Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing.

Virus-encoded microRNAs (miRNAs) have been shown to regulate a variety of biological processes involved in viral infection and viral-associated pathogenesis. Epstein-Barr virus (EBV) is a herpesvirus implicated in nasopharyngeal carcinoma (NPC) and other human malignancies. EBV-encoded miRNAs were a...

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Autores principales:	Shu-Jen Chen, Gian-Hung Chen, Yi-Hsuan Chen, Cheng-Yuan Liu, Kai-Ping Chang, Yu-Sun Chang, Hua-Chien Chen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8378acc250f3405bb005effa8ffa946f
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spelling	oai:doaj.org-article:8378acc250f3405bb005effa8ffa946f2021-11-18T06:35:02ZCharacterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing.1932-620310.1371/journal.pone.0012745https://doaj.org/article/8378acc250f3405bb005effa8ffa946f2010-09-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20862214/?tool=EBIhttps://doaj.org/toc/1932-6203Virus-encoded microRNAs (miRNAs) have been shown to regulate a variety of biological processes involved in viral infection and viral-associated pathogenesis. Epstein-Barr virus (EBV) is a herpesvirus implicated in nasopharyngeal carcinoma (NPC) and other human malignancies. EBV-encoded miRNAs were among the first group of viral miRNAs identified. To understand the roles of EBV miRNAs in the pathogenesis of NPC, we utilized deep sequencing technology to characterize the EBV miRNA transcriptome in clinical NPC tissues. We obtained more than 110,000 sequence reads in NPC samples and identified 44 EBV BART miRNAs, including four new mature miRNAs derived from previously identified BART miRNA precursor hairpins. Further analysis revealed extensive sequence variations (isomiRs) of EBV miRNAs, including terminal isomiRs at both the 5' and 3' ends and nucleotide variants. Analysis of EBV genomic sequences indicated that the majority of EBV miRNA nucleotide variants resulted from post-transcriptional modifications. Read counts of individual EBV miRNA in NPC tissue spanned from a few reads to approximately 18,000 reads, confirming the wide expression range of EBV miRNAs. Several EBV miRNAs were expressed at levels similar to highly abundant human miRNAs. Sequence analysis revealed that most of the highly abundant EBV miRNAs share their seed sequences (nucleotides 2-7) with human miRNAs, suggesting that seed sequence content may be an important factor underlying the differential accumulation of BART miRNAs. Interestingly, many of these human miRNAs have been found to be dysregulated in human malignancies, including NPC. These observations not only provide a potential linkage between EBV miRNAs and human malignancy but also suggest a highly coordinated mechanism through which EBV miRNAs may mimic or compete with human miRNAs to affect cellular functions.Shu-Jen ChenGian-Hung ChenYi-Hsuan ChenCheng-Yuan LiuKai-Ping ChangYu-Sun ChangHua-Chien ChenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 9 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Shu-Jen Chen Gian-Hung Chen Yi-Hsuan Chen Cheng-Yuan Liu Kai-Ping Chang Yu-Sun Chang Hua-Chien Chen Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing.
description	Virus-encoded microRNAs (miRNAs) have been shown to regulate a variety of biological processes involved in viral infection and viral-associated pathogenesis. Epstein-Barr virus (EBV) is a herpesvirus implicated in nasopharyngeal carcinoma (NPC) and other human malignancies. EBV-encoded miRNAs were among the first group of viral miRNAs identified. To understand the roles of EBV miRNAs in the pathogenesis of NPC, we utilized deep sequencing technology to characterize the EBV miRNA transcriptome in clinical NPC tissues. We obtained more than 110,000 sequence reads in NPC samples and identified 44 EBV BART miRNAs, including four new mature miRNAs derived from previously identified BART miRNA precursor hairpins. Further analysis revealed extensive sequence variations (isomiRs) of EBV miRNAs, including terminal isomiRs at both the 5' and 3' ends and nucleotide variants. Analysis of EBV genomic sequences indicated that the majority of EBV miRNA nucleotide variants resulted from post-transcriptional modifications. Read counts of individual EBV miRNA in NPC tissue spanned from a few reads to approximately 18,000 reads, confirming the wide expression range of EBV miRNAs. Several EBV miRNAs were expressed at levels similar to highly abundant human miRNAs. Sequence analysis revealed that most of the highly abundant EBV miRNAs share their seed sequences (nucleotides 2-7) with human miRNAs, suggesting that seed sequence content may be an important factor underlying the differential accumulation of BART miRNAs. Interestingly, many of these human miRNAs have been found to be dysregulated in human malignancies, including NPC. These observations not only provide a potential linkage between EBV miRNAs and human malignancy but also suggest a highly coordinated mechanism through which EBV miRNAs may mimic or compete with human miRNAs to affect cellular functions.
format	article
author	Shu-Jen Chen Gian-Hung Chen Yi-Hsuan Chen Cheng-Yuan Liu Kai-Ping Chang Yu-Sun Chang Hua-Chien Chen
author_facet	Shu-Jen Chen Gian-Hung Chen Yi-Hsuan Chen Cheng-Yuan Liu Kai-Ping Chang Yu-Sun Chang Hua-Chien Chen
author_sort	Shu-Jen Chen
title	Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing.
title_short	Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing.
title_full	Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing.
title_fullStr	Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing.
title_full_unstemmed	Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing.
title_sort	characterization of epstein-barr virus mirnaome in nasopharyngeal carcinoma by deep sequencing.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/8378acc250f3405bb005effa8ffa946f
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Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing.

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