LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes

Parmit Kumar Singh, Matthew R. Plumb, Andrea L. Ferris, James R. Iben, Xiaolin Wu, Hind Fadel, Brian T. Luke, Caroline Esnault, Eric M. Poeschla, Stephen H. Hughes, Mamuka Kvaratskhelia, Henry L. Levin

Research output: Contribution to journalArticle

37 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)2287-2297
Number of pages11
JournalGenes and Development
Volume29
Issue number21
DOIs
StatePublished - Nov 1 2015
Externally publishedYes

Fingerprint

Recombinant DNA
HIV-1
Messenger RNA
Introns
RNA Sequence Analysis
Integrases
Lentivirus
lens epithelium-derived growth factor
RNA Splicing Factors
Neoplasm Genes
Alternative Splicing
Genetic Therapy
Chromatin
Exons
Cultured Cells
Protein Isoforms
Multivariate Analysis
Fibroblasts

Keywords

  • HIV-1
  • Integration
  • LEDGF
  • MRNA splicing
  • P75
  • Retrovirus

ASJC Scopus subject areas

  • Genetics
  • Developmental Biology

Cite this

Singh, P. K., Plumb, M. R., Ferris, A. L., Iben, J. R., Wu, X., Fadel, H., ... Levin, H. L. (2015). LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes. Genes and Development, 29(21), 2287-2297. https://doi.org/10.1101/gad.267609

LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes. / Singh, Parmit Kumar; Plumb, Matthew R.; Ferris, Andrea L.; Iben, James R.; Wu, Xiaolin; Fadel, Hind; Luke, Brian T.; Esnault, Caroline; Poeschla, Eric M.; Hughes, Stephen H.; Kvaratskhelia, Mamuka; Levin, Henry L.

In: Genes and Development, Vol. 29, No. 21, 01.11.2015, p. 2287-2297.

Research output: Contribution to journalArticle

Singh, PK, Plumb, MR, Ferris, AL, Iben, JR, Wu, X, Fadel, H, Luke, BT, Esnault, C, Poeschla, EM, Hughes, SH, Kvaratskhelia, M & Levin, HL 2015, 'LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes', Genes and Development, vol. 29, no. 21, pp. 2287-2297. https://doi.org/10.1101/gad.267609
Singh, Parmit Kumar ; Plumb, Matthew R. ; Ferris, Andrea L. ; Iben, James R. ; Wu, Xiaolin ; Fadel, Hind ; Luke, Brian T. ; Esnault, Caroline ; Poeschla, Eric M. ; Hughes, Stephen H. ; Kvaratskhelia, Mamuka ; Levin, Henry L. / LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes. In: Genes and Development. 2015 ; Vol. 29, No. 21. pp. 2287-2297.
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