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


Authors: Janovitz, T.; Klein, I. A.; Oliveira, T.; Mukherjee, P.; Nussenzweig, M. C.; Sadelain, M.; Falck-Pedersen, E.
Article Title: High-throughput sequencing reveals principles of adeno-associated virus serotype 2 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. © 2013, American Society for Microbiology.
Keywords: controlled study; human cell; sequence analysis; nonhuman; protein dna binding; transcription initiation; gene locus; hela cells; gene expression regulation; genome analysis; human cell culture; recombination, genetic; binding site; dna sequence; virus replication; helicase; gene insertion; virus genome; genome, human; virus identification; dna binding motif; genome, viral; virus dna cell dna interaction; virus integration; high throughput sequencing; high-throughput nucleotide sequencing; adeno associated virus; dependovirus
Journal Title: Journal of Virology
Volume: 87
Issue: 15
ISSN: 0022-538X
Publisher: American Society for Microbiology  
Date Published: 2013-08-01
Start Page: 8559
End Page: 8568
Language: English
DOI: 10.1128/jvi.01135-13
PROVIDER: scopus
PMCID: PMC3719808
PUBMED: 23720718
DOI/URL:
Notes: --- - "Export Date: 1 August 2013" - "CODEN: JOVIA" - "Source: Scopus"
Altmetric
Citation Impact
MSK Authors
  1. Michel W J Sadelain
    500 Sadelain