Regulatory variation

The transcriptional regulatory structure of plant genomes is still relatively unexplored. We are using model genetic systems to analyze factors that influence expression variation in plants.

A first example was provided by the analysis of berry transcriptomes during fruit development and ripening in 10 grape sequenced varieties, which showed the association of gene expression variation with genetic and epigenetic properties.

Magris et al (2019) Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties. The Plant Journal 99:895-909

A second study made use of Hi-C, ChIP-seq and ATAC-seq to measure how chromatin features correlates to the expression of 31 845 grapevine genes. This study provided an inventory of intergenic open chromatin regions that can be considered potential candidates for cis-regulatory regions in the grapevine genome. 

Schwope et al (2021) Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression. The Plant Journal 107(6):1631-1647

 

Funded by the Italian Ministry of Agriculture (MIPAAF), project VIGNETO