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A Viral Genome Landscape of RNA Polyadenylation from KSHV Latent to Lytic Infection

RNA polyadenylation (pA) is one of the major steps in regulation of gene expression at the posttranscriptional level. In this report, a genome landscape of pA sites of viral transcripts in B lymphocytes with Kaposi sarcoma-associated herpesvirus (KSHV) infection was constructed using a modified PA-s...

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Autores principales: Majerciak, Vladimir, Ni, Ting, Yang, Wenjing, Meng, Bowen, Zhu, Jun, Zheng, Zhi-Ming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828183/
https://www.ncbi.nlm.nih.gov/pubmed/24244170
http://dx.doi.org/10.1371/journal.ppat.1003749
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author Majerciak, Vladimir
Ni, Ting
Yang, Wenjing
Meng, Bowen
Zhu, Jun
Zheng, Zhi-Ming
author_facet Majerciak, Vladimir
Ni, Ting
Yang, Wenjing
Meng, Bowen
Zhu, Jun
Zheng, Zhi-Ming
author_sort Majerciak, Vladimir
collection PubMed
description RNA polyadenylation (pA) is one of the major steps in regulation of gene expression at the posttranscriptional level. In this report, a genome landscape of pA sites of viral transcripts in B lymphocytes with Kaposi sarcoma-associated herpesvirus (KSHV) infection was constructed using a modified PA-seq strategy. We identified 67 unique pA sites, of which 55 could be assigned for expression of annotated ∼90 KSHV genes. Among the assigned pA sites, twenty are for expression of individual single genes and the rest for multiple genes (average 2.7 genes per pA site) in cluster-gene loci of the genome. A few novel viral pA sites that could not be assigned to any known KSHV genes are often positioned in the antisense strand to ORF8, ORF21, ORF34, K8 and ORF50, and their associated antisense mRNAs to ORF21, ORF34 and K8 could be verified by 3′RACE. The usage of each mapped pA site correlates to its peak size, the larger (broad and wide) peak size, the more usage and thus, the higher expression of the pA site-associated gene(s). Similar to mammalian transcripts, KSHV RNA polyadenylation employs two major poly(A) signals, AAUAAA and AUUAAA, and is regulated by conservation of cis-elements flanking the mapped pA sites. Moreover, we found two or more alternative pA sites downstream of ORF54, K2 (vIL6), K9 (vIRF1), K10.5 (vIRF3), K11 (vIRF2), K12 (Kaposin A), T1.5, and PAN genes and experimentally validated the alternative polyadenylation for the expression of KSHV ORF54, K11, and T1.5 transcripts. Together, our data provide not only a comprehensive pA site landscape for understanding KSHV genome structure and gene expression, but also the first evidence of alternative polyadenylation as another layer of posttranscriptional regulation in viral gene expression.
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spelling pubmed-38281832013-11-16 A Viral Genome Landscape of RNA Polyadenylation from KSHV Latent to Lytic Infection Majerciak, Vladimir Ni, Ting Yang, Wenjing Meng, Bowen Zhu, Jun Zheng, Zhi-Ming PLoS Pathog Research Article RNA polyadenylation (pA) is one of the major steps in regulation of gene expression at the posttranscriptional level. In this report, a genome landscape of pA sites of viral transcripts in B lymphocytes with Kaposi sarcoma-associated herpesvirus (KSHV) infection was constructed using a modified PA-seq strategy. We identified 67 unique pA sites, of which 55 could be assigned for expression of annotated ∼90 KSHV genes. Among the assigned pA sites, twenty are for expression of individual single genes and the rest for multiple genes (average 2.7 genes per pA site) in cluster-gene loci of the genome. A few novel viral pA sites that could not be assigned to any known KSHV genes are often positioned in the antisense strand to ORF8, ORF21, ORF34, K8 and ORF50, and their associated antisense mRNAs to ORF21, ORF34 and K8 could be verified by 3′RACE. The usage of each mapped pA site correlates to its peak size, the larger (broad and wide) peak size, the more usage and thus, the higher expression of the pA site-associated gene(s). Similar to mammalian transcripts, KSHV RNA polyadenylation employs two major poly(A) signals, AAUAAA and AUUAAA, and is regulated by conservation of cis-elements flanking the mapped pA sites. Moreover, we found two or more alternative pA sites downstream of ORF54, K2 (vIL6), K9 (vIRF1), K10.5 (vIRF3), K11 (vIRF2), K12 (Kaposin A), T1.5, and PAN genes and experimentally validated the alternative polyadenylation for the expression of KSHV ORF54, K11, and T1.5 transcripts. Together, our data provide not only a comprehensive pA site landscape for understanding KSHV genome structure and gene expression, but also the first evidence of alternative polyadenylation as another layer of posttranscriptional regulation in viral gene expression. Public Library of Science 2013-11-14 /pmc/articles/PMC3828183/ /pubmed/24244170 http://dx.doi.org/10.1371/journal.ppat.1003749 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
spellingShingle Research Article
Majerciak, Vladimir
Ni, Ting
Yang, Wenjing
Meng, Bowen
Zhu, Jun
Zheng, Zhi-Ming
A Viral Genome Landscape of RNA Polyadenylation from KSHV Latent to Lytic Infection
title A Viral Genome Landscape of RNA Polyadenylation from KSHV Latent to Lytic Infection
title_full A Viral Genome Landscape of RNA Polyadenylation from KSHV Latent to Lytic Infection
title_fullStr A Viral Genome Landscape of RNA Polyadenylation from KSHV Latent to Lytic Infection
title_full_unstemmed A Viral Genome Landscape of RNA Polyadenylation from KSHV Latent to Lytic Infection
title_short A Viral Genome Landscape of RNA Polyadenylation from KSHV Latent to Lytic Infection
title_sort viral genome landscape of rna polyadenylation from kshv latent to lytic infection
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828183/
https://www.ncbi.nlm.nih.gov/pubmed/24244170
http://dx.doi.org/10.1371/journal.ppat.1003749
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