The role of the zinc finger protein CTCF in organizing the genome within the 
nucleus is now well established. Widely separated sites on DNA, occupied by both 
CTCF and the cohesin complex, make physical contacts that create large loop 
domains. Additional contacts between loci within those domains, often also 
mediated by CTCF, tend to be favored over contacts between loci in different 
domains. A large number of studies during the past 2 years have addressed the 
questions: How are these loops generated? What are the effects of disrupting 
them? Are there rules governing large-scale genome organization? It now appears 
that the strongest and evolutionarily most conserved of these CTCF interactions 
have specific rules for the orientation of the paired CTCF sites, implying the 
existence of a nonequilibrium mechanism of generation. Recent experiments that 
invert, delete, or inactivate one of a mating CTCF pair result in major changes 
in patterns of organization and gene expression in the surrounding regions. What 
remain to be determined are the detailed molecular mechanisms for 
re-establishing loop domains and maintaining them after replication and mitosis. 
As recently published data show, some mechanisms may involve interactions with 
noncoding RNAs as well as protein cofactors. Many CTCF sites are also involved 
in other functions such as modulation of RNA splicing and specific regulation of 
gene expression, and the relationship between these activities and loop 
formation is another unanswered question that should keep investigators occupied 
for some time.