Chromatin conformation analysis in Vitis Vinifera

The three-dimensional structure of chromatin and the DNA function are in a strict relationship affecting each other. The present work is the first attempt in characterizing Vitis vinifera genome investigating its 3D structure. Chromatin structure can be assessed using Hi-C: a derivative method of Chromosome Conformation Capture (3C) that explores the three-dimensional architecture of whole genomes by coupling proximity-based ligation with next generation sequencing. Hi-C data provide information about contacts between genomic regions that can be transformed into two-dimensional interaction maps through bioinformatics analysis. We investigated the stability across grapevine varieties of structural features such as distance dependent decay of interactions, relative chromosome positioning inside the nucleus and polarization of telomeres and centromeres as in the Rabl conformation. We processed the obtained the grapevine interaction map via Principal Component Analysis (PCA) to reveal that chromatin appears organized into megabase-scale domains, namely A and B compartments. Comparing several genomic and epigenomic features across the chromatin compartments, we found that A compartment is positively related with open/active chromatin state, while B compartment is positively related with inactive chromatin. We investigated the presence of sub-megabase scale domains in grapevine genome, similar to what was found in mammalians, fly and in other plant species, generally called topologically associated domains (TADs). We also assessed the presence of long-range interactions (chromatin loops) and characterized the biological role of the genes involved in such kind of interactions. The genome variability across grapevine varieties is mainly due to thousands large insertions or deletions, known as structural variants (SV). SV can influence the activity of DNA and chromatin organization. We investigated the effect of SV on the chromatin spatial conformation by means of the simulation of large insertions, deletions and inversions and we reconstructed single haplotype Hi-C maps, observing allele-specific effects of heterozygous structural variation. Finally, we also investigated the possible effect of chromatin conformation on the occurrence of SVs in grapevine and we obtained results that pointed to physical interaction as a prerequisite for the occurrence of SVs. This study provides new insights into the role of grapevine chromatin conformation not only as the structural element that ensures DNA compression, but also as a player with functional implications in events that cause genomic variation and in the regulation of gene expression.