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.