High-Resolution ChIP-MNase Mapping of Nucleosome Positions at Selected Genomic Loci and Alleles

Methods Mol Biol. 2021:2351:123-145. doi: 10.1007/978-1-0716-1597-3_7.

Abstract

The positioning of nucleosomes regulates the accessibility of genomic DNA and can impact the activities of functional elements. Nucleosome positioning is highly consistent at each genomic location in any particular cell-type, but can vary in an orchestrated fashion between different cell-types and between genomic loci according to their activities. Here, we describe a technique-"ChIP-MNase" (chromatin immunoprecipitation linked to micrococcal nuclease mapping)-to determine nucleosome positions at chosen sets of genomic features that can be defined by their molecular composition and recovered by chromatin immunoprecipitation. ChIP-MNase enables high-resolution analysis of nucleosome positioning at genomic regions-of-interest and can allow differential analysis of alleles undergoing distinct molecular processes.

Keywords: Chromatin; Chromatin accessibility; Chromatin immunoprecipitation; Micrococcal nuclease; Nucleosomes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles*
  • Binding Sites
  • Cells, Cultured
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromatin Assembly and Disassembly
  • Chromatin Immunoprecipitation / methods*
  • Chromatin Immunoprecipitation Sequencing / methods*
  • Chromosome Mapping / methods*
  • Genetic Loci*
  • Micrococcal Nuclease / metabolism*
  • Nucleosomes / metabolism*
  • Protein Binding
  • Quality Control

Substances

  • Chromatin
  • Nucleosomes
  • Micrococcal Nuclease