The binding sites for the chromatin insulator protein CTCF map to DNA methylation-free domains genome-wide.
All known vertebrate chromatin insulators interact with the highly conserved, multivalent 11-zinc finger nuclear factor CTCF to demarcate expression domains by blocking enhancer or silencer signals in a position-dependent manner. Recent observations document that the properties of CTCF include reading and propagating the epigenetic state of the differentially methylated H19 imprinting control region. To assess whether these findings may reflect a universal role for CTCF targets, we identified more than 200 new CTCF target sites by generating DNA microarrays of clones derived from chromatin-immunopurified (ChIP) DNA followed by ChIP-on-chip hybridization analysis. Target sites include not only known loci involved in multiple cellular functions, such as metabolism, neurogenesis, growth, apoptosis, and signalling, but potentially also heterochromatic sequences. Using a novel insulator trapping assay, we also show that the majority of these targets manifest insulator functions with a continuous distribution of stringency. As these targets are generally DNA methylation-free as determined by antibodies against 5-methylcytidine and a methyl-binding protein (MBD2), a CTCF-based network correlates with genome-wide epigenetic states.
Mukhopadhyay
Rituparna
R
Department of Development & Genetics, Evolution Biology Centre, Uppsala University, Norbyvägen 18A, S-752 36 Uppsala, Sweden.
Yu
WenQiang
W
Whitehead
Joanne
J
Xu
JunWang
J
Lezcano
Magda
M
Pack
Svetlana
S
Kanduri
Chandrasekhar
C
Kanduri
Meena
M
Ginjala
Vasudeva
V
Vostrov
Alexander
A
Quitschke
Wolfgang
W
Chernukhin
Igor
I
Klenova
Elena
E
Lobanenkov
Victor
V
Ohlsson
Rolf
R
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D002874:Chromosome Mapping; D018899:CpG Islands; D019175:DNA Methylation; D015342:DNA Probes / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics*; D044127:Epigenesis, Genetic; D006824:Hybridization, Genetic; D008099:Liver / Q000166:cytology; D051379:Mice; D008969:Molecular Sequence Data; D012097:Repressor Proteins / Q000235:genetics*
D000076246:CCCTC-Binding Factor; C000619698:Ctcf protein, mouse; D015342:DNA Probes; D004268:DNA-Binding Proteins; D012097:Repressor Proteins