title: A genome-wide map of adeno-associated virus-mediated human gene targeting.
abstract: To determine which genomic features promote homologous recombination, we created a genome-wide map of gene targeting sites. We used an adeno-associated virus vector to target identical loci introduced as transcriptionally active retroviral vectors. A comparison of ~2,000 targeted and untargeted sites showed that targeting occurred throughout the human genome and was not influenced by the presence of nearby CpG islands, sequence repeats or DNase I-hypersensitive sites. Targeted sites were preferentially located within transcription units, especially when the target loci were transcribed in the opposite orientation to their surrounding chromosomal genes. We determined the impact of DNA replication by mapping replication forks, which revealed a preference for recombination at target loci transcribed toward an incoming fork. Our results constitute the first genome-wide screen of gene targeting in mammalian cells and demonstrate a strong recombinogenic effect of colliding polymerases.
authors.affiliation: Department of Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Deyle
authors.affiliation: Department of Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: R Scott
authors.initials: RS
authors.lastname: Hansen
authors.affiliation: Department of Molecular and Cellular Biology, University of Washington, Seattle, Washington, USA.
authors.forename: Anda M
authors.initials: AM
authors.lastname: Cornea
authors.affiliation: Department of Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: Li B
authors.initials: LB
authors.lastname: Li
authors.affiliation: Department of Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: Amber A
authors.initials: AA
authors.lastname: Burt
authors.affiliation: Gene Therapy Research Unit, Children's Medical Research Institute, Westmead, New South Wales, Australia.
authors.forename: Ian E
authors.initials: IE
authors.lastname: Alexander
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Richard S
authors.identifier: 0000000233561547
authors.initials: RS
authors.lastname: Sandstrom
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: John A
authors.initials: JA
authors.lastname: Stamatoyannopoulos
authors.affiliation: Genomic Technologies Department, Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.affiliation: 1] Department of Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Biochemistry, University of Washington, Seattle, Washington, USA.
authors.forename: David W
authors.initials: DW
authors.lastname: Russell
mesh_terms: D045744:Cell Line, Tumor; D002874:Chromosome Mapping; D018899:CpG Islands; D004261:DNA Replication; D003850:Deoxyribonuclease I / Q000235:genetics* / Q000378:metabolism; D000229:Dependovirus / Q000235:genetics*; D056426:Genetic Loci; D005822:Genetic Vectors; D015894:Genome, Human; D057809:HEK293 Cells; D059765:Homologous Recombination; D006801:Humans; D014158:Transcription, Genetic
chemical_list: D003850:Deoxyribonuclease I