Rasgrf1 imprinting is regulated by a CTCF-dependent methylation-sensitive enhancer blocker.
Imprinted methylation of the paternal Rasgrf1 allele in mice occurs at a differentially methylated domain (DMD) 30 kbp 5' of the promoter. A repeated sequence 3' of the DMD regulates imprinted methylation, which is required for imprinted expression. Here we identify the mechanism by which methylation controls imprinting. The DMD is an enhancer blocker that binds CTCF in a methylation-sensitive manner. CTCF bound to the unmethylated maternal allele silences expression. CTCF binding to the paternal allele is prevented by repeat-mediated methylation, allowing expression. Optimal in vitro enhancer-blocking activity requires CTCF binding sites. The enhancer blocker can be bypassed in vivo and imprinting abolished by placing an extra enhancer proximal to the promoter. Together, the repeats and the DMD constitute a binary switch that regulates Rasgrf1 imprinting.
Yoon
Bongjune
B
Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York 14263, USA.
Herman
Herry
H
Hu
Benjamin
B
Park
Yoon Jung
YJ
Lindroth
Anders
A
Bell
Adam
A
West
Adam G
AG
Chang
Yanjie
Y
Stablewski
Aimee
A
Piel
Jessica C
JC
Loukinov
Dmitri I
DI
Lobanenkov
Victor V
VV
Soloway
Paul D
PD
D000818:Animals; D000076246:CCCTC-Binding Factor; D002352:Carrier Proteins / Q000235:genetics*; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D020690:GTPase-Activating Proteins; D018392:Genomic Imprinting; D051379:Mice; D008957:Models, Genetic; D012097:Repressor Proteins / Q000378:metabolism*
C513041:Arhgap35 protein, mouse; D000076246:CCCTC-Binding Factor; D002352:Carrier Proteins; C000619698:Ctcf protein, mouse; D004268:DNA-Binding Proteins; D020690:GTPase-Activating Proteins; D012097:Repressor Proteins