ATAC-Seq Reveals the Landscape of Open Chromatin and  cis -Regulatory Elements in the Phytophthora sojae Genome

• Published in: Molecular plant-microbe interactions Vol. 35; no. 4; pp. 301 - 310
• Main Authors: Zhang, Zhichao, Lin, Long, Chen, Han, Ye, Wenwu, Dong, Suomeng, Zheng, Xiaobo, Wang, Yuanchao
• Format: Journal Article
• Language: English
• Published: United States American Phytopathological Society 01.04.2022; The American Phytopathological Society
• Subjects: Accessibility; ATAC-seq; Binding sites; Chromatin; Chromatin - genetics; Chromatin Immunoprecipitation Sequencing; cis-regulatory element; Genes; Genomes; High-Throughput Nucleotide Sequencing - methods; landscapes; Mycelia; mycelium; Next-generation sequencing; oomycete; open chromatin; Pathogenicity; Pathogens; Phytophthora - genetics; Phytophthora sojae; Place preferences; promoter; promoter regions; Regulatory mechanisms (biology); Regulatory sequences; transcription (genetics); transcription factor; transcription factors; Transcription Factors - genetics; Transposase; open chromatin; oomycete; transcription factor; promoter; cis-regulatory element; ATAC-seq
• ISSN: 0894-0282; 1943-7706; 1943-7706
• DOI: 10.1094/MPMI-11-21-0291-TA

Nucleosome-free open chromatin often harbors 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 candidate 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. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .