Does CTCF mediate between nuclear organization and gene expression

• Published in: BioEssays Vol. 32; no. 1; pp. 37 - 50
• Main Authors: Ohlsson, Rolf, Lobanenkov, Victor, Klenova, Elena
• Format: Journal Article
• Language: English
• Published: Weinheim Wiley-VCH Verlag 01.01.2010; WILEY-VCH Verlag; WILEY‐VCH Verlag; Wiley Subscription Services, Inc
• Subjects: Animals; Base Sequence; Binding sites; Binding Sites - genetics; CCCTC-Binding Factor; Cell Cycle Proteins - metabolism; Cell Nucleus - genetics; Cell Nucleus - metabolism; chromatin; Chromatin - genetics; Chromatin - metabolism; Chromosomal Proteins, Non-Histone - metabolism; Cohesins; Deoxyribonucleic acid; DNA; DNA - genetics; DNA - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Epigenesis, Genetic; epigenetics; Fibers; Gene Expression; genes; higher order structure; Humans; Mice; Models, Biological; Models, Genetic; Nucleosomes - genetics; Nucleosomes - metabolism; Protein Interaction Domains and Motifs; Repressor Proteins - chemistry; Repressor Proteins - genetics; Repressor Proteins - metabolism
• ISSN: 0265-9247; 1521-1878; 1521-1878
• DOI: 10.1002/bies.200900118

The multifunctional zinc-finger protein CCCTC-binding factor (CTCF) is a very strong candidate for the role of coordinating the expression level of coding sequences with their three-dimensional position in the nucleus, apparently responding to a "code" in the DNA itself. Dynamic interactions between chromatin fibers in the context of nuclear architecture have been implicated in various aspects of genome functions. However, the molecular basis of these interactions still remains elusive and is a subject of intense debate. Here we discuss the nature of CTCF-DNA interactions, the CTCF-binding specificity to its binding sites and the relationship between CTCF and chromatin, and we examine data linking CTCF with gene regulation in the three-dimensional nuclear space. We discuss why these features render CTCF a very strong candidate for the role and propose a unifying model, the "CTCF code," explaining the mechanistic basis of how the information encrypted in DNA may be interpreted by CTCF into diverse nuclear functions.