Profiling large-scale protein occupancy on bacterial genomes using IPOD-HR

Identifying genomic regions bound by individual proteins such as transcription factors is essential to understanding bacterial gene regulation; however, comprehensive understanding of the effect of protein occupancy on gene regulation would be prohibitively laborious and expensive to achieve using methods such as chromatin immunoprecipitation with sequencing (ChIP-seq) and ChIP with exonuclease treatment (ChIP-exo) for every protein and condition of interest. Here we describe a protocol for performing in vivo protein occupancy display-high resolution (IPOD-HR), a powerful method for genome-wide profiling of protein-bound DNA in prokaryotic systems. Although assay for transposase-accessible chromatin with sequencing (ATAC-seq) is the method of choice for assaying general protein occupancy in eukaryotic systems, bacterial nucleoid-associated proteins can affect ATAC-seq, rendering it unsuitable for use in bacteria. In contrast, IPOD-HR can be used to identify regions of bacterial genomes that are highly bound by proteins, regardless of the identity of the proteins bound, allowing the identification of condition- and genotype-dependent changes in protein occupancy associated with changes in gene regulation. The technique is coupled to RNA polymerase ChIP, followed by sequencing of the extracted samples and downstream analysis using open-source, automated software that we provide and actively maintain. Once cross-linked samples are obtained, the core DNA selection portion of the IPOD-HR protocol takes 3 calendar days to perform. The resulting DNA extracts are subjected to high-throughput sequencing, resulting in sequencing data that are analyzed, which typically requires a few additional days, depending on the number of samples and computing resources. The IPOD-HR experimental method requires familiarity with standard molecular biology techniques suitable for preparing Illumina sequencing inputs, and the computational post-processing pipeline requires basic knowledge of the Linux command line environment.