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Pathogens 2017, 6(1), 11; doi:10.3390/pathogens6010011

Quantitative Analysis of the KSHV Transcriptome Following Primary Infection of Blood and Lymphatic Endothelial Cells

1
Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
2
Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
3
Department of Microbiology, University of Washington, Seattle, WA 98101, USA
4
Department of Global Health, University of Washington, Seattle, WA 98101, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Angus Wilson
Received: 19 January 2017 / Revised: 7 March 2017 / Accepted: 15 March 2017 / Published: 19 March 2017
(This article belongs to the Special Issue Herpesviruses)
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Abstract

The transcriptome of the Kaposi’s sarcoma-associated herpesvirus (KSHV/HHV8) after primary latent infection of human blood (BEC), lymphatic (LEC) and immortalized (TIME) endothelial cells was analyzed using RNAseq, and compared to long-term latency in BCBL-1 lymphoma cells. Naturally expressed transcripts were obtained without artificial induction, and a comprehensive annotation of the KSHV genome was determined. A set of unique coding sequence (UCDS) features and a process to resolve overlapping transcripts were developed to accurately quantitate transcript levels from specific promoters. Similar patterns of KSHV expression were detected in BCBL-1 cells undergoing long-term latent infections and in primary latent infections of both BEC and LEC cultures. High expression levels of poly-adenylated nuclear (PAN) RNA and spliced and unspliced transcripts encoding the K12 Kaposin B/C complex and associated microRNA region were detected, with an elevated expression of a large set of lytic genes in all latently infected cultures. Quantitation of non-overlapping regions of transcripts across the complete KSHV genome enabled for the first time accurate evaluation of the KSHV transcriptome associated with viral latency in different cell types. Hierarchical clustering applied to a gene correlation matrix identified modules of co-regulated genes with similar correlation profiles, which corresponded with biological and functional similarities of the encoded gene products. Gene modules were differentially upregulated during latency in specific cell types indicating a role for cellular factors associated with differentiated and/or proliferative states of the host cell to influence viral gene expression. View Full-Text
Keywords: transcriptome; herpesvirus; Kaposi’s sarcoma-associated herpesvirus; promoter; deep sequencing; RNAseq; latency transcriptome; herpesvirus; Kaposi’s sarcoma-associated herpesvirus; promoter; deep sequencing; RNAseq; latency
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MDPI and ACS Style

Bruce, A.G.; Barcy, S.; DiMaio, T.; Gan, E.; Garrigues, H.J.; Lagunoff, M.; Rose, T.M. Quantitative Analysis of the KSHV Transcriptome Following Primary Infection of Blood and Lymphatic Endothelial Cells. Pathogens 2017, 6, 11.

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