KSHV 2.0: a comprehensive annotation of the Kaposi's sarcoma-associated herpesvirus genome using next-generation sequencing reveals novel genomic and functional features.
Productive herpesvirus infection requires a profound, time-controlled remodeling of the viral transcriptome and proteome. To gain insights into the genomic architecture and gene expression control in Kaposi's sarcoma-associated herpesvirus (KSHV), we performed a systematic genome-wide survey of viral transcriptional and translational activity throughout the lytic cycle. Using mRNA-sequencing and ribosome profiling, we found that transcripts encoding lytic genes are promptly bound by ribosomes upon lytic reactivation, suggesting their regulation is mainly transcriptional. Our approach also uncovered new genomic features such as ribosome occupancy of viral non-coding RNAs, numerous upstream and small open reading frames (ORFs), and unusual strategies to expand the virus coding repertoire that include alternative splicing, dynamic viral mRNA editing, and the use of alternative translation initiation codons. Furthermore, we provide a refined and expanded annotation of transcription start sites, polyadenylation sites, splice junctions, and initiation/termination codons of known and new viral features in the KSHV genomic space which we have termed KSHV 2.0. Our results represent a comprehensive genome-scale image of gene regulation during lytic KSHV infection that substantially expands our understanding of the genomic architecture and coding capacity of the virus.
Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America.
Carolina
C
Arias
Novartis Vaccines and Diagnostics, Bioinformatics, Emeryville, California, United States of America.
Ben
B
Weisburd
Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America.
Noam
N
Stern-Ginossar
Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America.
Alexandre
A
Mercier
Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America.
Alexis S
AS
Madrid
Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America.
Priya
P
Bellare
Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America.
Meghan
M
Holdorf
Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America.
Jonathan S
JS
Weissman
Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America.
Don
D
Ganem
D002460:Cell Line; D015967:Gene Expression Regulation, Viral / Q000235:genetics*; D016679:Genome, Viral; D019288:Herpesvirus 8, Human / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016366:Open Reading Frames; D022661:RNA, Untranslated / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*
D022661:RNA, Untranslated; D012367:RNA, Viral