Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression
Type
ArticleAuthors
Schwope, Rachel
Magris, Gabriele

Miculan, Mara
Paparelli, Eleonora
Celii, Mirko
Tocci, Aldo
Marroni, Fabio
Fornasiero, Alice
De Paoli, Emanuele
Morgante, Michele

KAUST Department
Biological and Environmental Science and Engineering (BESE) DivisionDate
2021-08-06Online Publication Date
2021-08-06Print Publication Date
2021-09Embargo End Date
2022-07-05Permanent link to this record
http://hdl.handle.net/10754/670027
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Show full item recordAbstract
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 >2kb from the nearest TSS. A motif search identified more than 480 transcription factor 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 transcription factor activity. The presence of a candidate cis-regulatory element (cCRE) >2kb 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 Vitis vinifera. Our findings enhance the characterization of a valuable agricultural crop and help to clarify the understanding of unique plant biology.Citation
Schwope, R., Magris, G., Miculan, M., Paparelli, E., Celii, M., Tocci, A., … Morgante, M. (2021). Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression. The Plant Journal. doi:10.1111/tpj.15404Publisher
WileyJournal
The Plant JournalAdditional Links
https://onlinelibrary.wiley.com/doi/10.1111/tpj.15404ae974a485f413a2113503eed53cd6c53
10.1111/tpj.15404