ATAC-Seq Reveals the Landscape of Open Chromatin and cis-Regulatory Elements in the Phytophthora sojae Genome
- 1 April 2022
- journal article
- research article
- Published by Scientific Societies in Molecular Plant-Microbe Interactions®
- Vol. 35 (4), 301-310
- https://doi.org/10.1094/mpmi-11-21-0291-ta
Abstract
Nucleosome-free open chromatin often harbor transcription factor (TF) binding sites that are associated with active cis-regulatory elements. However, analysis of open chromatin regions has rarely been applied to oomycete or fungal plant pathogens. In this study, we performed the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to identify open chromatin and cis-regulatory elements in Phytophthora sojae at the mycelial stage. We identified 10,389 peaks representing nucleosome-free regions (NFRs). The peaks were enriched in gene promoter regions and associated with 40% of P. sojae genes; transcription levels were higher for genes with multiple peaks than genes with a single peak and were higher for genes with a single peak than genes without peak. Chromatin accessibility was positively correlated with gene transcription level. Through motif discovery based on NFR peaks in core promoter regions, 25 candidates cis-regulatory motifs with evidence of TF-binding footprints were identified. These motifs exhibited various preferences for location in the promoter region and associations with the transcription level of their target genes, which included some putative pathogenicity-related genes. As the first study revealing the landscape of open chromatin and the correlation between chromatin accessibility and gene transcription level in oomycetes, the results provide a technical reference and data resources for future studies on the regulatory mechanisms of gene transcription.Keywords
Funding Information
- National Natural Science Foundation of China (31772140, 31721004)
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