MadID, a Versatile Approach to Map Protein-DNA Interactions, Highlights Telomere-Nuclear Envelope Contact Sites in Human Cells

Cell Rep. 2018 Dec 4;25(10):2891-2903.e5. doi: 10.1016/j.celrep.2018.11.027.

Abstract

Mapping the binding sites of DNA- or chromatin-interacting proteins is essential to understanding biological processes. DNA adenine methyltransferase identification (DamID) has emerged as a comprehensive method to map genome-wide occupancy of proteins of interest. A caveat of DamID is the specificity of Dam methyltransferase for GATC motifs that are not homogenously distributed in the genome. Here, we developed an optimized method named MadID, using proximity labeling of DNA by the methyltransferase M.EcoGII. M.EcoGII mediates N6-adenosine methylation in any DNA sequence context, resulting in deeper and unbiased coverage of the genome. We demonstrate, using m6A-specific immunoprecipitation and deep sequencing, that MadID is a robust method to identify protein-DNA interactions at the whole-genome level. Using MadID, we revealed contact sites between human telomeres, repetitive sequences devoid of GATC sites, and the nuclear envelope. Overall, MadID opens the way to identification of binding sites in genomic regions that were largely inaccessible.

Keywords: LADs; M.EcoGII; MadID; m6A; methylation; nuclear envelope; proximity labeling; telomeres.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine / analogs & derivatives
  • Adenosine / metabolism
  • Cell Cycle
  • Cell Line
  • DNA / metabolism*
  • DNA Methylation
  • DNA Modification Methylases / metabolism
  • DNA-Binding Proteins / metabolism*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Lamins / metabolism
  • Nuclear Envelope / metabolism*
  • Protein Binding
  • Telomere / metabolism*

Substances

  • DNA-Binding Proteins
  • Lamins
  • N6-methyladenosine (m6A)
  • DNA
  • DNA Modification Methylases
  • Adenosine