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Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome
tRNAs and tRNA-derived RNA fragments (tRFs) play various roles in many cellular processes outside of protein synthesis. However, comprehensive investigations of tRNA/tRF regulation are rare. In this study, we used new algorithms to extensively analyze the publicly available data from 1332 ChIP-Seq a...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7933247/ https://www.ncbi.nlm.nih.gov/pubmed/33664286 http://dx.doi.org/10.1038/s41598-021-83469-6 |
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author | Sun, Zefang Tan, Jia Zhao, Minqiong Peng, Qiyao Zhou, Mingqing Zuo, Shanru Wu, Feilong Li, Xueguang Dong, Yangyang Xie, Ming Yang, Yide Zhou, Junhua Liu, Xianghua He, Quanze He, Zuping Yu, Xing He, Quanyuan |
author_facet | Sun, Zefang Tan, Jia Zhao, Minqiong Peng, Qiyao Zhou, Mingqing Zuo, Shanru Wu, Feilong Li, Xueguang Dong, Yangyang Xie, Ming Yang, Yide Zhou, Junhua Liu, Xianghua He, Quanze He, Zuping Yu, Xing He, Quanyuan |
author_sort | Sun, Zefang |
collection | PubMed |
description | tRNAs and tRNA-derived RNA fragments (tRFs) play various roles in many cellular processes outside of protein synthesis. However, comprehensive investigations of tRNA/tRF regulation are rare. In this study, we used new algorithms to extensively analyze the publicly available data from 1332 ChIP-Seq and 42 small-RNA-Seq experiments in human cell lines and tissues to investigate the transcriptional and posttranscriptional regulatory mechanisms of tRNAs. We found that histone acetylation, cAMP, and pluripotency pathways play important roles in the regulation of the tRNA gene transcription in a cell-specific manner. Analysis of RNA-Seq data identified 950 high-confidence tRFs, and the results suggested that tRNA pools are dramatically distinct across the samples in terms of expression profiles and tRF composition. The mismatch analysis identified new potential modification sites and specific modification patterns in tRNA families. The results also show that RNA library preparation technologies have a considerable impact on tRNA profiling and need to be optimized in the future. |
format | Online Article Text |
id | pubmed-7933247 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-79332472021-03-05 Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome Sun, Zefang Tan, Jia Zhao, Minqiong Peng, Qiyao Zhou, Mingqing Zuo, Shanru Wu, Feilong Li, Xueguang Dong, Yangyang Xie, Ming Yang, Yide Zhou, Junhua Liu, Xianghua He, Quanze He, Zuping Yu, Xing He, Quanyuan Sci Rep Article tRNAs and tRNA-derived RNA fragments (tRFs) play various roles in many cellular processes outside of protein synthesis. However, comprehensive investigations of tRNA/tRF regulation are rare. In this study, we used new algorithms to extensively analyze the publicly available data from 1332 ChIP-Seq and 42 small-RNA-Seq experiments in human cell lines and tissues to investigate the transcriptional and posttranscriptional regulatory mechanisms of tRNAs. We found that histone acetylation, cAMP, and pluripotency pathways play important roles in the regulation of the tRNA gene transcription in a cell-specific manner. Analysis of RNA-Seq data identified 950 high-confidence tRFs, and the results suggested that tRNA pools are dramatically distinct across the samples in terms of expression profiles and tRF composition. The mismatch analysis identified new potential modification sites and specific modification patterns in tRNA families. The results also show that RNA library preparation technologies have a considerable impact on tRNA profiling and need to be optimized in the future. Nature Publishing Group UK 2021-03-04 /pmc/articles/PMC7933247/ /pubmed/33664286 http://dx.doi.org/10.1038/s41598-021-83469-6 Text en © The Author(s) 2021 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 Sun, Zefang Tan, Jia Zhao, Minqiong Peng, Qiyao Zhou, Mingqing Zuo, Shanru Wu, Feilong Li, Xueguang Dong, Yangyang Xie, Ming Yang, Yide Zhou, Junhua Liu, Xianghua He, Quanze He, Zuping Yu, Xing He, Quanyuan Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome |
title | Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome |
title_full | Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome |
title_fullStr | Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome |
title_full_unstemmed | Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome |
title_short | Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome |
title_sort | integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the trna transcriptome |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7933247/ https://www.ncbi.nlm.nih.gov/pubmed/33664286 http://dx.doi.org/10.1038/s41598-021-83469-6 |
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