RT Journal
A1 Mukhopadhyay, Rituparna
A1 Yu, WenQiang
A1 Whitehead, Joanne
A1 Xu, JunWang
A1 Lezcano, Magda
A1 Pack, Svetlana
A1 Kanduri, Chandrasekhar
A1 Kanduri, Meena
A1 Ginjala, Vasudeva
A1 Vostrov, Alexander
A1 Quitschke, Wolfgang
A1 Chernukhin, Igor
A1 Klenova, Elena
A1 Lobanenkov, Victor
A1 Ohlsson, Rolf
T1 The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide
JF Genome Research 
JO Genome Research 
YR 2004 
FD August 01 
VO 14 
IS 8 
SP 1594 
OP 1602 
DO 10.1101/gr.2408304 
UL http://genome.cshlp.org/content/14/8/1594.abstract 
AB 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.