Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression. (6th August 2021)

• Record Type: Journal Article
• Authors: Schwope, Rachel; Magris, Gabriele; Miculan, Mara; Paparelli, Eleonora; Celii, Mirko; Tocci, Aldo; Marroni, Fabio; Fornasiero, Alice; De Paoli, Emanuele; Morgante, Michele
• Is Part Of: Plant journal. Volume 107:Number 6(2021)
• Page Start: 1631
• Page End: 1647
• Publication Date: 2021-08-06
• Subjects: chromatin -- epigenetics -- transcription factors -- gene expression -- plant biology -- Vitis vinifera; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.15404
• Languages: English
• ISSNs: 0960-7412

Abstract

Summary: Vitis vinifera is an economically important crop and a useful model in which to study chromatin dynamics. In contrast to the small and relatively simple genome of Arabidopsis thaliana, grapevine contains a complex genome of 487 Mb that exhibits extensive colonization by transposable elements. We used Hi‐C, ChIP‐seq and ATAC‐seq to measure how chromatin features correlate to the expression of 31 845 grapevine genes. ATAC‐seq revealed the presence of more than 16 000 open chromatin regions, of which we characterize nearly 5000 as possible distal enhancer candidates that occur in intergenic space > 2 kb from the nearest transcription start site (TSS). A motif search identified more than 480 transcription factor (TF) binding sites in these regions, with those for TCP family proteins in greatest abundance. These open chromatin regions are typically within 15 kb from their nearest promoter, and a gene ontology analysis indicated that their nearest genes are significantly enriched for TF activity. The presence of a candidate cis‐regulatory element (cCRE) > 2 kb upstream of the TSS, location in the active nuclear compartment as determined by Hi‐C, and the enrichment of H3K4me3, H3K4me1 and H3K27ac at the gene are correlated with gene expression. Taken together, these results suggest that regions of intergenic open chromatin identified by ATAC‐seq can be considered potential candidates for cis‐regulatory regions in V. vinifera . Our findings enhance the characterization of a valuable agricultural crop, and help to clarify the understanding of unique plant biology. Significance Statement: We use ATAC‐seq to identify open chromatin regions in Vitis vinifera, and show that they contain transcription factor binding sites and are correlated with gene expression, making them likely enhancer candidates. These findings add to the knowledge of biology of horticultural crops and provide possible targets for improved grape breeding strategies.