The rhox homeobox gene cluster is imprinted and selectively targeted for regulation by histone h1 and DNA methylation.
Histone H1 is an abundant and essential component of chromatin whose precise role in regulating gene expression is poorly understood. Here, we report that a major target of H1-mediated regulation in embryonic stem (ES) cells is the X-linked Rhox homeobox gene cluster. To address the underlying mechanism, we examined the founding member of the Rhox gene cluster-Rhox5-and found that its distal promoter (Pd) loses H1, undergoes demethylation, and is transcriptionally activated in response to loss of H1 genes in ES cells. Demethylation of the Pd is required for its transcriptional induction and we identified a single cytosine in the Pd that, when methylated, is sufficient to inhibit Pd transcription. Methylation of this single cytosine prevents the Pd from binding GA-binding protein (GABP), a transcription factor essential for Pd transcription. Thus, H1 silences Rhox5 transcription by promoting methylation of one of its promoters, a mechanism likely to extend to other H1-regulated Rhox genes, based on analysis of ES cells lacking DNA methyltransferases. The Rhox cluster genes targeted for H1-mediated transcriptional repression are also subject to another DNA methylation-regulated process: Xp imprinting. Remarkably, we found that only H1-regulated Rhox genes are imprinted, not those immune to H1-mediated repression. Together, our results indicate that the Rhox gene cluster is a major target of H1-mediated transcriptional repression in ES cells and that H1 is a candidate to have a role in Xp imprinting.
Department of Reproductive Medicine, University of California-San Diego School of Medicine, La Jolla, CA 92093, USA.
James A
JA
Maclean
Anilkumar
A
Bettegowda
Byung Ju
BJ
Kim
Chih-Hong
CH
Lou
Seung-Min
SM
Yang
Anjana
A
Bhardwaj
Sreenath
S
Shanker
Zhiying
Z
Hu
Yuhong
Y
Fan
Sigrid
S
Eckardt
K John
KJ
McLaughlin
Arthur I
AI
Skoultchi
Miles F
MF
Wilkinson
D000818:Animals; D002478:Cells, Cultured; D003596:Cytosine / Q000378:metabolism; D019175:DNA Methylation; D015254:DNA Modification Methylases / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000378:metabolism*; D051268:GA-Binding Protein Transcription Factor / Q000378:metabolism; D017353:Gene Deletion; D005801:Genes, Homeobox; D018392:Genomic Imprinting; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D018398:Homeodomain Proteins / Q000235:genetics* / Q000378:metabolism; D051379:Mice; D005810:Multigene Family; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
D051268:GA-Binding Protein Transcription Factor; D006657:Histones; D018398:Homeodomain Proteins; C498048:Rhox5 protein, mouse; D014157:Transcription Factors; D003596:Cytosine; D015254:DNA Modification Methylases
Methods Enzymol. 2004;377:85-107
14979020
Dev Biol. 1998 Oct 15;202(2):196-214
9769172
Biol Reprod. 2008 Sep;79(3):468-74
18562707
J Biol Chem. 1996 Jul 19;271(29):17536-46
8663309
Mol Hum Reprod. 2002 Oct;8(10):923-9
12356942
Hum Mol Genet. 2005 Apr 15;14 Spec No 1:R59-64
15809274
Nat Genet. 2001 Jan;27(1):31-9
11137995
Cell. 2005 Feb 11;120(3):369-82
15707895
Gene. 2002 Nov 13;301(1-2):1-11
12490318
Mol Pharmacol. 2009 Nov;76(5):1072-81
19679824
Cell. 2005 Dec 29;123(7):1199-212
16377562
Mol Reprod Dev. 2000 Feb;55(2):146-51
10618653
Genes Dev. 1994 May 15;8(10):1147-59
7926720
Bioinformatics. 2002 Nov;18(11):1427-31
12424112
Oncogene. 2005 Apr 28;24(19):3091-9
15735669
Biol Reprod. 2005 Dec;73(6):1126-34
16093360
Cell. 1992 Jun 12;69(6):915-26
1606615
Mol Cell Biol. 2008 Apr;28(7):2138-53
18212046
Cell. 1996 Aug 9;86(3):475-83
8756729
Mol Cell Biol. 2003 Jul;23(13):4559-72
12808097
Dev Cell. 2004 Jan;6(1):117-31
14723852
Stem Cells. 2007 Jan;25(1):2-9
17023513
Mol Cell Biol. 2001 Dec;21(23):8197-202
11689708
BMC Genomics. 2006 Aug 17;7:212
16916441
Nat Rev Genet. 2005 May;6(5):410-8
15818384
Cell. 2005 Dec 29;123(7):1178-9
16377556
Crit Rev Eukaryot Gene Expr. 1997;7(3):215-30
9399071
Nat Cell Biol. 2009 Feb;11(2):172-82
19151705
Genes Dev. 2007 Feb 15;21(4):409-19
17322401
Genes Dev. 2006 Dec 15;20(24):3382-94
17182866
Biochem J. 2002 Aug 15;366(Pt 1):367-75
11980563
Cell. 1999 Oct 29;99(3):247-57
10555141
Hum Mol Genet. 2005 Apr 15;14 Spec No 1:R47-58
15809273
Genomics. 2006 Jul;88(1):34-43
16574372
Nat Rev Genet. 2001 Jan;2(1):33-8
11253066
Int J Biochem Cell Biol. 1997 Dec;29(12):1463-6
9570139
Dev Biol. 1994 Nov;166(1):170-9
7958444
Biol Reprod. 2004 Mar;70(3):828-36
14627546
Genesis. 2006 Mar;44(3):122-9
16496311
Curr Biol. 2006 Jan 24;16(2):166-72
16431368
Bioessays. 2009 Dec;31(12):1318-26
19921658
Mol Cell Biol. 2007 Jan;27(2):732-42
17101788
Mol Endocrinol. 2003 Feb;17(2):223-33
12554750
Science. 2004 Jun 11;304(5677):1675-8
15192231
Cell. 2000 Sep 29;103(1):17-27
11051544
Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):7257-61
8041776
Genomics. 1996 Jun 15;34(3):304-16
8786129
Cell Stem Cell. 2008 Feb 7;2(2):160-9
18371437
Nature. 1975 Aug 21;256(5519):640-2
1152998
J Biol Chem. 2002 Oct 11;277(41):38683-92
12087094
Dev Biol. 1990 Oct;141(2):451-5
2210045
Dev Biol. 2000 Jul 1;223(1):181-93
10864470
J Biol Chem. 2002 Jul 19;277(29):26036-45
11986330
Cell. 1976 Sep;9(1):57-70
975240
Mech Dev. 1991 Jun;34(2-3):155-64
1680379
Genes Dev. 2002 Jan 1;16(1):6-21
11782440
Mol Cell Biol. 1998 Sep;18(9):5492-9
9710633
Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5198-203
19273861
Mamm Genome. 2006 Feb;17(2):178-87
16465597
J Biol Chem. 2001 Apr 27;276(17):13587-92
11278859