title: Methods for integration site distribution analyses in animal cell genomes.
abstract: The question of where retroviral DNA becomes integrated in chromosomes is important for understanding (i) the mechanisms of viral growth, (ii) devising new anti-retroviral therapy, (iii) understanding how genomes evolve, and (iv) developing safer methods for gene therapy. With the completion of genome sequences for many organisms, it has become possible to study integration targeting by cloning and sequencing large numbers of host-virus DNA junctions, then mapping the host DNA segments back onto the genomic sequence. This allows statistical analysis of the distribution of integration sites relative to the myriad types of genomic features that are also being mapped onto the sequence scaffold. Here we present methods for recovering and analyzing integration site sequences.
authors.affiliation: Institute of Microbiology, University Hospital Center and University of Lausanne, Bugnon 48, Lausanne 1011, Switzerland.
authors.forename: Angela
authors.initials: A
authors.lastname: Ciuffi
authors.forename: Keshet
authors.initials: K
authors.lastname: Ronen
authors.forename: Troy
authors.initials: T
authors.lastname: Brady
authors.forename: Nirav
authors.initials: N
authors.lastname: Malani
authors.forename: Gary
authors.initials: G
authors.lastname: Wang
authors.forename: Charles C
authors.initials: CC
authors.lastname: Berry
authors.forename: Frederic D
authors.initials: FD
authors.lastname: Bushman
mesh_terms: D000818:Animals; D002875:Chromosomes / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D018390:Gene Targeting / Q000379:methods*; D016679:Genome, Viral / Q000235:genetics*; D006801:Humans; D042541:Intracellular Space / Q000821:virology*; D016662:Virus Integration / Q000235:genetics*
chemical_list: D004279:DNA, Viral