DNA binding factors are essential for regulating gene expression. CTCF and 
cohesin are DNA binding factors with central roles in chromatin organization and 
gene expression. We determined the sites of CTCF and cohesin binding to DNA in 
mouse brain, genome wide and in an allele-specific manner with high read-depth 
ChIP-seq. By comparing our results with existing data for mouse liver and 
embryonic stem (ES) cells, we investigated the tissue specificity of CTCF 
binding sites. ES cells have fewer unique CTCF binding sites occupied than liver 
and brain, consistent with a ground-state pattern of CTCF binding that is 
elaborated during differentiation. CTCF binding sites without the canonical 
consensus motif were highly tissue specific. In brain, a third of CTCF and 
cohesin binding sites coincide, consistent with the potential for many 
interactions between cohesin and CTCF but also many instances of independent 
action. In the context of genomic imprinting, CTCF and/or cohesin bind to a 
majority but not all differentially methylated regions, with preferential 
binding to the unmethylated parental allele. Whether the parental 
allele-specific methylation was established in the parental germlines or 
post-fertilization in the embryo is not a determinant in CTCF or cohesin 
binding. These findings link CTCF and cohesin with the control regions of a 
subset of imprinted genes, supporting the notion that imprinting control is 
mechanistically diverse.