title: High-resolution mapping of h1 linker histone variants in embryonic stem cells.
abstract: H1 linker histones facilitate higher-order chromatin folding and are essential for mammalian development. To achieve high-resolution mapping of H1 variants H1d and H1c in embryonic stem cells (ESCs), we have established a knock-in system and shown that the N-terminally tagged H1 proteins are functionally interchangeable to their endogenous counterparts in vivo. H1d and H1c are depleted from GC- and gene-rich regions and active promoters, inversely correlated with H3K4me3, but positively correlated with H3K9me3 and associated with characteristic sequence features. Surprisingly, both H1d and H1c are significantly enriched at major satellites, which display increased nucleosome spacing compared with bulk chromatin. While also depleted at active promoters and enriched at major satellites, overexpressed H1(0) displays differential binding patterns in specific repetitive sequences compared with H1d and H1c. Depletion of H1c, H1d, and H1e causes pericentric chromocenter clustering and de-repression of major satellites. These results integrate the localization of an understudied type of chromatin proteins, namely the H1 variants, into the epigenome map of mouse ESCs, and we identify significant changes at pericentric heterochromatin upon depletion of this epigenetic mark.
authors: School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA.
authors: Kaixiang
authors: K
authors: Cao
authors: Nathalie
authors: N
authors: Lailler
authors: Yunzhe
authors: Y
authors: Zhang
authors: Ashwath
authors: A
authors: Kumar
authors: Karan
authors: K
authors: Uppal
authors: Zheng
authors: Z
authors: Liu
authors: Eva K
authors: EK
authors: Lee
authors: Hongwei
authors: H
authors: Wu
authors: Magdalena
authors: M
authors: Medrzycki
authors: Chenyi
authors: C
authors: Pan
authors: Po-Yi
authors: PY
authors: Ho
authors: Guy P
authors: GP
authors: Cooper
authors: Xiao
authors: X
authors: Dong
authors: Christoph
authors: C
authors: Bock
authors: Eric E
authors: EE
authors: Bouhassira
authors: Yuhong
authors: Y
authors: Fan
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics*; D042002:Chromatin Assembly and Disassembly / Q000235:genetics; D002874:Chromosome Mapping; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D044127:Epigenesis, Genetic; D055879:Gene Knock-In Techniques; D006570:Heterochromatin / Q000235:genetics*; D011495:Histone-Lysine N-Methyltransferase; D006657:Histones / Q000235:genetics*; D051379:Mice
chemical_list: D002843:Chromatin; D006570:Heterochromatin; D006657:Histones; D011495:Histone-Lysine N-Methyltransferase
references: Mol Cell Biol. 1999 Apr;19(4):2803-16
references: 10082546
references: EMBO Rep. 2009 Sep;10(9):973-82
references: 19680288
references: Methods Enzymol. 2004;377:85-107
references: 14979020
references: Bioinformatics. 2009 Oct 1;25(19):2605-6
references: 19689956
references: J Struct Biol. 2010 Jan;169(1):124-33
references: 19766725
references: Dev Biol. 2007 Dec 1;312(1):419-26
references: 17964565
references: Dev Cell. 2010 Oct 19;19(4):625-38
references: 20951352
references: Mol Cell. 2001 Apr;7(4):729-39
references: 11336697
references: J Mol Biol. 1984 Jun 15;176(1):105-29
references: 6330367
references: BMC Bioinformatics. 2009 Dec 22;10:442
references: 20028554
references: J Biol Chem. 2005 Nov 11;280(45):38090-5
references: 16127177
references: Cell. 2005 Dec 29;123(7):1199-212
references: 16377562
references: PLoS One. 2009 Oct 01;4(10):e0007243
references: 19794910
references: Nat Biotechnol. 2010 Oct;28(10):1045-8
references: 20944595
references: Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21931-6
references: 21106759
references: Genome Biol. 2009;10(3):R25
references: 19261174
references: Nature. 2001 Mar 1;410(6824):116-20
references: 11242053
references: Nature. 2007 Jun 14;447(7146):799-816
references: 17571346
references: PLoS Genet. 2008 Oct;4(10):e1000227
references: 18927631
references: EMBO J. 2009 Dec 2;28(23):3635-45
references: 19834459
references: Nature. 2009 Nov 19;462(7271):358-62
references: 19924215
references: Cytogenet Genome Res. 2005;110(1-4):462-7
references: 16093699
references: Gene. 2009 Feb 15;431(1-2):1-12
references: 19059319
references: Cell. 1985 Aug;42(1):281-90
