Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome

Abstract 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 C...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Zefang Sun, Jia Tan, Minqiong Zhao, Qiyao Peng, Mingqing Zhou, Shanru Zuo, Feilong Wu, Xueguang Li, Yangyang Dong, Ming Xie, Yide Yang, Junhua Zhou, Xianghua Liu, Quanze He, Zuping He, Xing Yu, Quanyuan He
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8ff731984d084a34b79a1143651f40e5
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:8ff731984d084a34b79a1143651f40e5
record_format	dspace
spelling	oai:doaj.org-article:8ff731984d084a34b79a1143651f40e52021-12-02T11:37:25ZIntegrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome10.1038/s41598-021-83469-62045-2322https://doaj.org/article/8ff731984d084a34b79a1143651f40e52021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83469-6https://doaj.org/toc/2045-2322Abstract 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.Zefang SunJia TanMinqiong ZhaoQiyao PengMingqing ZhouShanru ZuoFeilong WuXueguang LiYangyang DongMing XieYide YangJunhua ZhouXianghua LiuQuanze HeZuping HeXing YuQuanyuan HeNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Zefang Sun Jia Tan Minqiong Zhao Qiyao Peng Mingqing Zhou Shanru Zuo Feilong Wu Xueguang Li Yangyang Dong Ming Xie Yide Yang Junhua Zhou Xianghua Liu Quanze He Zuping He Xing Yu Quanyuan He Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome
description	Abstract 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	article
author	Zefang Sun Jia Tan Minqiong Zhao Qiyao Peng Mingqing Zhou Shanru Zuo Feilong Wu Xueguang Li Yangyang Dong Ming Xie Yide Yang Junhua Zhou Xianghua Liu Quanze He Zuping He Xing Yu Quanyuan He
author_facet	Zefang Sun Jia Tan Minqiong Zhao Qiyao Peng Mingqing Zhou Shanru Zuo Feilong Wu Xueguang Li Yangyang Dong Ming Xie Yide Yang Junhua Zhou Xianghua Liu Quanze He Zuping He Xing Yu Quanyuan He
author_sort	Zefang Sun
title	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_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_sort	integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the trna transcriptome
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/8ff731984d084a34b79a1143651f40e5
work_keys_str_mv	AT zefangsun integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT jiatan integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT minqiongzhao integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT qiyaopeng integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT mingqingzhou integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT shanruzuo integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT feilongwu integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT xueguangli integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT yangyangdong integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT mingxie integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT yideyang integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT junhuazhou integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT xianghualiu integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT quanzehe integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT zupinghe integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT xingyu integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome AT quanyuanhe integratedgenomicanalysisrevealsregulatorypathwaysanddynamiclandscapesofthetrnatranscriptome
_version_	1718395773670916096

Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome

Ejemplares similares