title: Pervasive transcription constitutes a new level of eukaryotic genome regulation.
abstract: 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.
authors.affiliation: Centre de Génétique Moléculaire-Centre National de la Recherche Scientifique, Université of Pierre et Marie Curie, 91198 Gif-sur-Yvette, Paris 6, France.
authors.forename: Julia
authors.initials: J
authors.lastname: Berretta
authors.forename: Antonin
authors.initials: A
authors.lastname: Morillon
mesh_terms: D000818:Animals; D005057:Eukaryotic Cells / Q000378:metabolism*; D005786:Gene Expression Regulation; D016678:Genome; D006801:Humans; D034622:RNA Interference; D022661:RNA, Untranslated; D014158:Transcription, Genetic
chemical_list: D022661:RNA, Untranslated
references.citation: Science. 2005 Sep 2;309(5740):1564-6
references.pmid: 16141073
references.citation: EMBO J. 2007 Dec 12;26(24):4996-5006
references.pmid: 18007593
references.citation: Curr Opin Cell Biol. 2009 Jun;21(3):359-66
references.pmid: 19477626
references.citation: Mol Cell. 2008 Oct 24;32(2):232-46
references.pmid: 18951091
references.citation: Nature. 2008 Jun 26;453(7199):1239-43
references.pmid: 18488015
references.citation: Nature. 2007 Feb 8;445(7128):666-70
references.pmid: 17237763
references.citation: Mol Cell. 2006 Dec 8;24(5):735-746
references.pmid: 17157256
references.citation: Science. 2008 Dec 19;322(5909):1849-51
references.pmid: 19056940
references.citation: Genes Dev. 2005 Mar 15;19(6):697-708
references.pmid: 15741315
references.citation: Science. 2008 Dec 19;322(5909):1855-7
references.pmid: 19056939
references.citation: Science. 2007 May 4;316(5825):744-7
references.pmid: 17446352
references.citation: Nature. 2008 Nov 6;456(7218):130-4
references.pmid: 18820678
references.citation: PLoS Biol. 2005 Jun;3(6):e189
references.pmid: 15828860
references.citation: Cell. 2009 Feb 20;136(4):642-55
references.pmid: 19239886
references.citation: Science. 2008 Dec 12;322(5908):1717-20
references.pmid: 18988810
references.citation: Cell. 2005 Nov 18;123(4):581-92
references.pmid: 16286007
references.citation: Genes Dev. 2009 Jul 1;23(13):1534-45
references.pmid: 19571181
references.citation: Nat Genet. 2008 Aug;40(8):977-86
references.pmid: 18641648
references.citation: PLoS Biol. 2008 Dec 23;6(12):2817-30
references.pmid: 19108609
references.citation: Mol Biol Cell. 2006 Sep;17(9):3848-59
references.pmid: 16807355
references.citation: Annu Rev Genet. 2008;42:733-72
references.pmid: 18729722
references.citation: Science. 2007 Jun 8;316(5830):1484-8
references.pmid: 17510325
references.citation: Nat Rev Genet. 2007 Jun;8(6):413-23
references.pmid: 17486121
references.citation: Nature. 2009 Feb 19;457(7232):1033-7
references.pmid: 19169243
references.citation: Mol Cell. 2008 Sep 26;31(6):785-99
references.pmid: 18922463
references.citation: Mol Cell. 2006 Sep 15;23(6):853-64
references.pmid: 16973437
references.citation: Science. 2004 Oct 22;306(5696):655-60
references.pmid: 15499012
references.citation: Nat Cell Biol. 2008 Feb;10(2):228-36
references.pmid: 18157120
references.citation: Nat Genet. 2009 May;41(5):572-8
references.pmid: 19377478
references.citation: Nature. 2009 Feb 19;457(7232):1038-42
references.pmid: 19169244
references.citation: Science. 2008 Dec 19;322(5909):1845-8
references.pmid: 19056941
references.citation: Genes Dev. 2008 Mar 1;22(5):615-26
references.pmid: 18316478
references.citation: Science. 2004 Dec 24;306(5705):2242-6
references.pmid: 15539566
references.citation: Mol Cell. 2006 Sep 15;23(6):841-51
references.pmid: 16973436
references.citation: Mol Cell. 2008 Jul 25;31(2):201-11
references.pmid: 18657503
references.citation: Science. 2005 Sep 2;309(5740):1559-63
references.pmid: 16141072
references.citation: Cell. 2007 Jun 29;129(7):1311-23
references.pmid: 17604720
references.citation: PLoS Genet. 2008 Dec;4(12):e1000299
references.pmid: 19096707
references.citation: Cell. 2007 Mar 23;128(6):1089-103
references.pmid: 17346786
references.citation: Cell. 2005 Jun 3;121(5):713-24
references.pmid: 15935758
references.citation: Nat Genet. 2006 Jun;38(6):626-35
references.pmid: 16645617
references.citation: Science. 2008 Jun 6;320(5881):1344-9
references.pmid: 18451266
references.citation: Nat Genet. 2006 Jan;38(1):124-9
references.pmid: 16369532
references.citation: Science. 2003 Aug 22;301(5636):1096-9
references.pmid: 12934008
references.citation: Nature. 2005 Aug 11;436(7052):876-80
references.pmid: 15988478
references.citation: Mol Cell Biol. 2007 Jan;27(1):92-101
references.pmid: 17074811
references.citation: Nature. 2007 Dec 13;450(7172):1031-5
references.pmid: 18075583
references.citation: EMBO J. 1997 Dec 1;16(23):7184-95
references.pmid: 9384595
references.citation: EMBO J. 2009 Jun 17;28(12):1697-707
references.pmid: 19407817
references.citation: Nature. 2008 Jul 3;454(7200):126-30
references.pmid: 18509338
references.citation: Mol Cell. 2008 Nov 21;32(4):465-77
references.pmid: 19026778
references.citation: Science. 2008 Dec 19;322(5909):1851-4
references.pmid: 19056938
references.citation: Cell. 2007 Nov 16;131(4):706-17
references.pmid: 18022365
references.citation: Science. 2007 Nov 2;318(5851):798-801
references.pmid: 17916692
references.citation: Proc Natl Acad Sci U S A. 2007 May 8;104(19):8011-6
references.pmid: 17470801
references.citation: Mol Cell. 2008 Feb 15;29(3):313-23
references.pmid: 18280237
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5320-5
references.pmid: 16569694
references.citation: Science. 2005 May 20;308(5725):1149-54
references.pmid: 15790807
references.citation: Mol Cell. 2008 Dec 5;32(5):685-95
references.pmid: 19061643
references.citation: Nature. 2009 Mar 12;458(7235):223-7
references.pmid: 19182780
references.citation: Nature. 2004 Jun 3;429(6991):571-4
references.pmid: 15175754
references.citation: Mol Cell. 2008 Sep 5;31(5):671-82
references.pmid: 18775327
references.citation: Cell. 1997 Jan 24;88(2):243-51
references.pmid: 9008165
references.citation: Genome Res. 2008 Jul;18(7):1073-83
references.pmid: 18550805
references.citation: Cell. 2005 Jun 3;121(5):725-37
references.pmid: 15935759