Home LiteratureArticle Details
PMID: 19596240 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Control of inducible gene expression by signal-dependent transcriptional elongation.

Cell ·Vol. 138 ·No. 1 ·2009-07-10 ·Pages 129-45

Hargreaves DC, Horng T, Medzhitov R

Abstract

Most inducible transcriptional programs consist of primary and secondary response genes (PRGs and SRGs) that differ in their kinetics of expression and in their requirements for new protein synthesis and chromatin remodeling. Here we show that many PRGs, in contrast to SRGs, have preassembled RNA polymerase II (Pol II) and positive histone modifications at their promoters in the basal state. Pol II at PRGs generates low levels of full-length unspliced transcripts but fails to make mature, protein-coding transcripts in the absence of stimulation. Induction of PRGs is controlled at the level of transcriptional elongation and mRNA processing, through the signal-dependent recruitment of P-TEFb. P-TEFb is in turn recruited by the bromodomain-containing protein Brd4, which detects H4K5/8/12Ac inducibly acquired at PRG promoters. Our findings suggest that the permissive structure of PRGs both stipulates their unique regulation in the basal state by corepressor complexes and enables their rapid induction in multiple cell types.

MeSH Terms
Animals Cell Line Chromatin Assembly and Disassembly Histone Code Histones/metabolism Humans Lipopolysaccharides/immunology,metabolism Macrophages/metabolism Mice Mice, Inbred C57BL Phosphorylation Protein Structure, Tertiary RNA Polymerase II/chemistry,metabolism Regulatory Sequences, Nucleic Acid Transcriptional Activation
Chemicals
Histones Lipopolysaccharides RNA Polymerase II
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Hargreaves Diana C
Howard Hughes Medical Institute and Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA.
Horng Tiffany
Medzhitov Ruslan
References (45)
45 references, click to expand
  1. Deciphering the transcriptional histone acetylation code for a human gene.
    Cell. 2002 Nov 1;111(3):381-92 PMID: 12419248
  2. Missing pieces in the NF-kappaB puzzle.
    Cell. 2002 Apr;109 Suppl:S81-96 PMID: 11983155
  3. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II.
    Cell. 2006 May 19;125(4):703-17 PMID: 16713563
  4. Brd4 coactivates transcriptional activation of NF-kappaB via specific binding to acetylated RelA.
    Mol Cell Biol. 2009 Mar;29(5):1375-87 PMID: 19103749
  5. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote.
    Genes Dev. 2004 Jun 1;18(11):1263-71 PMID: 15175259
  6. Genome-wide map of nucleosome acetylation and methylation in yeast.
    Cell. 2005 Aug 26;122(4):517-27 PMID: 16122420
  7. Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells.
    Nat Cell Biol. 2007 Dec;9(12):1428-35 PMID: 18037880
  8. Intracellular delivery of acetyl-histone peptides inhibits native bromodomain-chromatin interactions and impairs mitotic progression.
    FEBS Lett. 2008 Apr 30;582(10):1501-7 PMID: 18396160
  9. Gene-specific control of inflammation by TLR-induced chromatin modifications.
    Nature. 2007 Jun 21;447(7147):972-8 PMID: 17538624
  10. Chromatin modifications and their function.
    Cell. 2007 Feb 23;128(4):693-705 PMID: 17320507
  11. Transcriptional responses of human epidermal keratinocytes to cytokine interleukin-1.
    J Cell Physiol. 2008 Jan;214(1):1-13 PMID: 17941080
  12. Eloquent silence: developmental functions of Class I histone deacetylases.
    Curr Opin Genet Dev. 2008 Oct;18(5):404-10 PMID: 18929655
  13. P-TEFb is not an essential elongation factor for the intronless human U2 snRNA and histone H2b genes.
    EMBO J. 2005 Dec 7;24(23):4154-65 PMID: 16308568
  14. A corepressor/coactivator exchange complex required for transcriptional activation by nuclear receptors and other regulated transcription factors.
    Cell. 2004 Feb 20;116(4):511-26 PMID: 14980219
  15. P-TEFb kinase recruitment and function at heat shock loci.
    Genes Dev. 2000 Apr 1;14(7):792-803 PMID: 10766736
  16. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4.
    Mol Cell. 2005 Aug 19;19(4):535-45 PMID: 16109377
  17. Genomic characterization reveals a simple histone H4 acetylation code.
    Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5501-6 PMID: 15795371
  18. Combinatorial patterns of histone acetylations and methylations in the human genome.
