Study of Vitis vinifera gene regulation using ChIP-seq, ATAC-seq, BS-seq, Hi-C, and RNA-seq

We use ATAC-seq to search for regions of open chromatin in the grapevine leaf tissue. We perform sequence analysis of these open chromatin regions and find that they contain more than 480 transcription factor motifs and are enriched near transcription factor genes. Additionally, we use ChIP-seq and BS-seq to search for known epigenetic signatures of putative CREs. We exploit the high levels of individual heterozygosity to perform an allele-specific analysis of open chromatin regions and to relate this information to patterns of allele specific expression. Finally, we use Hi-C to define nuclear organization patterns and provide a comprehensive linear model to show the additive effects of global and local gene regulation.

本研究采用转座酶可及性测序（ATAC-seq）筛选葡萄叶片组织中的开放染色质区域，随后对该类区域开展序列分析，发现其包含超过480个转录因子结合基序，且在转录因子基因附近显著富集。此外，本研究借助染色质免疫共沉淀测序（ChIP-seq）与亚硫酸氢盐测序（BS-seq），对推定顺式调控元件（CREs）的已知表观遗传特征进行鉴定。研究利用个体较高的杂合性水平，针对开放染色质区域开展等位基因特异性分析，并将该分析结果与等位基因特异性表达模式相关联。最后，本研究通过染色体构象捕获测序（Hi-C）明确细胞核组织模式，并构建全面的线性模型以阐释全局与局部基因调控的累加效应。