Genome-wide identification of HexA binding sites in Pectobacterium carotovorum PCC27 using ChIP-seq

HexA is a global transcriptional regulator involved in quorum sensing and virulence regulation in Pectobacterium carotovorum PCC27. To identify genome-wide DNA binding sites of HexA, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using a FLAG-tagged HexA strain. Samples were collected at two different growth phases—mid-log and early stationary—to investigate condition-dependent differences in HexA binding profiles. A total of six samples (three biological replicates per condition) were sequenced on the Illumina NovaSeq 6000 platform using paired-end 101 bp reads. Peaks were called using MACS2, and downstream analysis was performed with ChIPseeker. This study provides insight into the dynamic regulation of HexA across bacterial growth stages. ChIP-seq was performed on P. carotovorum PCC27 expressing FLAG-tagged HexA. Samples were collected at mid-log and early stationary growth phases, with three biological replicates per condition (n=6 total). Paired-end sequencing was performed using the Illumina NovaSeq 6000 platform (2 × 101 bp). ChIP DNA was enriched using anti-FLAG antibody and libraries were prepared with the TruSeq ChIP Sample Preparation Kit. Peaks were called using MACS2 and annotated with ChIPseeker.