Identification of the accessible chromatin regions in six tissues in the soybean

• Published in: Genomics (San Diego, Calif.) Calif.), 2022-05, Vol.114 (3), p.110364-110364, Article 110364
• Main Authors: Huang, Mingkun, Zhang, Ling, Zhou, Limeng, Yung, Wai-Shing, Wang, Zhili, Xiao, Zhixia, Wang, Qianwen, Wang, Xin, Li, Man-Wah, Lam, Hon-Ming
• Format: Article
• Language: English
• Subjects: Accessible chromatin region (ACR); ATAC-seq; Chromatin - genetics; Chromatin Immunoprecipitation Sequencing; Genome architecture; Genomics; Glycine max; Glycine max - genetics; Glycine max - metabolism; Soybean; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2022.110364

Accessible chromatin regions (ACRs) are tightly associated with gene expressions in the genome. Conserved non-coding cis-regulatory elements, such as transcription factor binding motifs, are usually found in ACRs, indicating an essential regulatory role of ACRs in the plant genome architecture. However, there have been few studies on soybean ACRs, especially those focusing on specific tissues. Hence, in this study, with the convenient ATAC-seq, we identified the ACRs in six soybean tissues, including root, leaf bud, flower, flower bud, developing seed, and pod. In total, the ACRs occupied about 3.3% of the entire soybean genome. By integrating the results from RNA-seq and transcription factor (TF) ChIP-seq, ACRs were found to be tightly associated with gene expressions and TF binding capacities in soybean. Together, these data provide a comprehensive understanding of the genomic features of ACRs in soybean. As a collection of essential genomic resources, these processed data are made available at datahub.wildsoydb.org. •Identification of the ACRs in six tissues in soybean genome.•ACRs are important for soybean genome architecture, such as TF binding.•The information of ACRs is available in our website for further investigation.