Determination of the Chromatin Openness in Bacterial Genomes

Mahmoud M Al-Bassam; Karsten Zengler

doi:10.1007/978-1-0716-2899-7_5

Determination of the Chromatin Openness in Bacterial Genomes

Methods Mol Biol. 2023:2611:63-69. doi: 10.1007/978-1-0716-2899-7_5.

Authors

Mahmoud M Al-Bassam¹, Karsten Zengler^{2

3

4}

Affiliations

¹ Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA. malbassam@eng.ucsd.edu.
² Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
³ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
⁴ Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.

PMID: 36807064
DOI: 10.1007/978-1-0716-2899-7_5

Abstract

The hyperactive Tn5 transposase in the ATAC-seq method has been widely used to determine the open DNA regions and understand the overall epigenomic regulation in the chromatins of eukaryotic cells. Here, we describe POP-seq (Prokaryotic chromatin Openness Profiling sequencing), an adaptation of the ATAC-seq method, to interrogate changes in the openness of prokaryotic nucleoids.

Keywords: Chromatin structure; H-NS; HiC; Nucleoid structure; Nucleoid-associated proteins; POP-seq; Tn5 transposase; Transcription factor binding sites.

MeSH terms

Chromatin*
DNA
Genome, Bacterial
High-Throughput Nucleotide Sequencing* / methods
Sequence Analysis, DNA / methods

Substances

Chromatin
DNA