Bioinformatic Analysis of Nucleosome and Histone Variant Positioning

Methods Mol Biol. 2018:1832:185-203. doi: 10.1007/978-1-4939-8663-7_10.

Abstract

Assays profiling nucleosome positioning and occupancy are often coupled with high-throughput sequencing, which results in generation of large data sets. These data sets require processing in specialized computational pipelines to yield useful information. Here, we describe main steps of such a pipeline, and discuss bioinformatic and statistical aspects of assessing data quality, as well as data visualization and further analysis.

Keywords: Data processing and analysis; Histone variants; MNase; Next generation sequencing; Nucleosome positioning.

MeSH terms

  • Algorithms
  • Base Composition / genetics
  • Computational Biology / methods*
  • Gene Expression Regulation
  • Histones / metabolism*
  • Micrococcal Nuclease / metabolism
  • Nucleosomes / metabolism*
  • Protein Isoforms / metabolism
  • Sequence Alignment
  • Transcription Initiation Site

Substances

  • Histones
  • Nucleosomes
  • Protein Isoforms
  • Micrococcal Nuclease