title: LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes.
abstract: The host chromatin-binding factor LEDGF/p75 interacts with HIV-1 integrase and directs integration to active transcription units. To understand how LEDGF/p75 recognizes transcription units, we sequenced 1 million HIV-1 integration sites isolated from cultured HEK293T cells. Analysis of integration sites showed that cancer genes were preferentially targeted, raising concerns about using lentivirus vectors for gene therapy. Additional analysis led to the discovery that introns and alternative splicing contributed significantly to integration site selection. These correlations were independent of transcription levels, size of transcription units, and length of the introns. Multivariate analysis with five parameters previously found to predict integration sites showed that intron density is the strongest predictor of integration density in transcription units. Analysis of previously published HIV-1 integration site data showed that integration density in transcription units in mouse embryonic fibroblasts also correlated strongly with intron number, and this correlation was absent in cells lacking LEDGF. Affinity purification showed that LEDGF/p75 is associated with a number of splicing factors, and RNA sequencing (RNA-seq) analysis of HEK293T cells lacking LEDGF/p75 or the LEDGF/p75 integrase-binding domain (IBD) showed that LEDGF/p75 contributes to splicing patterns in half of the transcription units that have alternative isoforms. Thus, LEDGF/p75 interacts with splicing factors, contributes to exon choice, and directs HIV-1 integration to transcription units that are highly spliced.
authors.affiliation: Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA;
authors.forename: Parmit Kumar
authors.initials: PK
authors.lastname: Singh
authors.affiliation: Center for Retrovirus Research, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA;
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Plumb
authors.affiliation: HIV Drug Resistance Program, National Cancer Institute, Frederick, Maryland 21702, USA;
authors.forename: Andrea L
authors.initials: AL
authors.lastname: Ferris
authors.affiliation: Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA;
authors.forename: James R
authors.initials: JR
authors.lastname: Iben
authors.affiliation: Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA;
authors.forename: Xiaolin
authors.initials: X
authors.lastname: Wu
authors.affiliation: Department of Molecular Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA;
authors.forename: Hind J
authors.initials: HJ
authors.lastname: Fadel
authors.affiliation: Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702, USA;
authors.forename: Brian T
authors.initials: BT
authors.lastname: Luke
authors.affiliation: Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA;
authors.forename: Caroline
authors.initials: C
authors.lastname: Esnault
authors.affiliation: Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.
authors.forename: Eric M
authors.initials: EM
authors.lastname: Poeschla
authors.affiliation: HIV Drug Resistance Program, National Cancer Institute, Frederick, Maryland 21702, USA;
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Hughes
authors.affiliation: Center for Retrovirus Research, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA;
authors.forename: Mamuka
authors.initials: M
authors.lastname: Kvaratskhelia
authors.affiliation: Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA;
authors.forename: Henry L
authors.initials: HL
authors.lastname: Levin
mesh_terms: D057809:HEK293 Cells; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics / Q000378:metabolism*; D007438:Introns / Q000235:genetics; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012326:RNA Splicing; D016662:Virus Integration / Q000235:genetics*
chemical_list: D036341:Intercellular Signaling Peptides and Proteins; C119380:lens epithelium-derived growth factor
keywords: HIV-1; LEDGF; integration; mRNA splicing; p75; retrovirus