title: The histone deacetylase inhibitor sodium valproate causes limited transcriptional change in mouse embryonic stem cells but selectively overrides Polycomb-mediated Hoxb silencing.
abstract: BACKGROUND
  Histone deacetylase inhibitors (HDACi) cause histone hyperacetylation and H3K4 hypermethylation in various cell types. They find clinical application as anti-epileptics and chemotherapeutic agents, but the pathways through which they operate remain unclear. Surprisingly, changes in gene expression caused by HDACi are often limited in extent and can be positive or negative. Here we have explored the ability of the clinically important HDACi valproic acid (VPA) to alter histone modification and gene expression, both globally and at specific genes, in mouse embryonic stem (ES) cells.
  
  
  RESULTS
  Microarray expression analysis of ES cells exposed to VPA (1 mM, 8 h), showed that only 2.4% of genes showed a significant, >1.5-fold transcriptional change. Of these, 33% were down-regulated. There was no correlation between gene expression and VPA-induced changes in histone acetylation or H3K4 methylation at gene promoters, which were usually minimal. In contrast, all Hoxb genes showed increased levels of H3K9ac after exposure to VPA, but much less change in other modifications showing bulk increases. VPA-induced changes were lost within 24 h of inhibitor removal. VPA significantly increased the low transcription of Hoxb4 and Hoxb7, but not other Hoxb genes. Expression of Hoxb genes increased in ES cells lacking functional Polycomb silencing complexes PRC1 and PRC2. Surprisingly, VPA caused no further increase in Hoxb transcription in these cells, except for Hoxb1, whose expression increased several fold. Retinoic acid (RA) increased transcription of all Hoxb genes in differentiating ES cells within 24 h, but thereafter transcription remained the same, increased progressively or fell progressively in a locus-specific manner.
  
  
  CONCLUSIONS
  Hoxb genes in ES cells are unusual in being sensitive to VPA, with effects on both cluster-wide and locus-specific processes. VPA increases H3K9ac at all Hoxb loci but significantly overrides PRC-mediated silencing only at Hoxb4 and Hoxb7. Hoxb1 is the only Hoxb gene that is further up-regulated by VPA in PRC-deficient cells. Our results demonstrate that VPA can exert both cluster-wide and locus-specific effects on Hoxb regulation.
authors: Chromatin and Gene Expression Group, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham B15 2TT, UK. b.m.turner@bham.ac.uk.
authors: Elsa
authors: E
authors: Boudadi
authors: Hannah
authors: H
authors: Stower
authors: John A
authors: JA
authors: Halsall
authors: Charlotte E
authors: CE
authors: Rutledge
authors: Martin
authors: M
authors: Leeb
authors: Anton
authors: A
authors: Wutz
authors: Laura P
authors: LP
authors: O'Neill
authors: Karl P
authors: KP
authors: Nightingale
authors: Bryan M
authors: BM
authors: Turner
references: Cell. 2011 Feb 18;144(4):513-25
references: 21335234
references: Nucleic Acids Res. 2010 Aug;38(15):4958-69
references: 20385584
references: Gene Expr. 1996;5(4-5):245-53
references: 8723390
references: Nature. 2008 Aug 7;454(7205):711-5
references: 18685699
references: Genes Dev. 2006 Nov 1;20(21):2913-21
references: 17079682
references: J Biol Chem. 2007 Feb 16;282(7):4408-4416
references: 17166833
references: Cold Spring Harb Symp Quant Biol. 2010;75:71-8
references: 21502416
references: Pharmacogenet Genomics. 2005 Nov;15(11):787-800
references: 16220111
references: Nat Genet. 2011 Nov 28;43(12):1169-70; author reply 1171-2
references: 22120049
references: Mol Cell. 2006 Jun 9;22(5):669-79
references: 16762839
references: Methods. 1999 Nov;19(3):417-24
references: 10579937
references: PLoS Biol. 2007 Dec;5(12):e326
references: 18076287
references: EMBO J. 1994 Nov 15;13(22):5274-83
references: 7957093
references: Genes Dev. 2010 Feb 1;24(3):265-76
references: 20123906
references: J Cell Biochem. 2009 Jul 1;107(4):600-8
references: 19459166
references: Trends Genet. 2011 Oct;27(10):389-96
references: 21764166
references: J Pathol. 2005 Jan;205(2):154-71
references: 15643670
references: Cell. 2009 Sep 4;138(5):1019-31
references: 19698979
references: Genome Res. 2007 Jun;17(6):708-19
references: 17567991
references: J Natl Cancer Inst. 2010 Feb 24;102(4):219
references: 20145211
references: Cancer Treat Rev. 2008 May;34(3):206-22
references: 18226465
references: Nat Genet. 2001 May;28(1):17-8
references: 11326268
references: Biomaterials. 2011 Oct;32(30):7363-74
references: 21762983
references: Biochim Biophys Acta. 2009 Jan;1789(1):58-68
references: 18722564
references: J Biol Chem. 2002 Mar 15;277(11):9590-7
references: 11777905
references: Semin Neurol. 2008 Jul;28(3):328-35
references: 18777479
references: Am J Med Genet. 1988 Jan;29(1):171-85
references: 3125743
references: Hum Mol Genet. 2000 Jan 22;9(2):227-36
references: 10607833
references: EMBO J. 2011 Jan 19;30(2):249-62
references: 21131905
references: Nat Cell Biol. 2006 May;8(5):532-8
references: 16570078
references: Nature. 2007 Aug 2;448(7153):553-60
references: 17603471
references: Cancer Lett. 2009 Aug 8;280(2):192-200
references: 19345475
references: J Biol Chem. 2011 Oct 14;286(41):35977-35988
references: 21849501
references: Expert Opin Drug Saf. 2005 Mar;4(2):345-53
references: 15794725
references: Trends Genet. 2012 Sep;28(9):436-44
references: 22633123
references: Cell Res. 2011 Mar;21(3):381-95
references: 21321607
references: Expert Opin Pharmacother. 2008 Feb;9(2):285-92
references: 18201150
references: Cell. 2006 Apr 21;125(2):315-26
references: 16630819
references: Nature. 2012 Sep 6;489(7414):57-74
references: 22955616
references: PLoS One. 2009 Jun 30;4(6):e6086
references: 19564914
references: J Biol Chem. 2002 Apr 26;277(17):15171-81
references: 11821430
references: PLoS One. 2012;7(9):e43692
references: 23028466
references: J Biol Chem. 2001 Sep 28;276(39):36734-41
references: 11473107
references: J Biol Chem. 2011 Feb 4;286(5):3250-60
references: 21087926
references: Mol Pharmacol. 2011 Dec;80(6):979-87
references: 21868484
references: Bioessays. 2008 Feb;30(2):110-21
references: 18200528
references: Mol Cell. 2006 Aug;23(4):607-18
references: 16916647
references: Nat Rev Genet. 2009 Jan;10(1):32-42
references: 19065135
references: Pharmacol Res. 2010 Jul;62(1):18-34
references: 20219679
references: Methods. 2003 Sep;31(1):76-82
references: 12893176
references: Somatic Cell Genet. 1977 Mar;3(2):217-25
references: 605381
references: Oncogene. 2007 Aug 13;26(37):5541-52
references: 17694093
references: Genes Dev. 2004 May 15;18(10):1119-30
references: 15155579
references: Nature. 2002 Sep 26;419(6905):407-11
references: 12353038
references: Nature. 1989 Dec 14;342(6251):767-72
references: 2574828
references: PLoS One. 2012;7(3):e33453
references: 22479401