Dissection of affinity captured LINE-1 macromolecular complexes

Elife. 2018 Jan 8:7:e30094. doi: 10.7554/eLife.30094.

Abstract

Long Interspersed Nuclear Element-1 (LINE-1, L1) is a mobile genetic element active in human genomes. L1-encoded ORF1 and ORF2 proteins bind L1 RNAs, forming ribonucleoproteins (RNPs). These RNPs interact with diverse host proteins, some repressive and others required for the L1 lifecycle. Using differential affinity purifications, quantitative mass spectrometry, and next generation RNA sequencing, we have characterized the proteins and nucleic acids associated with distinctive, enzymatically active L1 macromolecular complexes. Among them, we describe a cytoplasmic intermediate that we hypothesize to be the canonical ORF1p/ORF2p/L1-RNA-containing RNP, and we describe a nuclear population containing ORF2p, but lacking ORF1p, which likely contains host factors participating in target-primed reverse transcription.

Keywords: LINE-1; affinity proteomics; biochemistry; chemical biology; computational biology; human; interactome; retrotransposon; ribonucleoprotein; systems biology.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatography, Affinity
  • Endonucleases / analysis*
  • HeLa Cells
  • Humans
  • Long Interspersed Nucleotide Elements*
  • Macromolecular Substances / chemistry*
  • Mass Spectrometry
  • RNA / analysis*
  • RNA-Directed DNA Polymerase / analysis*
  • Ribonucleoproteins / analysis*

Substances

  • L1 ORF1 protein, human
  • L1 ORF2 protein, human
  • Macromolecular Substances
  • Ribonucleoproteins
  • RNA
  • RNA-Directed DNA Polymerase
  • Endonucleases