Cargando…

Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts

RNA decay is an important regulatory mechanism for gene expression at the posttranscriptional level. Although the main pathways and major enzymes that facilitate this process are well defined, global analysis of RNA turnover remains under-investigated. Recent advances in the application of next-gene...

Descripción completa

Detalles Bibliográficos
Autores principales: Won, Jung-Im, Shin, JaeMoon, Park, So Young, Yoon, JeeHee, Jeong, Dong-Hoon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7555781/
https://www.ncbi.nlm.nih.gov/pubmed/32899599
http://dx.doi.org/10.3390/ijms21186452
_version_ 1783594087493926912
author Won, Jung-Im
Shin, JaeMoon
Park, So Young
Yoon, JeeHee
Jeong, Dong-Hoon
author_facet Won, Jung-Im
Shin, JaeMoon
Park, So Young
Yoon, JeeHee
Jeong, Dong-Hoon
author_sort Won, Jung-Im
collection PubMed
description RNA decay is an important regulatory mechanism for gene expression at the posttranscriptional level. Although the main pathways and major enzymes that facilitate this process are well defined, global analysis of RNA turnover remains under-investigated. Recent advances in the application of next-generation sequencing technology enable its use in order to examine various RNA decay patterns at the genome-wide scale. In this study, we investigated human RNA decay patterns using parallel analysis of RNA end-sequencing (PARE-seq) data from XRN1-knockdown HeLa cell lines, followed by a comparison of steady state and degraded mRNA levels from RNA-seq and PARE-seq data, respectively. The results revealed 1103 and 1347 transcripts classified as stable and unstable candidates, respectively. Of the unstable candidates, we found that a subset of the replication-dependent histone transcripts was polyadenylated and rapidly degraded. Additionally, we identified 380 endonucleolytically cleaved candidates by analyzing the most abundant PARE sequence on a transcript. Of these, 41.4% of genes were classified as unstable genes, which implied that their endonucleolytic cleavage might affect their mRNA stability. Furthermore, we identified 1877 decapped candidates, including HSP90B1 and SWI5, having the most abundant PARE sequences at the 5′-end positions of the transcripts. These results provide a useful resource for further analysis of RNA decay patterns in human cells.
format Online
Article
Text
id pubmed-7555781
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-75557812020-10-19 Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts Won, Jung-Im Shin, JaeMoon Park, So Young Yoon, JeeHee Jeong, Dong-Hoon Int J Mol Sci Article RNA decay is an important regulatory mechanism for gene expression at the posttranscriptional level. Although the main pathways and major enzymes that facilitate this process are well defined, global analysis of RNA turnover remains under-investigated. Recent advances in the application of next-generation sequencing technology enable its use in order to examine various RNA decay patterns at the genome-wide scale. In this study, we investigated human RNA decay patterns using parallel analysis of RNA end-sequencing (PARE-seq) data from XRN1-knockdown HeLa cell lines, followed by a comparison of steady state and degraded mRNA levels from RNA-seq and PARE-seq data, respectively. The results revealed 1103 and 1347 transcripts classified as stable and unstable candidates, respectively. Of the unstable candidates, we found that a subset of the replication-dependent histone transcripts was polyadenylated and rapidly degraded. Additionally, we identified 380 endonucleolytically cleaved candidates by analyzing the most abundant PARE sequence on a transcript. Of these, 41.4% of genes were classified as unstable genes, which implied that their endonucleolytic cleavage might affect their mRNA stability. Furthermore, we identified 1877 decapped candidates, including HSP90B1 and SWI5, having the most abundant PARE sequences at the 5′-end positions of the transcripts. These results provide a useful resource for further analysis of RNA decay patterns in human cells. MDPI 2020-09-04 /pmc/articles/PMC7555781/ /pubmed/32899599 http://dx.doi.org/10.3390/ijms21186452 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Won, Jung-Im
Shin, JaeMoon
Park, So Young
Yoon, JeeHee
Jeong, Dong-Hoon
Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts
title Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts
title_full Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts
title_fullStr Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts
title_full_unstemmed Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts
title_short Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts
title_sort global analysis of the human rna degradome reveals widespread decapped and endonucleolytic cleaved transcripts
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7555781/
https://www.ncbi.nlm.nih.gov/pubmed/32899599
http://dx.doi.org/10.3390/ijms21186452
work_keys_str_mv AT wonjungim globalanalysisofthehumanrnadegradomerevealswidespreaddecappedandendonucleolyticcleavedtranscripts
AT shinjaemoon globalanalysisofthehumanrnadegradomerevealswidespreaddecappedandendonucleolyticcleavedtranscripts
AT parksoyoung globalanalysisofthehumanrnadegradomerevealswidespreaddecappedandendonucleolyticcleavedtranscripts
AT yoonjeehee globalanalysisofthehumanrnadegradomerevealswidespreaddecappedandendonucleolyticcleavedtranscripts
AT jeongdonghoon globalanalysisofthehumanrnadegradomerevealswidespreaddecappedandendonucleolyticcleavedtranscripts