Integrative Analysis of CUT&Tag and RNA-Seq Data Through Bioinformatics: A Unified Workflow for Enhanced Insights

Methods Mol Biol. 2024:2846:191-213. doi: 10.1007/978-1-0716-4071-5_13.

Abstract

Cleavage Under Targets and Tagmentation (CUT&Tag) is a recent methodology used for robust epigenomic profiling that, unlike conventional chromatin immunoprecipitation (ChIP-Seq), requires only a limited amount of cells as starting material. RNA sequencing (RNA-Seq) reveals the presence and quantity of RNA in a biological sample, describing the continuously changing cellular transcriptome. The integrated analysis of transcriptional activity, histone modifications, and chromatin accessibility via CUT&Tag is still in its infancy compared to the well-established ChIP-Seq. This chapter describes a robust bioinformatics methodology and workflow to perform an integrative CUT&Tag/RNA-Seq analysis.

Keywords: Bioinformatics; Chromatin immunoprecipitation sequencing (ChIP-Seq); Cleavage under targets and tagmentation (CUT&Tag); Histone marks; Next-generation sequencing (NGS); RNA sequencing (RNA-Seq).

MeSH terms

  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation / methods
  • Chromatin Immunoprecipitation Sequencing / methods
  • Computational Biology* / methods
  • Epigenomics / methods
  • Gene Expression Profiling / methods
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • RNA-Seq / methods
  • Sequence Analysis, RNA / methods
  • Software
  • Transcriptome
  • Workflow*

Substances

  • Chromatin