Nuclear protein LEDGF/p75 recognizes supercoiled DNA by a novel DNA-binding domain

Nucleic Acids Res. 2011 Jul;39(12):5067-81. doi: 10.1093/nar/gkr088. Epub 2011 Feb 23.


Lens epithelium-derived growth factor (LEDGF) or p75 is a co-activator of general transcription and also involved in insertion of human immunodeficiency virus type I (HIV-1) cDNA into host cell genome, which occurs preferentially to active transcription units. These phenomena may share an underlying molecular mechanism in common. We report here that LEDGF/p75 binds negatively supercoiled DNA selectively over unconstrained DNA. We identified a novel DNA-binding domain in the protein and termed it 'supercoiled DNA-recognition domain' (SRD). Recombinant protein fragments containing SRD showed a preferential binding to supercoiled DNA in vitro. SRD harbors a characteristic cluster of lysine and glutamic/aspartic acid residues. A polypeptide mimicking the cluster (K(9)E(9)K(9)) also showed this specificity, suggesting that the cluster is an essential element for the supercoil recognition. eGFP-tagged LEDGF/p75 expressed in the nucleus distributed partially in transcriptionally active regions that were identified by immunostaining of methylated histone H3 (H3K4me3) or incorporation of Br-UTP. This pattern of localization was observed with SRD alone but abolished if the protein lacked SRD. Thus, these results imply that LEDGF/p75 guides its binding partners, including HIV-1 integrase, to the active transcription site through recognition of negative supercoils generated around it.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Cell Nucleus / genetics
  • DNA, Superhelical / metabolism*
  • HeLa Cells
  • Humans
  • Intercellular Signaling Peptides and Proteins / analysis
  • Intercellular Signaling Peptides and Proteins / chemistry*
  • Intercellular Signaling Peptides and Proteins / metabolism
  • Molecular Sequence Data
  • Nuclear Proteins / analysis
  • Nuclear Proteins / chemistry*
  • Nuclear Proteins / metabolism
  • Protein Structure, Tertiary
  • Rats
  • Rats, Sprague-Dawley
  • Transcription, Genetic


  • DNA, Superhelical
  • Intercellular Signaling Peptides and Proteins
  • Nuclear Proteins
  • lens epithelium-derived growth factor

Associated data

  • GENBANK/AB285525