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dc.contributor.authorSchwope, Rachel
dc.contributor.authorMagris, Gabriele
dc.contributor.authorMiculan, Mara
dc.contributor.authorPaparelli, Eleonora
dc.contributor.authorCelii, Mirko
dc.contributor.authorTocci, Aldo
dc.contributor.authorMarroni, Fabio
dc.contributor.authorFornasiero, Alice
dc.contributor.authorDe Paoli, Emanuele
dc.contributor.authorMorgante, Michele
dc.date.accessioned2021-07-06T11:16:55Z
dc.date.available2021-07-06T11:16:55Z
dc.date.issued2021-08-06
dc.identifier.citationSchwope, 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.15404
dc.identifier.issn0960-7412
dc.identifier.issn1365-313X
dc.identifier.doi10.1111/tpj.15404
dc.identifier.urihttp://hdl.handle.net/10754/670027
dc.description.abstractVitis 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.
dc.publisherWiley
dc.relation.urlhttps://onlinelibrary.wiley.com/doi/10.1111/tpj.15404
dc.rightsArchived with thanks to The Plant Journal
dc.titleOpen chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression
dc.typeArticle
dc.contributor.departmentBiological and Environmental Science and Engineering (BESE) Division
dc.identifier.journalThe Plant Journal
dc.rights.embargodate2022-07-05
dc.eprint.versionPost-print
dc.contributor.institutionDipartimento di Scienze Agroalimentari Ambientali e Animali (DI4A) Udine I-33100 Italy
dc.contributor.institutionIstituto di Genomica Applicata Udine I-33100 Italy
dc.contributor.institutionScuola Superiore Sant'Anna Pisa Institute of Life Sciences Pisa 56127 Italy
dc.contributor.institutionIGA Technology Services Udine I-33100 Italy
dc.contributor.institutionScuola Internazionale Superiore di Studi Avanzati Trieste, Friuli-Venezia Giulia, IT
kaust.personCelii, Mirko
kaust.personFornasiero, Alice
refterms.dateFOA2021-07-06T11:18:25Z
dc.date.published-online2021-08-06
dc.date.published-print2021-09


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