State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; College of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China.
College of Life Science, Northeast Forestry University, Harbin 150040, China.
Genomics Proteomics Bioinformatics. 2023 Apr;21(2):311-323. doi: 10.1016/j.gpb.2022.10.005. Epub 2022 Oct 31.
Chromatin accessibility landscapes are essential for detecting regulatory elements, illustrating the corresponding regulatory networks, and, ultimately, understanding the molecular basis underlying key biological processes. With the advancement of sequencing technologies, a large volume of chromatin accessibility data has been accumulated and integrated for humans and other mammals. These data have greatly advanced the study of disease pathogenesis, cancer survival prognosis, and tissue development. To advance the understanding of molecular mechanisms regulating plant key traits and biological processes, we developed a comprehensive plant chromatin accessibility database (PlantCADB) from 649 samples of 37 species. These samples are abiotic stress-related (such as heat, cold, drought, and salt; 159 samples), development-related (232 samples), and/or tissue-specific (376 samples). Overall, 18,339,426 accessible chromatin regions (ACRs) were compiled. These ACRs were annotated with genomic information, associated genes, transcription factor footprint, motif, and single-nucleotide polymorphisms (SNPs). Additionally, PlantCADB provides various tools to visualize ACRs and corresponding annotations. It thus forms an integrated, annotated, and analyzed plant-related chromatin accessibility resource, which can aid in better understanding genetic regulatory networks underlying development, important traits, stress adaptations, and evolution.PlantCADB is freely available at https://bioinfor.nefu.edu.cn/PlantCADB/.
染色质可及性图谱对于检测调控元件、阐明相应的调控网络以及最终理解关键生物学过程的分子基础至关重要。随着测序技术的进步，大量的染色质可及性数据已经在人类和其他哺乳动物中得到了积累和整合。这些数据极大地推动了疾病发病机制、癌症生存预后和组织发育的研究。为了深入了解调控植物关键性状和生物学过程的分子机制，我们从 37 个物种的 649 个样本中开发了一个全面的植物染色质可及性数据库（PlantCADB）。这些样本与非生物胁迫有关（如热、冷、干旱和盐胁迫；159 个样本）、与发育有关（232 个样本）或组织特异性有关（376 个样本）。总体上，共编译了 18339426 个可及染色质区域（ACRs）。这些 ACRs 被注释了基因组信息、相关基因、转录因子足迹、基序和单核苷酸多态性（SNPs）。此外，PlantCADB 还提供了各种可视化 ACRs 和相应注释的工具。因此，它形成了一个集成的、注释的和分析的植物相关染色质可及性资源，这有助于更好地理解发育、重要性状、应激适应和进化背后的遗传调控网络。PlantCADB 可在 https://bioinfor.nefu.edu.cn/PlantCADB/ 免费获取。
