Wang Yiduo, Wang Shuai, Wu Yufeng, Cheng Jiawen, Wang Haiyan
National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.
Genes (Basel). 2024 Dec 20;15(12):1630. doi: 10.3390/genes15121630.
BACKGROUND/OBJECTIVES: Chromatin accessibility is closely associated with transcriptional regulation during maize () leaf development. However, its precise role in controlling gene expression at different developmental stages remains poorly understood. This study aimed to investigate the dynamics of chromatin accessibility and its influence on genome-wide gene expression during the BBCH_11, BBCH_13, and BBCH_17 stages of maize leaf development.
Maize leaves were collected at the BBCH_11, BBCH_13, and BBCH_17 developmental stages, and chromatin accessibility was assessed using ATAC-seq. RNA-seq was performed to profile gene expression. Integrated analysis of ATAC-seq and RNA-seq data was conducted to elucidate the relationship between chromatin accessibility and transcriptional regulation.
A total of 46,808, 38,242, and 41,084 accessible chromatin regions (ACRs) were identified at the BBCH_11, BBCH_13, and BBCH_17 stages, respectively, with 23.4%, 12.2%, and 21.9% of these regions located near transcription start sites (TSSs). Integrated analyses revealed that both the number and intensity of ACRs significantly influence gene expression levels. Motif analysis identified key transcription factors associated with leaf development and potential transcriptional repressors among genes, showing divergent regulation patterns in ATAC-seq and RNA-seq datasets.
These findings demonstrate that chromatin accessibility plays a crucial role in regulating the spatial and temporal expression of key genes during maize leaf development by modulating transcription factor binding. This study provides novel insights into the regulatory mechanisms underlying maize leaf development, contributing to a deeper understanding of chromatin-mediated gene expression.
背景/目的：染色质可及性与玉米叶片发育过程中的转录调控密切相关。然而，其在不同发育阶段控制基因表达的确切作用仍知之甚少。本研究旨在探究玉米叶片发育的BBCH_11、BBCH_13和BBCH_17阶段染色质可及性的动态变化及其对全基因组基因表达的影响。
在BBCH_11、BBCH_13和BBCH_17发育阶段采集玉米叶片，采用ATAC-seq评估染色质可及性。进行RNA-seq以分析基因表达谱。对ATAC-seq和RNA-seq数据进行综合分析，以阐明染色质可及性与转录调控之间的关系。
在BBCH_11、BBCH_13和BBCH_17阶段分别鉴定出46,808、38,242和41,084个可及染色质区域（ACR），其中23.4%、12.2%和21.9%的区域位于转录起始位点（TSS）附近。综合分析表明，ACR的数量和强度均显著影响基因表达水平。基序分析确定了与叶片发育相关的关键转录因子以及基因中的潜在转录抑制因子，显示出ATAC-seq和RNA-seq数据集中不同的调控模式。
这些发现表明，染色质可及性通过调节转录因子结合，在玉米叶片发育过程中调控关键基因的时空表达方面发挥着关键作用。本研究为玉米叶片发育的调控机制提供了新的见解，有助于更深入地理解染色质介导的基因表达。
