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High-throughput sequencing reveals principles of adeno-associated virus serotype 2 integration.

TitleHigh-throughput sequencing reveals principles of adeno-associated virus serotype 2 integration.
Publication TypeJournal Article
Year of Publication2013
AuthorsJanovitz T, Klein IA, Oliveira T, Mukherjee P, Nussenzweig MC, Sadelain M, Falck-Pedersen E
JournalJ Virol
Volume87
Issue15
Pagination8559-68
Date Published2013 Aug
ISSN1098-5514
KeywordsDependovirus, Genome, Human, Genome, Viral, HeLa Cells, High-Throughput Nucleotide Sequencing, Humans, Recombination, Genetic, Virus Integration
Abstract

Viral integrations are important in human biology, yet genome-wide integration profiles have not been determined for many viruses. Adeno-associated virus (AAV) infects most of the human population and is a prevalent gene therapy vector. AAV integrates into the human genome with preference for a single locus, termed AAVS1. However, the genome-wide integration of AAV has not been defined, and the principles underlying this recombination remain unclear. Using a novel high-throughput approach, integrant capture sequencing, nearly 12 million AAV junctions were recovered from a human cell line, providing five orders of magnitude more data than were previously available. Forty-five percent of integrations occurred near AAVS1, and several thousand novel integration hotspots were identified computationally. Most of these occurred in genes, with dozens of hotspots targeting known oncogenes. Viral replication protein binding sites (RBS) and transcriptional activity were major factors favoring integration. In a first for eukaryotic viruses, the data reveal a unique asymmetric integration profile with distinctive directional orientation of viral genomes. These studies provide a new understanding of AAV integration biology through the use of unbiased high-throughput data acquisition and bioinformatics.

DOI10.1128/JVI.01135-13
Alternate JournalJ Virol
PubMed ID23720718
PubMed Central IDPMC3719808
Grant ListR01 AI037526 / AI / NIAID NIH HHS / United States
T32GM07739 / GM / NIGMS NIH HHS / United States
R01 AI094050 / AI / NIAID NIH HHS / United States
/ / Howard Hughes Medical Institute / United States
AI037526 / AI / NIAID NIH HHS / United States
R37 AI037526 / AI / NIAID NIH HHS / United States
T32 GM007739 / GM / NIGMS NIH HHS / United States

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