title: Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes.
abstract: BACKGROUND
  The genomic binding of CTCF is highly conserved across mammals, but the mechanisms that underlie its stability are poorly understood. One transcription factor known to functionally interact with CTCF in the context of X-chromosome inactivation is the ubiquitously expressed YY1. Because combinatorial transcription factor binding can contribute to the evolutionary stabilization of regulatory regions, we tested whether YY1 and CTCF co-binding could in part account for conservation of CTCF binding.
  
  
  RESULTS
  Combined analysis of CTCF and YY1 binding in lymphoblastoid cell lines from seven primates, as well as in mouse and human livers, reveals extensive genome-wide co-localization specifically at evolutionarily stable CTCF-bound regions. CTCF-YY1 co-bound regions resemble regions bound by YY1 alone, as they enrich for active histone marks, RNA polymerase II and transcription factor binding. Although these highly conserved, transcriptionally active CTCF-YY1 co-bound regions are often promoter-proximal, gene-distal regions show similar molecular features.
  
  
  CONCLUSIONS
  Our results reveal that these two ubiquitously expressed, multi-functional zinc-finger proteins collaborate in functionally active regions to stabilize one another's genome-wide binding across primate evolution.
authors.forename: Petra C
authors.initials: PC
authors.lastname: Schwalie
authors.forename: Michelle C
authors.initials: MC
authors.lastname: Ward
authors.forename: Carolyn E
authors.initials: CE
authors.lastname: Cain
authors.forename: Andre J
authors.initials: AJ
authors.lastname: Faure
authors.forename: Yoav
authors.initials: Y
authors.lastname: Gilad
authors.forename: Duncan T
authors.initials: DT
authors.lastname: Odom
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
mesh_terms: D000818:Animals; D000076246:CCCTC-Binding Factor; D002460:Cell Line; D019143:Evolution, Molecular; D016678:Genome; D006801:Humans; D051379:Mice; D011323:Primates / Q000235:genetics*; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism*; D050986:YY1 Transcription Factor / Q000378:metabolism*
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; C000619698:Ctcf protein, mouse; D012097:Repressor Proteins; D050986:YY1 Transcription Factor