science. 2005 May 20;308(5725):1149-54
15790807
Mol Cell. 2008 Dec 5;32(5):685-95
19061643
Nature. 2009 Mar 12;458(7235):223-7
19182780
Nature. 2004 Jun 3;429(6991):571-4
15175754
Mol Cell. 2008 Sep 5;31(5):671-82
18775327
Cell. 1997 Jan 24;88(2):243-51
9008165
Genome Res. 2008 Jul;18(7):1073-83
18550805
Cell. 2005 Jun 3;121(5):725-37
15935759