State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
PLoS One. 2012;7(2):e31416. doi: 10.1371/journal.pone.0031416. Epub 2012 Feb 8.
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.
染色质环在细胞核中基因的动态空间组织中发挥重要作用。越来越多的证据表明，多价功能锌指蛋白 CCCTC 结合因子（CTCF）是基因组空间组织的主要调节剂，并介导基因组内普遍存在的染色质环。使用环形染色体构象捕获（4C）方法，我们发现 CTCF 可能是介导 kcnq5 基因座空间组织的主要组织者。我们使用染色体构象捕获（3C）和 3C 衍生技术详细描述了 CTCF 介导的 kcnq5 基因座的细胞类型特异性空间组织。凝聚也参与调节这个基因座的组织。CTCF 的 RNAi 介导的敲低显着降低了 kcnq5 基因座染色质环之间的相互作用频率，并下调了局部基因表达。功能分析表明，kcnq5 基因座的相互作用染色质环可以在荧光素酶报告基因测定中抑制基因表达。这些相互作用的染色质片段是一系列抑制元件，其接触由 CTCF 介导。因此，这些发现表明 kcnq5 基因座的动态空间组织调节局部基因表达。