    Nat Genet. 2008 Jul;40(7):897-903 PMID: 18552846
  19. NF-kappaB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II.
    Mol Cell. 2001 Aug;8(2):327-37 PMID: 11545735
  20. Selective and antagonistic functions of SWI/SNF and Mi-2beta nucleosome remodeling complexes during an inflammatory response.
    Genes Dev. 2006 Feb 1;20(3):282-96 PMID: 16452502
  21. PU.1 and C/EBPalpha/beta convert fibroblasts into macrophage-like cells.
    Proc Natl Acad Sci U S A. 2008 Apr 22;105(16):6057-62 PMID: 18424555
  22. NEMO/IKK gamma-deficient mice model incontinentia pigmenti.
    Mol Cell. 2000 Jun;5(6):981-92 PMID: 10911992
  23. Exchange of N-CoR corepressor and Tip60 coactivator complexes links gene expression by NF-kappaB and beta-amyloid precursor protein.
    Cell. 2002 Jul 12;110(1):55-67 PMID: 12150997
  24. Phosphorylation of histone H3 at Ser10 facilitates RNA polymerase II release from promoter-proximal pausing in Drosophila.
    Genes Dev. 2007 Nov 1;21(21):2818-31 PMID: 17942706
  25. In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes.
    Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):7923-7 PMID: 8367444
  26. A nuclear receptor corepressor transcriptional checkpoint controlling activator protein 1-dependent gene networks required for macrophage activation.
    Proc Natl Acad Sci U S A. 2004 Oct 5;101(40):14461-6 PMID: 15452344
  27. Regulation of transcript elongation through cooperative and ordered recruitment of cofactors.
    J Biol Chem. 2007 Jul 20;282(29):20887-96 PMID: 17535807
  28. NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila.
    Genes Dev. 2003 Jun 1;17(11):1402-14 PMID: 12782658
  29. A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells.
    Nature. 1986 Jun 12-18;321(6071):702-6 PMID: 3520340
  30. The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription.
    Mol Cell. 2005 Aug 19;19(4):523-34 PMID: 16109376
  31. A chromatin landmark and transcription initiation at most promoters in human cells.
    Cell. 2007 Jul 13;130(1):77-88 PMID: 17632057
  32. Breaking barriers to transcription elongation.
    Nat Rev Mol Cell Biol. 2006 Aug;7(8):557-67 PMID: 16936696
  33. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo.
    Nat Genet. 2007 Dec;39(12):1512-6 PMID: 17994019
  34. RNA polymerase is poised for activation across the genome.
    Nat Genet. 2007 Dec;39(12):1507-11 PMID: 17994021
  35. Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors.
    Cell. 2004 Jan 23;116(2):247-57 PMID: 14744435
  36. Elongation by RNA polymerase II: the short and long of it.
    Genes Dev. 2004 Oct 15;18(20):2437-68 PMID: 15489290
  37. A BAF-centred view of the immune system.
    Nat Rev Immunol. 2004 Dec;4(12):965-77 PMID: 15573131
  38. A human RNA polymerase II complex containing factors that modify chromatin structure.
    Mol Cell Biol. 1998 Sep;18(9):5355-63 PMID: 9710619
  39. Class-specific regulation of pro-inflammatory genes by MyD88 pathways and IkappaBzeta.
    J Biol Chem. 2008 May 2;283(18):12468-77 PMID: 18319258
  40. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4.
    Cell. 2007 Oct 5;131(1):58-69 PMID: 17884155
  41. Control of formation of two distinct classes of RNA polymerase II elongation complexes.
    Mol Cell Biol. 1992 May;12(5):2078-90 PMID: 1569941
  42. XIAP regulates bi-phasic NF-kappaB induction involving physical interaction and ubiquitination of MEKK2.
    Cell Signal. 2008 Nov;20(11):2107-12 PMID: 18761086
  43. A conserved AU sequence from the 3' untranslated region of GM-CSF mRNA mediates selective mRNA degradation.
    Cell. 1986 Aug 29;46(5):659-67 PMID: 3488815
  44. Sp1: emerging roles--beyond constitutive activation of TATA-less housekeeping genes.
    Biochem Biophys Res Commun. 2008 Jul 18;372(1):1-13 PMID: 18364237
  45. The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis.
    Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):8758-63 PMID: 12840145
Article Info
Journal
Cell
Abbr.
Cell
ISSN
1097-4172
Published
2009-07-10
Pages
129-45
Language
English
Region
United States
NLM ID
0413066
PMCID
PMC2828818
Subset
IM
Grants
Howard Hughes Medical Institute · United States
NIAID NIH HHS · R37 AI046688 · United States
NIAID NIH HHS · R01 AI046688 · United States
NIAID NIH HHS · R37 AI046688-08 · United States
NIAID NIH HHS · U01 AI061360 · United States
Corrections
CommentIn
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com