CTCF Mediates the Cell-Type Specific Spatial Organization of the Kcnq5 Locus and the Local Gene Regulation

• Published in: PloS one Vol. 7; no. 2; p. e31416
• Main Authors: Ren, Licheng, Wang, Yang, Shi, Minglei, Wang, Xiaoning, Yang, Zhong, Zhao, Zhihu
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 08.02.2012; Public Library of Science (PLoS)
• Subjects: Analysis; Binding sites; Biology; CCCTC-Binding Factor; Cell Line, Tumor; Chromatin; Chromosomes; DNA binding proteins; DNA methylation; Fragments; Functional analysis; Gene expression; Gene Expression Regulation; Gene regulation; Genes; Genetic engineering; Genetic Loci; Genome, Human; Genomes; Genomics; Humans; KCNQ Potassium Channels - metabolism; KCNQ5 protein; Luciferase; Nuclei; Potassium channels (voltage-gated); Protein binding; Repressor Proteins - physiology; RNA-mediated interference; Zinc; Zinc finger proteins; Beijing China; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0031416

Chromatin loops play important roles in the dynamic spatial organization of genes in the nucleus. Growing evidence has revealed that the multivalent functional zinc finger protein CCCTC-binding factor (CTCF) is a master regulator of genome spatial organization, and mediates the ubiquitous chromatin loops within the genome. Using circular chromosome conformation capture (4C) methodology, we discovered that CTCF may be a master organizer in mediating the spatial organization of the kcnq5 gene locus. We characterized the cell-type specific spatial organization of the kcnq5 gene locus mediated by CTCF in detail using chromosome conformation capture (3C) and 3C-derived techniques. Cohesion also participated in mediating the organization of this locus. RNAi-mediated knockdown of CTCF sharply diminished the interaction frequencies between the chromatin loops of the kcnq5 gene locus and down-regulated local gene expression. Functional analysis showed that the interacting chromatin loops of the kcnq5 gene locus can repress the gene expression in a luciferase reporter assay. These interacting chromatin fragments were a series of repressing elements whose contacts were mediated by CTCF. Therefore, these findings suggested that the dynamical spatial organization of the kcnq5 locus regulates local gene expression.