CTCF regulates allelic expression of Igf2 by orchestrating a promoter-polycomb repressive complex 2 intrachromosomal loop.
CTCF is a zinc finger DNA-binding protein that regulates the epigenetic states of numerous target genes. Using allelic regulation of mouse insulin-like growth factor II (Igf2) as a model, we demonstrate that CTCF binds to the unmethylated maternal allele of the imprinting control region (ICR) in the Igf2/H19 imprinting domain and forms a long-range intrachromosomal loop to interact with the three clustered Igf2 promoters. Polycomb repressive complex 2 is recruited through the interaction of CTCF with Suz12, leading to allele-specific methylation at lysine 27 of histone H3 (H3-K27) and to suppression of the maternal Igf2 promoters. Targeted mutation or deletion of the maternal ICR abolishes this chromatin loop, decreases allelic H3-K27 methylation, and causes loss of Igf2 imprinting. RNA interference knockdown of Suz12 also leads to reactivation of the maternal Igf2 allele and biallelic Igf2 expression. CTCF and Suz12 are coprecipitated from nuclear extracts with antibodies specific for either protein, and they interact with each other in a two-hybrid system. These findings offer insight into general epigenetic mechanisms by which CTCF governs gene expression by orchestrating chromatin loop structures and by serving as a DNA-binding protein scaffold to recruit and bind polycomb repressive complexes.
Li
Tao
T
Medical Service, VA Palo Alto Health Care System, Palo Alto, California 94304, USA.
Hu
Ji-Fan
JF
Qiu
Xinwen
X
Ling
Jianqun
J
Chen
Huiling
H
Wang
Shukui
S
Hou
Aiju
A
Vu
Thanh H
TH
Hoffman
Andrew R
AR
D000483:Alleles; D000818:Animals; D000076246:CCCTC-Binding Factor; D002460:Cell Line; D033481:Chromosomes, Mammalian / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D005260:Female; D017353:Gene Deletion; D018392:Genomic Imprinting; D006657:Histones / Q000378:metabolism; D007335:Insulin-Like Growth Factor II / Q000235:genetics*; D008745:Methylation; D051379:Mice; D008810:Mice, Inbred C57BL; D009690:Nucleic Acid Conformation; D063151:Polycomb Repressive Complex 2; D063146:Polycomb-Group Proteins; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011485:Protein Binding; D034622:RNA Interference; D012097:Repressor Proteins / Q000378:metabolism*; D013489:Suppression, Genetic
D000076246:CCCTC-Binding Factor; C000619698:Ctcf protein, mouse; D004268:DNA-Binding Proteins; D006657:Histones; D063146:Polycomb-Group Proteins; D012097:Repressor Proteins; C494163:Suz12 protein, mouse; D007335:Insulin-Like Growth Factor II; D063151:Polycomb Repressive Complex 2