Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology

Methods Enzymol. 2012:513:297-313. doi: 10.1016/B978-0-12-391938-0.00013-6.

Abstract

Gene transcription can be regulated through alteration of chromatin structure, such as changes in nucleosome positioning and histone-modification patterns. Recent development of techniques based on the next-generation sequencing technology has allowed high-resolution analysis of genome-wide distribution of these chromatin features. In this chapter, we describe in detail the protocols of ChIP-Seq and MNase-Seq, which have been developed to detect the genome-wide profiles of transcription factor binding, histone modifications, and nucleosome occupancy. We also describe RNA-Seq protocols used to map global gene expression profiles.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Base Sequence
  • Chromatin Assembly and Disassembly
  • Chromatin Immunoprecipitation / methods*
  • Chromosome Mapping / methods*
  • Computational Biology / methods
  • Gene Expression Profiling / methods*
  • High-Throughput Nucleotide Sequencing / methods
  • Histones / genetics
  • Histones / metabolism*
  • Micrococcal Nuclease / metabolism
  • Nucleosomes / metabolism*
  • Protein Binding
  • Transcription Factors / metabolism
  • Transcriptome

Substances

  • Histones
  • Nucleosomes
  • Transcription Factors
  • Micrococcal Nuclease