Transfer RNA-derived fragments in aging Caenorhabditis elegans originate from abundant homologous gene copies

Abstract Small RNAs that originate from transfer RNA (tRNA) species, tRNA-derived fragments (tRFs), play diverse biological functions but little is known for their association with aging. Moreover, biochemical aspects of tRNAs limit discovery of functional tRFs by high throughput sequencing. In part...

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Autores principales:	GiWon Shin, Hee Jung Koo, Mihwa Seo, Seung-Jae V. Lee, Hong Gil Nam, Gyoo Yeol Jung
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/671708ab310442aba73295f37f88d034
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spelling	oai:doaj.org-article:671708ab310442aba73295f37f88d0342021-12-02T17:47:18ZTransfer RNA-derived fragments in aging Caenorhabditis elegans originate from abundant homologous gene copies10.1038/s41598-021-91724-z2045-2322https://doaj.org/article/671708ab310442aba73295f37f88d0342021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-91724-zhttps://doaj.org/toc/2045-2322Abstract Small RNAs that originate from transfer RNA (tRNA) species, tRNA-derived fragments (tRFs), play diverse biological functions but little is known for their association with aging. Moreover, biochemical aspects of tRNAs limit discovery of functional tRFs by high throughput sequencing. In particular, genes encoding tRNAs exist as multiple copies throughout genome, and mature tRNAs have various modified bases, contributing to ambiguities for RNA sequencing-based analysis of tRFs. Here, we report age-dependent changes of tRFs in Caenorhabditis elegans. We first analyzed published RNA sequencing data by using a new strategy for tRNA-associated sequencing reads. Our current method used unique mature tRNAs as a reference for the sequence alignment, and properly filtered out false positive enrichment for tRFs. Our analysis successfully distinguished de novo mutation sites from differences among homologous copies, and identified potential RNA modification sites. Overall, the majority of tRFs were upregulated during aging and originated from 5′-ends, which we validated by using Northern blot analysis. Importantly, we revealed that the major source of tRFs upregulated during aging was the tRNAs with abundant gene copy numbers. Our analysis suggests that tRFs are useful biomarkers of aging particularly when they originate from abundant homologous gene copies.GiWon ShinHee Jung KooMihwa SeoSeung-Jae V. LeeHong Gil NamGyoo Yeol JungNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q GiWon Shin Hee Jung Koo Mihwa Seo Seung-Jae V. Lee Hong Gil Nam Gyoo Yeol Jung Transfer RNA-derived fragments in aging Caenorhabditis elegans originate from abundant homologous gene copies
description	Abstract Small RNAs that originate from transfer RNA (tRNA) species, tRNA-derived fragments (tRFs), play diverse biological functions but little is known for their association with aging. Moreover, biochemical aspects of tRNAs limit discovery of functional tRFs by high throughput sequencing. In particular, genes encoding tRNAs exist as multiple copies throughout genome, and mature tRNAs have various modified bases, contributing to ambiguities for RNA sequencing-based analysis of tRFs. Here, we report age-dependent changes of tRFs in Caenorhabditis elegans. We first analyzed published RNA sequencing data by using a new strategy for tRNA-associated sequencing reads. Our current method used unique mature tRNAs as a reference for the sequence alignment, and properly filtered out false positive enrichment for tRFs. Our analysis successfully distinguished de novo mutation sites from differences among homologous copies, and identified potential RNA modification sites. Overall, the majority of tRFs were upregulated during aging and originated from 5′-ends, which we validated by using Northern blot analysis. Importantly, we revealed that the major source of tRFs upregulated during aging was the tRNAs with abundant gene copy numbers. Our analysis suggests that tRFs are useful biomarkers of aging particularly when they originate from abundant homologous gene copies.
format	article
author	GiWon Shin Hee Jung Koo Mihwa Seo Seung-Jae V. Lee Hong Gil Nam Gyoo Yeol Jung
author_facet	GiWon Shin Hee Jung Koo Mihwa Seo Seung-Jae V. Lee Hong Gil Nam Gyoo Yeol Jung
author_sort	GiWon Shin
title	Transfer RNA-derived fragments in aging Caenorhabditis elegans originate from abundant homologous gene copies
title_short	Transfer RNA-derived fragments in aging Caenorhabditis elegans originate from abundant homologous gene copies
title_full	Transfer RNA-derived fragments in aging Caenorhabditis elegans originate from abundant homologous gene copies
title_fullStr	Transfer RNA-derived fragments in aging Caenorhabditis elegans originate from abundant homologous gene copies
title_full_unstemmed	Transfer RNA-derived fragments in aging Caenorhabditis elegans originate from abundant homologous gene copies
title_sort	transfer rna-derived fragments in aging caenorhabditis elegans originate from abundant homologous gene copies
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/671708ab310442aba73295f37f88d034
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Transfer RNA-derived fragments in aging Caenorhabditis elegans originate from abundant homologous gene copies

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