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Implication of a new function of human tDNAs in chromatin organization

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 divi...

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Autores principales: Iwasaki, Yuki, Ikemura, Toshimichi, Kurokawa, Ken, Okada, Norihiro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7567086/
https://www.ncbi.nlm.nih.gov/pubmed/33060757
http://dx.doi.org/10.1038/s41598-020-74499-7
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author Iwasaki, Yuki
Ikemura, Toshimichi
Kurokawa, Ken
Okada, Norihiro
author_facet Iwasaki, Yuki
Ikemura, Toshimichi
Kurokawa, Ken
Okada, Norihiro
author_sort Iwasaki, Yuki
collection PubMed
description 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.
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spelling pubmed-75670862020-10-19 Implication of a new function of human tDNAs in chromatin organization Iwasaki, Yuki Ikemura, Toshimichi Kurokawa, Ken Okada, Norihiro Sci Rep Article 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. Nature Publishing Group UK 2020-10-15 /pmc/articles/PMC7567086/ /pubmed/33060757 http://dx.doi.org/10.1038/s41598-020-74499-7 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Iwasaki, Yuki
Ikemura, Toshimichi
Kurokawa, Ken
Okada, Norihiro
Implication of a new function of human tDNAs in chromatin organization
title Implication of a new function of human tDNAs in chromatin organization
title_full Implication of a new function of human tDNAs in chromatin organization
title_fullStr Implication of a new function of human tDNAs in chromatin organization
title_full_unstemmed Implication of a new function of human tDNAs in chromatin organization
title_short Implication of a new function of human tDNAs in chromatin organization
title_sort implication of a new function of human tdnas in chromatin organization
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7567086/
https://www.ncbi.nlm.nih.gov/pubmed/33060757
http://dx.doi.org/10.1038/s41598-020-74499-7
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