Abstract
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.
Highlights
IntroductionTransfer 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
Transfer RNA genes are essential genes that encode tRNAs in all species
We previously showed that TF binding sites (TFBSs) cluster in pericentric regions in the human g enome[22,23,24], providing an interesting possibility for the role of TFBSs in the association of pericentric DNAs of homologous and nonhomologous chromosomes[24,25]
Summary
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. Various TF binding sites (TFBSs) located in non-transcriptional regions have been observed, suggesting the presence of a novel functional significance of TFs such as affecting the functional concentration of various factors, induction of chromatin looping, changing chromatin and nuclear structure and the evolution of new transcriptional regulatory n etworks[20,21]. We previously showed that TFBSs cluster in pericentric regions in the human g enome[22,23,24], providing an interesting possibility for the role of TFBSs in the association of pericentric DNAs of homologous and nonhomologous chromosomes[24,25]
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