references: 4016952
references: Mol Cell Biol. 2003 Jul;23(13):4559-72
references: 12808097
references: Nucleic Acids Res. 1999 Aug 15;27(16):3355-63
references: 10454644
references: Nat Biotechnol. 2010 Oct;28(10):1106-14
references: 20852634
references: Bioessays. 2000 Feb;22(2):124-37
references: 10655032
references: Mamm Genome. 1995 Feb;6(2):76-83
references: 7767009
references: Nature. 2007 Aug 2;448(7153):553-60
references: 17603471
references: Dev Biol. 1993 May;157(1):281-3
references: 7683285
references: Mol Biol Cell. 2008 Aug;19(8):3554-63
references: 18508923
references: Cell. 2008 Nov 14;135(4):649-61
references: 18992931
references: J Cell Biol. 2004 Aug 16;166(4):493-505
references: 15302854
references: J Vis Exp. 2012 Mar 19;(61):
references: 22453355
references: J Mol Biol. 1998 Sep 25;282(3):683-97
references: 9737930
references: J Cell Biol. 2005 Jun 6;169(5):733-43
references: 15939760
references: Cell. 2006 Apr 21;125(2):315-26
references: 16630819
references: J Mol Biol. 1997 Aug 8;271(1):124-38
references: 9300059
references: Cell. 1984 Nov;39(1):223-32
references: 6091913
references: J Mol Biol. 1989 Dec 5;210(3):573-85
references: 2614834
references: Nature. 2001 Mar 1;410(6824):120-4
references: 11242054
references: Mol Cell Biol. 2001 Dec;21(23):7933-43
references: 11689686
references: Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8872-7
references: 18583476
references: J Biol Chem. 1983 Jan 10;258(1):262-8
references: 6848501
references: Cell. 2007 Jul 13;130(1):77-88
references: 17632057
references: Proc Natl Acad Sci U S A. 1995 Feb 28;92(5):1520-4
references: 7878012
references: J Cell Biol. 2007 May 7;177(3):401-11
references: 17485486
references: Trends Genet. 2000 Sep;16(9):418-20
references: 10973072
references: J Mol Biol. 1989 Dec 5;210(3):587-99
references: 2614835
references: PLoS Genet. 2012;8(5):e1002691
references: 22589736
references: Mol Cell Biol. 2000 Mar;20(6):2122-8
references: 10688658
references: Chromosoma. 1971;34(1):73-87
references: 4105528
references: Exp Cell Res. 2000 Feb 25;255(1):114-24
references: 10666340
references: EMBO J. 2005 Feb 23;24(4):800-12
references: 15678104
references: Cell. 2001 Nov 2;107(3):323-37
references: 11701123
references: BMC Cancer. 2008 Dec 24;8:388
references: 19108733
references: Proc Natl Acad Sci U S A. 1998 Nov 24;95(24):14173-8
references: 9826673
references: DNA Cell Biol. 1997 Sep;16(9):1041-9
references: 9324306
references: PLoS Genet. 2012;8(8):e1002879
references: 22956909
references: Proc Natl Acad Sci U S A. 2006 Jun 6;103(23):8709-14
references: 16731634
references: J Mol Biol. 2012 Jun 8;419(3-4):183-97
references: 22446683
references: Bioinformatics. 2009 Aug 1;25(15):1952-8
references: 19505939
references: J Immunol. 2005 Aug 15;175(4):2317-20
references: 16081801
references: Chromosome Res. 2006;14(1):17-25
references: 16506093
references: Nature. 2006 May 18;441(7091):349-53
references: 16625203
references: J Biol Chem. 2005 Jul 29;280(30):27809-14
references: 15911621
references: Nucleic Acids Res. 2010 Jul;38(12):3909-22
references: 20215437
references: Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6506-11
references: 16617109
references: Front Biosci (Landmark Ed). 2012 Jan 01;17:396-406
references: 22201751
references: Proc Natl Acad Sci U S A. 2001 Oct 9;98(21):11949-54
references: 11593003
references: Proc Natl Acad Sci U S A. 2003 May 13;100(10):5920-5
references: 12719535
references: Differentiation. 2008 Jan;76(1):15-23
references: 17825083
references: Science. 2008 Feb 8;319(5864):819-21
references: 18258916
references: PLoS One. 2012;7(6):e38829
references: 22701719
references: Bioinformatics. 2011 Jul 15;27(14):1889-93
references: 21596789
references: Genome Biol. 2009 Feb 10;10(2):R14
references: 19208250
references: Nat Biotechnol. 2010 Oct;28(10):1079-88
references: 20944600
references: Nucleic Acids Res. 1992 Jan 25;20(2):187-94
references: 1741245
references: PLoS One. 2008;3(12):e3932
references: 19079543
references: Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6434-8
references: 7604008
references: Genes Dev. 2009 Feb 15;23(4):452-65
references: 19196654
references: Bioinformatics. 2005 Nov 1;21(21):4067-8
references: 16141249
references: FASEB J. 1994 Dec;8(15):1260-8
references: 8001738