title: Regulation of gene expression via the core promoter and the basal transcriptional machinery.
abstract: The RNA polymerase II core promoter is a structurally and functionally diverse transcriptional regulatory element. There are two main strategies for transcription initiation - focused and dispersed initiation. In focused initiation, transcription starts from a single nucleotide or within a cluster of several nucleotides, whereas in dispersed initiation, there are several weak transcription start sites over a broad region of about 50 to 100 nucleotides. Focused initiation is the predominant means of transcription in simpler organisms, whereas dispersed initiation is observed in approximately two-thirds of vertebrate genes. Regulated genes tend to have focused promoters, and constitutive genes typically have dispersed promoters. Hence, in vertebrates, focused promoters are used in a small but biologically important fraction of genes. The properties of focused core promoters are dependent upon the presence or absence of sequence motifs such as the TATA box and DPE. For example, Caudal, a key regulator of the homeotic gene network, preferentially activates transcription from DPE- versus TATA-dependent promoters. The basal transcription factors, which act in conjunction with the core promoter, are another important component in the regulation of gene expression. For instance, upon differentiation of myoblasts to myotubes, the cells undergo a switch from a TFIID-based transcription system to a TRF3-TAF3-based system. These findings suggest that the core promoter and basal transcription factors are important yet mostly unexplored components in the regulation of gene expression.
authors.affiliation: Section of Molecular Biology, 0347, University of California, San Diego, La Jolla, CA 92093-0347, USA.
authors.forename: Tamar
authors.initials: T
authors.lastname: Juven-Gershon
authors.forename: James T
authors.initials: JT
authors.lastname: Kadonaga
mesh_terms: D000818:Animals; D001665:Binding Sites; D005786:Gene Expression Regulation; D006801:Humans; D008954:Models, Biological; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D016385:TATA Box / Q000235:genetics; D035362:Transcription Factor TFIID / Q000235:genetics / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D012333:RNA, Messenger; D035362:Transcription Factor TFIID; D012319:RNA Polymerase II
references.citation: Cell Mol Life Sci. 2007 Feb;64(4):386-400
references.pmid: 17171231
references.citation: Mol Cell. 2005 May 13;18(4):471-81
references.pmid: 15893730
references.citation: Genes Dev. 1998 Jan 1;12(1):34-44
references.pmid: 9420329
references.citation: Genes Dev. 2001 Oct 1;15(19):2515-9
references.pmid: 11581157
references.citation: Genome Biol. 2006;7(8):R78
references.pmid: 16916456
references.citation: Mol Cell Biol. 2000 Jul;20(13):4754-64
references.pmid: 10848601
references.citation: Genes Dev. 2007 Nov 15;21(22):2936-49
references.pmid: 17978101
references.citation: Genes Dev. 1997 Nov 15;11(22):3020-31
references.pmid: 9367984
references.citation: Mol Cell. 2008 Oct 10;32(1):96-105
references.pmid: 18851836
references.citation: Genes Dev. 2008 Oct 15;22(20):2823-30
references.pmid: 18923080
references.citation: J Biol Chem. 2007 May 18;282(20):14685-9
references.pmid: 17395580
references.citation: Mol Microbiol. 2003 May;48(3):587-98
references.pmid: 12694606
references.citation: Genes Dev. 2002 Oct 15;16(20):2583-92
references.pmid: 12381658
references.citation: Genes Dev. 1994 Apr 1;8(7):830-42
references.pmid: 7926771
references.citation: Nature. 2003 Jul 10;424(6945):147-51
references.pmid: 12853946
references.citation: Science. 2000 Nov 3;290(5493):982-5
references.pmid: 11062130
references.citation: Genome Res. 2008 Jan;18(1):1-12
references.pmid: 18032727
references.citation: Genes Dev. 1996 Mar 15;10(6):711-24
references.pmid: 8598298
references.citation: BMC Genomics. 2006 Jun 21;7:161
references.pmid: 16790048
references.citation: Genes Dev. 1998 Feb 15;12(4):547-56
references.pmid: 9472023
references.citation: Cell. 2000 May 26;101(5):459-69
references.pmid: 10850489
references.citation: Nature. 2007 Dec 13;450(7172):1082-5
references.pmid: 18046332
references.citation: Cell. 1989 Apr 7;57(1):103-13
references.pmid: 2467742
references.citation: Nat Rev Genet. 2007 Jun;8(6):424-36
references.pmid: 17486122
references.citation: Nat Methods. 2006 Nov;3(11):917-22
references.pmid: 17124735
references.citation: Genome Biol. 2006;7(7):R53
references.pmid: 16827941
references.citation: Curr Opin Cell Biol. 2008 Jun;20(3):253-9
references.pmid: 18436437
references.citation: Biochem Soc Trans. 2006 Dec;34(Pt 6):1047-50
references.pmid: 17073747
references.citation: Genes Dev. 2008 Sep 1;22(17):2359-69
references.pmid: 18703679
references.citation: Genes Dev. 2007 Sep 1;21(17):2137-49
references.pmid: 17704303
references.citation: Genes Dev. 2007 Nov 15;21(22):2855-60
references.pmid: 18006682
references.citation: Nat Genet. 2006 Jun;38(6):626-35
references.pmid: 16645617
references.citation: Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9715-20
references.pmid: 18621688
references.citation: Genome Res. 2006 Jan;16(1):1-10
references.pmid: 16344566
references.citation: EMBO J. 1999 Sep 1;18(17):4835-45
references.pmid: 10469661
references.citation: Genes Dev. 2005 Oct 15;19(20):2418-23
references.pmid: 16230532
references.citation: Genes Dev. 2004 Jul 1;18(13):1606-17
references.pmid: 15231738
references.citation: Annu Rev Biochem. 2003;72:449-79
references.pmid: 12651739
references.citation: BMC Genomics. 2005 Feb 25;6:25
references.pmid: 15733318
references.citation: Gene. 2007 Mar 1;389(1):52-65
references.pmid: 17123746
references.citation: Genome Biol. 2002;3(12):RESEARCH0087
references.pmid: 12537576
references.citation: Genes Dev. 2001 Oct 1;15(19):2503-8
references.pmid: 11581155
references.citation: Nature. 2005 Aug 11;436(7052):876-80
references.pmid: 15988478
references.citation: Curr Biol. 2004 Apr 6;14(7):593-8
references.pmid: 15062100
references.citation: Crit Rev Biochem Mol Biol. 2006 May-Jun;41(3):105-78
references.pmid: 16858867
references.citation: BMC Genomics. 2007 Mar 08;8:67
references.pmid: 17346352
references.citation: Chromosoma. 2007 Oct;116(5):417-29
references.pmid: 17593382
references.citation: Proc Natl Acad Sci U S A. 2004 Sep 14;101(37):13525-30
references.pmid: 15345743
references.citation: Genes Dev. 2001 Nov 15;15(22):2945-9
references.pmid: 11711430
references.citation: Nucleic Acids Res. 2007;35(18):6219-26
references.pmid: 17855401
references.citation: EMBO Rep. 2007 Nov;8(11):1016-8
references.pmid: 17972900
references.citation: Genes Dev. 2008 Sep 1;22(17):2353-8
references.pmid: 18703680
references.citation: Genes Dev. 2007 Sep 1;21(17):2113-7
references.pmid: 17785521