Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan.
Evolutionary Morphology Laboratory, RIKEN, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan.
Sci Rep. 2017 Jul 10;7(1):4957. doi: 10.1038/s41598-017-04506-x.
The nuclear protein CCCTC-binding factor (CTCF) contributes as an insulator to chromatin organization in animal genomes. Currently, our knowledge of its binding property is confined mainly to mammals. In this study, we identified CTCF homologs in extant jawless fishes and performed ChIP-seq for the CTCF protein in the Arctic lamprey. Our phylogenetic analysis suggests that the lamprey lineage experienced gene duplication that gave rise to its unique paralog, designated CTCF2, which is independent from the previously recognized duplication between CTCF and CTCFL. The ChIP-seq analysis detected comparable numbers of CTCF binding sites between lamprey, chicken, and human, and revealed that the lamprey CTCF protein binds to the two-part motif, consisting of core and upstream motifs previously reported for mammals. These findings suggest that this mode of CTCF binding was established in the last common ancestor of extant vertebrates (more than 500 million years ago). We analyzed CTCF binding inside Hox clusters, which revealed a reinforcement of CTCF binding in the region spanning Hox1-4 genes that is unique to lamprey. Our study provides not only biological insights into the antiquity of CTCF-based epigenomic regulation known in mammals but also a technical basis for comparative epigenomic studies encompassing the whole taxon Vertebrata.
CCCTC 结合因子（CTCF）是一种核蛋白，它作为一种绝缘子，有助于动物基因组中的染色质组织。目前，我们对其结合特性的了解主要局限于哺乳动物。在这项研究中，我们在现存的无颌鱼类中鉴定出 CTCF 同源物，并在北极七鳃鳗中进行 CTCF 蛋白的 ChIP-seq 实验。我们的系统发育分析表明，七鳃鳗的谱系经历了基因复制，产生了其独特的旁系同源物，命名为 CTCF2，它与之前在 CTCF 和 CTCFL 之间识别的复制无关。ChIP-seq 分析在七鳃鳗、鸡和人类之间检测到可比数量的 CTCF 结合位点，并揭示了七鳃鳗 CTCF 蛋白结合到以前报道的哺乳动物的两部分基序，包括核心和上游基序。这些发现表明，这种 CTCF 结合模式是在现存脊椎动物（5 亿多年前）的最后共同祖先中建立的。我们分析了 Hox 簇内的 CTCF 结合，发现 CTCF 结合在跨越 Hox1-4 基因的区域得到了加强，这是七鳃鳗所特有的。我们的研究不仅为哺乳动物中已知的基于 CTCF 的表观基因组调控的古老性提供了生物学见解，而且为包括整个脊椎动物门的比较表观基因组研究提供了技术基础。
