title: 5-hydroxymethylcytosine represses the activity of enhancers in embryonic stem cells: a new epigenetic signature for gene regulation.
abstract: BACKGROUND
  Recent mapping of 5-hydroxymethylcytosine (5hmC) provides a genome-wide view of the distribution of this important chromatin mark. However, the role of 5hmC in specific regulatory regions is not clear, especially at enhancers.
  
  
  RESULTS
  We found a group of distal transcription factor binding sites highly enriched for 5-hdroxymethylcytosine (5hmC), but lacking any known activating histone marks and being depleted for nascent transcripts, suggesting a repressive role for 5hmC in mouse embryonic stem cells (mESCs). 5-formylcytosine (5fC), which is known to mark poised enhancers where H3K4me1 is enriched, is also observed at these sites. Furthermore, the 5hmC levels were inversely correlated with RNA polymerase II (PolII) occupancy in mESCs as well as in fully differentiated adipocytes. Interestingly, activating H3K4me1/2 histone marks were enriched at these sites when the associated genes become activated following lineage specification. These putative enhancers were shown to be functional in embryonic stem cells when unmethylated. Together, these data suggest that 5hmC suppresses the activity of this group of enhancers, which we termed "silenced enhancers".
  
  
  CONCLUSIONS
  Our findings indicate that 5hmC has a repressive role at specific proximal and distal regulatory regions in mESCs, and suggest that 5hmC is a new epigenetic mark for silenced enhancers.
authors.forename: Inchan
authors.initials: I
authors.lastname: Choi
authors.forename: Rinho
authors.initials: R
authors.lastname: Kim
authors.forename: Hee-Woong
authors.initials: HW
authors.lastname: Lim
authors.affiliation: Department of Genetics, Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, 3400 Civic Center Blvd, 19104 Philadelphia, PA, USA. kaestner@mail.med.upenn.edu.
authors.forename: Klaus H
authors.initials: KH
authors.lastname: Kaestner
authors.forename: Kyoung-Jae
authors.initials: KJ
authors.lastname: Won
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives; D000818:Animals; D001665:Binding Sites; D019070:Cell Lineage; D003596:Cytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D044127:Epigenesis, Genetic; D006657:Histones / Q000378:metabolism; D051379:Mice; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D006657:Histones; D012333:RNA, Messenger; D014157:Transcription Factors; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine
references.citation: Mol Syst Biol. 2011 Dec 20;7:562
references.pmid: 22186736
references.citation: Nature. 2008 Aug 7;454(7205):766-70
references.pmid: 18600261
references.citation: Proc Natl Acad Sci U S A. 1993 Sep 15;90(18):8424-8
references.pmid: 8378314
references.citation: Genes Dev. 2008 Nov 1;22(21):2953-67
references.pmid: 18981474
references.citation: Nat Biotechnol. 2010 May;28(5):503-10
references.pmid: 20436462
references.citation: Cell. 2008 Jun 13;133(6):1106-17
references.pmid: 18555785
references.citation: Nat Biotechnol. 2010 May;28(5):495-501
references.pmid: 20436461
references.citation: Cell Cycle. 2011 Aug 1;10(15):2428-36
references.pmid: 21750410
references.citation: Nature. 2009 Mar 12;458(7235):223-7
references.pmid: 19182780
references.citation: Genome Biol. 2011 Jun 20;12(6):R54
references.pmid: 21689397
references.citation: Nature. 2011 May 19;473(7347):398-402
references.pmid: 21460836
references.citation: Nucleic Acids Res. 2013 Apr;41(7):e84
references.pmid: 23408859
references.citation: J Biol Chem. 2011 Oct 14;286(41):35334-35338
references.pmid: 21862836
references.citation: Biochem Biophys Res Commun. 2011 Jul 22;411(1):40-3
references.pmid: 21703242
references.citation: Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1361-6
references.pmid: 24474761
references.citation: Cell. 2012 Dec 21;151(7):1417-30
references.pmid: 23260135
references.citation: Nat Biotechnol. 2010 Oct;28(10):1045-8
references.pmid: 20944595
references.citation: Mol Cell. 2011 May 20;42(4):451-64
references.pmid: 21514197
references.citation: Science. 2009 May 15;324(5929):929-30
references.pmid: 19372393
references.citation: Curr Genomics. 2009 Aug;10(5):294-302
references.pmid: 20119526
references.citation: Nature. 2011 May 19;473(7347):394-7
references.pmid: 21552279
references.citation: Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21931-6
references.pmid: 21106759
references.citation: Genes Dev. 2011 Apr 1;25(7):679-84
references.pmid: 21460036
references.citation: Cell. 2010 Apr 30;141(3):432-45
references.pmid: 20434984
references.citation: PLoS Genet. 2011 Jun;7(6):e1002154
references.pmid: 21731508
references.citation: Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2876-81
references.pmid: 23382218
references.citation: Science. 2011 Sep 2;333(6047):1303-7
references.pmid: 21817016
references.citation: Cell. 2005 Sep 23;122(6):947-56
references.pmid: 16153702
references.citation: Cell. 2012 Jun 8;149(6):1368-80
references.pmid: 22608086
references.citation: Nature. 2007 Aug 2;448(7153):553-60
references.pmid: 17603471
references.citation: Science. 2008 Dec 19;322(5909):1845-8
references.pmid: 19056941
references.citation: Nucleic Acids Res. 2012 Sep 1;40(17):8255-65
references.pmid: 22730288
references.citation: Cell. 2013 Apr 25;153(3):678-91
references.pmid: 23602153
references.citation: Nature. 2009 Nov 19;462(7271):315-22
references.pmid: 19829295
references.citation: Science. 2009 May 15;324(5929):930-5
references.pmid: 19372391
references.citation: Cell Rep. 2013 Feb 21;3(2):291-300
references.pmid: 23403289
references.citation: Nature. 2011 Feb 10;470(7333):279-83
references.pmid: 21160473
references.citation: Nat Biotechnol. 2011 Jan;29(1):68-72
references.pmid: 21151123
references.citation: Hum Mol Genet. 2014 Feb 1;23(3):657-67
references.pmid: 24087792
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: Nat Genet. 2007 Mar;39(3):311-8
references.pmid: 17277777
references.citation: Methods Enzymol. 2006;411:134-93
references.pmid: 16939790
references.citation: Nature. 2013 Dec 12;504(7479):306-310
references.pmid: 24213634
references.citation: Nature. 2011 May 15;474(7351):390-4
references.pmid: 21572438
references.citation: Genome Res. 2013 Feb;23(2):352-64
references.pmid: 23033340
references.citation: Genes Dev. 2011 Apr 1;25(7):742-54
references.pmid: 21460038
references.citation: Science. 2011 Sep 2;333(6047):1300-3
references.pmid: 21778364
references.citation: Nature. 2011 May 19;473(7347):343-8
references.pmid: 21490601
references.citation: Mech Dev. 2001 Feb;100(2):335-8
references.pmid: 11165493