Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan.
Center for Information Biology, National Institute of Genetics, Mishima, Japan.
Sci Rep. 2020 Oct 15;10(1):17440. doi: 10.1038/s41598-020-74499-7.
Transfer RNA genes (tDNAs) are essential genes that encode tRNAs in all species. To understand new functions of tDNAs, other than that of encoding tRNAs, we used ENCODE data to examine binding characteristics of transcription factors (TFs) for all tDNA regions (489 loci) in the human genome. We divided the tDNAs into three groups based on the number of TFs that bound to them. At the two extremes were tDNAs to which many TFs bound (Group 1) and those to which no TFs bound (Group 3). Several TFs involved in chromatin remodeling such as ATF3, EP300 and TBL1XR1 bound to almost all Group 1 tDNAs. Furthermore, almost all Group 1 tDNAs included DNase I hypersensitivity sites and may thus interact with other chromatin regions through their bound TFs, and they showed highly conserved synteny across tetrapods. In contrast, Group 3 tDNAs did not possess these characteristics. These data suggest the presence of a previously uncharacterized function of these tDNAs. We also examined binding of CTCF to tDNAs and their involvement in topologically associating domains (TADs) and lamina-associated domains (LADs), which suggest a new perspective on the evolution and function of tDNAs.
转移 RNA 基因（tDNAs）是所有物种中编码 tRNA 的必需基因。为了了解 tDNAs 的新功能（除编码 tRNA 以外的功能），我们利用 ENCODE 数据研究了人类基因组中所有 tDNA 区域（489 个基因座）的转录因子（TFs）的结合特征。我们根据与 tDNA 结合的 TF 数量将 tDNA 分为三组。TFs 大量结合的 tDNA（第 1 组）和几乎没有 TF 结合的 tDNA（第 3 组）处于两个极端。一些参与染色质重塑的 TF，如 ATF3、EP300 和 TBL1XR1，几乎与所有第 1 组 tDNA 结合。此外，几乎所有第 1 组 tDNA 都包含 DNA 酶 I 超敏位点，因此可能通过结合的 TF 与其他染色质区域相互作用，并且它们在四足动物中具有高度保守的同线性。相比之下，第 3 组 tDNA 不具有这些特征。这些数据表明这些 tDNA 具有以前未被描述的功能。我们还检查了 CTCF 与 tDNA 的结合及其在拓扑关联域（TADs）和核纤层相关域（LADs）中的作用，这为 tDNA 的进化和功能提供了一个新的视角。
