Project description:NKD1, 2 and O2 are key transcription factors interactively regulating endosperm development. Their mutation combinations may diversely alter the global gene regulatory landscape. To investigate how interactions between NKD1, 2 and O2 affect endosperm regulatome, which is indicated by accessible regions for regulators on chromatins, Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed for 16 DAP endosperms of all 8 genotype combinations (2 biological replicate per genotype). Among 16 sequenced samples, 20,478 to 49,640 (mean: 34,766) peaks were called, and these peaks represent potential chromatin accessible regions. Distribution of the peaks on chromatins varies among samples: 54.35% - 66.73% peaks are located at distal intergenic region (>3kb upstream and >300 bp downstream of a gene) and 6.7% - 12.1% are located at promoter region (within 3 kb flanking transcription starting site), and 4.62% - 8.88% peaks are located within 1kb flanking transcription starting site. Also, in WT background, nkd1 and nkd2 single mutants have overall greater number of opening regions (upregulated peaks) than closing regions (downregulated peaks), whereas nkd1,2 double mutant has similar number of opening and closing regions. In contrast, in o2-background, all nkd1, nkd2 and nkd1,2 mutants have greater number of closing than opening regions. This indicates that o2 may alter differential accessibility of nkd1, nkd2 single or nkd1,2 double mutants.
Project description:We report the Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) for high-throughput profiling of accessible chromatin regions after cold treatment in Vitis amurensis
Project description:Bumblebees (Hymenoptera: Apidae) are important pollinating insects that play pivotal roles in crop production and natural ecosystem services. To achieve a comprehensive profile of accessible chromatin regions and provide clues for all possible regulatory elements in the bumblebee genome, we did ATAC-seq for Bombus terrestris samples derived from its four developmental stages: egg, larva, pupa, and adult, respectively. The sequencing reads of ATAC-seq were mapped to B. terrestris reference genome, and its accessible chromatin regions were identified and characterized using bioinformatic methods. Our study will provide important resources not only for uncovering regulatory elements in the bumblebee genome, but also for expanding our understanding of bumblebee biology.