Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.
Research Center for Genome and Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
Sci Rep. 2020 Sep 3;10(1):14629. doi: 10.1038/s41598-020-71602-w.
The nuclear protein CCCTC-binding factor (CTCF) contributes as an insulator to chromatin organization in diverse animals. The gene encoding this protein has a paralog which was first identified to be expressed exclusively in the testis in mammals and designated as CTCFL (also called BORIS). CTCFL orthologs were reported only among amniotes, and thus CTCFL was once thought to have arisen in the amniote lineage. In this study, we identified elasmobranch CTCFL orthologs, and investigated its origin with the aid of a shark genome assembly improved by proximity-guided scaffolding. Our analysis employing evolutionary interpretation of syntenic gene location suggested an earlier timing of the gene duplication between CTCF and CTCFL than previously thought, that is, around the common ancestor of extant vertebrates. Also, our transcriptomic sequencing revealed a biased expression of the catshark CTCFL in the testis, suggesting the origin of the tissue-specific localization in mammals more than 400 million years ago. To understand the historical process of the functional consolidation of the long-standing chromatin regulator CTCF, its additional paralogs remaining in some of the descendant lineages for spatially restricted transcript distribution should be taken into consideration.
核蛋白 CCCTC 结合因子（CTCF）作为绝缘子有助于不同动物的染色质组织。编码该蛋白的基因有一个旁系同源物，最初在哺乳动物中被鉴定为仅在睾丸中表达，并被命名为 CTCFL（也称为 BORIS）。CTCFL 的直系同源物仅在羊膜动物中报道，因此 CTCFL 曾经被认为是在羊膜动物谱系中产生的。在这项研究中，我们鉴定了软骨鱼的 CTCFL 直系同源物，并借助通过邻近引导支架改进的鲨鱼基因组组装来研究其起源。我们的分析通过对基因位置的协同进化解释表明，CTCF 和 CTCFL 之间的基因复制时间比以前认为的要早，即在现存脊椎动物的共同祖先附近。此外，我们的转录组测序揭示了猫鲨 CTCFL 在睾丸中的偏表达，表明组织特异性定位在 4 亿多年前就在哺乳动物中起源。为了了解长期存在的染色质调节因子 CTCF 的功能整合的历史过程，应该考虑到其在一些后代谱系中仍然存在的其他旁系同源物，这些旁系同源物具有空间限制的转录分布。
