Simultaneous Profiling of DNA Accessibility and Gene Expression Dynamics with ATAC-Seq and RNA-Seq

Methods Mol Biol. 2018:1819:317-333. doi: 10.1007/978-1-4939-8618-7_15.

Abstract

This chapter describes sequencing-based methods for profiling dynamic changes in DNA accessibility and gene expression in Saccharomyces cerevisiae. Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) is a powerful technique for identifying nucleosome-free regions of the genome. Combining ATAC-Seq with RNA Sequencing (RNA-Seq) is a rapid approach for studying the relationship between genome structure and changes in global patterns of gene expression from a single experiment. A laboratory protocol is presented for these methods as well as examples of typical results and visualizations.

Keywords: Chromatin; Gene regulation; Genomics; Transcription; Transcription factors.

MeSH terms

  • DNA, Fungal / genetics*
  • DNA, Fungal / metabolism
  • Gene Expression Profiling / methods*
  • Genome, Fungal*
  • High-Throughput Nucleotide Sequencing / methods*
  • RNA, Fungal / genetics*
  • RNA, Fungal / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism

Substances

  • DNA, Fungal
  • RNA, Fungal