Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences.
The completion of the human genome sequence has made possible genome-wide studies of retroviral DNA integration. Here we report an analysis of 3,127 integration site sequences from human cells. We compared retroviral vectors derived from human immunodeficiency virus (HIV), avian sarcoma-leukosis virus (ASLV), and murine leukemia virus (MLV). Effects of gene activity on integration targeting were assessed by transcriptional profiling of infected cells. Integration by HIV vectors, analyzed in two primary cell types and several cell lines, strongly favored active genes. An analysis of the effects of tissue-specific transcription showed that it resulted in tissue-specific integration targeting by HIV, though the effect was quantitatively modest. Chromosomal regions rich in expressed genes were favored for HIV integration, but these regions were found to be interleaved with unfavorable regions at CpG islands. MLV vectors showed a strong bias in favor of integration near transcription start sites, as reported previously. ASLV vectors showed only a weak preference for active genes and no preference for transcription start regions. Thus, each of the three retroviruses studied showed unique integration site preferences, suggesting that virus-specific binding of integration complexes to chromatin features likely guides site selection.
Mitchell
Rick S
RS
Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.
Beitzel
Brett F
BF
Schroder
Astrid R W
AR
Shinn
Paul
P
Chen
Huaming
H
Berry
Charles C
CC
Ecker
Joseph R
JR
Bushman
Frederic D
FD
D001358:Avian Sarcoma Viruses / Q000235:genetics; D001665:Binding Sites; D002460:Cell Line; D002843:Chromatin / Q000737:chemistry; D002877:Chromosomes, Human / Q000235:genetics; D018899:CpG Islands; D004279:DNA, Viral; D015894:Genome, Human; D006678:HIV / Q000235:genetics; D006367:HeLa Cells; D006801:Humans; D009052:Leukemia Virus, Murine / Q000235:genetics; D007963:Leukocytes, Mononuclear / Q000821:virology; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000737:chemistry; D017434:Protein Structure, Tertiary; D012190:Retroviridae / Q000235:genetics*; D014158:Transcription, Genetic; D016662:Virus Integration
D002843:Chromatin; D004279:DNA, Viral; D009841:Oligonucleotides