Methods for integration site distribution analyses in animal cell genomes |
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| Authors: | Angela Ciuffi Keshet Ronen Troy Brady Nirav Malani Gary Wang Charles C Berry Frederic D Bushman |
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| Institution: | aDepartment of Microbiology, University of Pennsylvania School of Medicine, 402 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA;bInstitute of Microbiology, University Hospital Center and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland;cDepartment of Family/Preventive Medicine, University of California, San Diego School of Medicine, San Diego, CA 9209, USA |
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| 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. |
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| Keywords: | Integration sites HIV Retroviral DNA Genomic |
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