Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide.
A prime goal in systems biology is the comprehensive use of existing high-throughput genomic datasets to gain a better understanding of chromatin organization and genome function. In this report, we use chromatin immunoprecipitation (ChIP) data that map protein-binding sites on the genome, and Hi-C data that map interactions between DNA fragments in the genome in an integrative approach. We first reanalyzed the contact map of the human genome as determined with Hi-C and found that long-range interactions are highly nonrandom; the same DNA fragments are often found interacting together. We then show using ChIP data that these interactions can be explained by the action of the CCCTC-binding factor (CTCF). These CTCF-mediated interactions are found both within chromosomes and in between different chromosomes. This makes CTCF a major organizer of both the structure of the chromosomal fiber within each individual chromosome and of the chromosome territories within the cell nucleus.
Computer Laboratory, Cambridge University, Cambridge, UK.
Marco
M
Botta
Syed
S
Haider
Ian X Y
IX
Leung
Pietro
P
Lio
Julien
J
Mozziconacci
D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D002460:Cell Line; D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism; D002843:Chromatin / Q000737:chemistry; D047369:Chromatin Immunoprecipitation; D002877:Chromosomes, Human / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D053263:Gene Regulatory Networks; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006801:Humans; D011485:Protein Binding; D012097:Repressor Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D049490:Systems Biology / Q000379:methods*
D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D002843:Chromatin; D012097:Repressor Proteins; D004247:DNA