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    Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression

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    tpj.15404.pdf
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    25.17Mb
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    PDF
    Description:
    Accepted manuscript
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    Type
    Article
    Authors
    Schwope, Rachel cc
    Magris, Gabriele cc
    Miculan, Mara
    Paparelli, Eleonora
    Celii, Mirko
    Tocci, Aldo
    Marroni, Fabio
    Fornasiero, Alice
    De Paoli, Emanuele
    Morgante, Michele cc
    KAUST Department
    Biological and Environmental Science and Engineering (BESE) Division
    Date
    2021-08-06
    Online Publication Date
    2021-08-06
    Print Publication Date
    2021-09
    Embargo End Date
    2022-07-05
    Permanent link to this record
    http://hdl.handle.net/10754/670027
    
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    Abstract
    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.15404
    Publisher
    Wiley
    Journal
    The Plant Journal
    DOI
    10.1111/tpj.15404
    Additional Links
    https://onlinelibrary.wiley.com/doi/10.1111/tpj.15404
    ae974a485f413a2113503eed53cd6c53
    10.1111/tpj.15404
    Scopus Count
    Collections
    Articles; Biological and Environmental Science and Engineering (BESE) Division

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