Journal
GENOMICS
Volume 114, Issue 3, Pages -Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ygeno.2022.110364
Keywords
Soybean; Glycine max; ATAC-seq; Accessible chromatin region (ACR); Genome architecture
Funding
- Hong Kong Research Grants Council Area of Excellence Scheme [AoE/M-403/16]
- Lo Kwee-Seong Biomedical Research Fund
- Lushan Botanical Garden Research Fund [2021ZWZX31, 2022ZWZX01]
- Impact Postdoctoral Fellowship Scheme of The Chinese University of Hong Kong
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In this study, ACRs were identified in six soybean tissues using ATAC-seq, and they were found to be tightly associated with gene expressions and TF binding capacities in soybean.
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.
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