CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2.
It is thought that the H19 imprinting control region (ICR) directs the silencing of the maternally inherited Igf2 allele through a CTCF-dependent chromatin insulator. The ICR has been shown to interact physically with a silencer region in Igf2, differentially methylated region (DMR)1, but the role of CTCF in this chromatin loop and whether it restricts the physical access of distal enhancers to Igf2 is not known. We performed systematic chromosome conformation capture analyses in the Igf2/H19 region over >160 kb, identifying sequences that interact physically with the distal enhancers and the ICR. We found that, on the paternal chromosome, enhancers interact with the Igf2 promoters but that, on the maternal allele, this is prevented by CTCF binding within the H19 ICR. CTCF binding in the maternal ICR regulates its interaction with matrix attachment region (MAR)3 and DMR1 at Igf2, thus forming a tight loop around the maternal Igf2 locus, which may contribute to its silencing. Mutation of CTCF binding sites in the H19 ICR leads to loss of CTCF binding and de novo methylation of a CTCF target site within Igf2 DMR1, showing that CTCF can coordinate regional epigenetic marks. This systematic chromosome conformation capture analysis of an imprinting cluster reveals that CTCF has a critical role in the epigenetic regulation of higher-order chromatin structure and gene silencing over considerable distances in the genome.
Kurukuti
Sreenivasulu
S
Department of Development and Genetics, Uppsala University, Norbyvägen 18A, S-752 36 Uppsala, Sweden.
Tiwari
Vijay Kumar
VK
Tavoosidana
Gholamreza
G
Pugacheva
Elena
E
Murrell
Adele
A
Zhao
Zhihu
Z
Lobanenkov
Victor
V
Reik
Wolf
W
Ohlsson
Rolf
R
D000818:Animals; D000076246:CCCTC-Binding Factor; D004268:DNA-Binding Proteins / Q000378:metabolism* / Q000502:physiology; D004742:Enhancer Elements, Genetic; D044127:Epigenesis, Genetic / Q000502:physiology; D005260:Female; D020868:Gene Silencing; D018392:Genomic Imprinting / Q000502:physiology*; D006570:Heterochromatin / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D007335:Insulin-Like Growth Factor II / Q000235:genetics* / Q000378:metabolism; D008297:Male; D051379:Mice; D011485:Protein Binding / Q000235:genetics; D011487:Protein Conformation; D011506:Proteins / Q000235:genetics*; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated / Q000378:metabolism* / Q000502:physiology; D012097:Repressor Proteins / Q000378:metabolism* / Q000502:physiology
D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; C000619698:Ctcf protein, mouse; D004268:DNA-Binding Proteins; C094335:H19 long non-coding RNA; D006570:Heterochromatin; C035170:IGF2 protein, human; D011506:Proteins; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated; D012097:Repressor Proteins; D007335:Insulin-Like Growth Factor II