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" |
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