Differential Analysis of Protein-DNA Binding Using ChIP-Seq Data

Methods Mol Biol. 2024:2846:63-89. doi: 10.1007/978-1-0716-4071-5_5.

Abstract

Chromatin immunoprecipitation in combination with next-generation sequencing (ChIP-Seq) allows probing of protein-DNA binding in a rapid and genome-wide fashion. Herein we describe the required steps to preprocess ChIP-Seq data and to analyze the differential binding of proteins to DNA for perturbation experiments. In these experiments, different conditions are compared to find the underlying biological mechanisms caused by the stimulus or treatment. In addition, we provide a sample analysis using the steps outlined in the chapter.

Keywords: DiffBind; Differential ChIP-Seq analysis; ChIP-Seq.

MeSH terms

  • Binding Sites
  • Chromatin Immunoprecipitation / methods
  • Chromatin Immunoprecipitation Sequencing* / methods
  • Computational Biology / methods
  • DNA* / genetics
  • DNA* / metabolism
  • DNA-Binding Proteins* / genetics
  • DNA-Binding Proteins* / metabolism
  • High-Throughput Nucleotide Sequencing* / methods
  • Humans
  • Protein Binding*
  • Sequence Analysis, DNA / methods
  • Software

Substances

  • DNA
  • DNA-Binding Proteins