Quantitative Analysis of the KSHV Transcriptome Following Primary Infection of Blood and Lymphatic Endothelial Cells
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 trans...
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MDPI AG
2017-03-01
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| Series: | Pathogens |
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| Online Access: | http://www.mdpi.com/2076-0817/6/1/11 |
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| author | A. Gregory Bruce Serge Barcy Terri DiMaio Emilia Gan H. Jacques Garrigues Michael Lagunoff Timothy M. Rose |
| author_facet | A. Gregory Bruce Serge Barcy Terri DiMaio Emilia Gan H. Jacques Garrigues Michael Lagunoff Timothy M. Rose |
| author_sort | A. Gregory Bruce |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T19:25:07Z |
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| id | doaj.art-81dec590e9d54719af527d125babbb59 |
| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-04-12T19:25:07Z |
| publishDate | 2017-03-01 |
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| record_format | Article |
| series | Pathogens |
| spelling | doaj.art-81dec590e9d54719af527d125babbb592022-12-22T03:19:30ZengMDPI AGPathogens2076-08172017-03-01611110.3390/pathogens6010011pathogens6010011Quantitative Analysis of the KSHV Transcriptome Following Primary Infection of Blood and Lymphatic Endothelial CellsA. Gregory Bruce0Serge Barcy1Terri DiMaio2Emilia Gan3H. Jacques Garrigues4Michael Lagunoff5Timothy M. Rose6Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98101, USACenter for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98101, USADepartment of Microbiology, University of Washington, Seattle, WA 98101, USADepartment of Global Health, University of Washington, Seattle, WA 98101, USACenter for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98101, USADepartment of Microbiology, University of Washington, Seattle, WA 98101, USACenter for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98101, USAThe 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.http://www.mdpi.com/2076-0817/6/1/11transcriptomeherpesvirusKaposi’s sarcoma-associated herpesviruspromoterdeep sequencingRNAseqlatency |
| spellingShingle | A. Gregory Bruce Serge Barcy Terri DiMaio Emilia Gan H. Jacques Garrigues Michael Lagunoff Timothy M. Rose Quantitative Analysis of the KSHV Transcriptome Following Primary Infection of Blood and Lymphatic Endothelial Cells Pathogens transcriptome herpesvirus Kaposi’s sarcoma-associated herpesvirus promoter deep sequencing RNAseq latency |
| title | Quantitative Analysis of the KSHV Transcriptome Following Primary Infection of Blood and Lymphatic Endothelial Cells |
| title_full | Quantitative Analysis of the KSHV Transcriptome Following Primary Infection of Blood and Lymphatic Endothelial Cells |
| title_fullStr | Quantitative Analysis of the KSHV Transcriptome Following Primary Infection of Blood and Lymphatic Endothelial Cells |
| title_full_unstemmed | Quantitative Analysis of the KSHV Transcriptome Following Primary Infection of Blood and Lymphatic Endothelial Cells |
| title_short | Quantitative Analysis of the KSHV Transcriptome Following Primary Infection of Blood and Lymphatic Endothelial Cells |
| title_sort | quantitative analysis of the kshv transcriptome following primary infection of blood and lymphatic endothelial cells |
| topic | transcriptome herpesvirus Kaposi’s sarcoma-associated herpesvirus promoter deep sequencing RNAseq latency |
| url | http://www.mdpi.com/2076-0817/6/1/11 |
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