ArticleThe Plant journal : for cell and molecular biology2021
Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression.
Article in The Plant journal : for cell and molecular biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 30 citations in OpenAlex.
- Multi-omics revolution to promote plant breeding efficiency.Frontiers in plant science · 2022Pooled it
- A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation.Plant physiology · 2026Article
- Dissecting gene regulatory networks driving grape berry ripening using comparative systems biology across nonclimacteric fleshy fruits: the NAC-centered hierarchy revisited.Horticulture research · 2026Review
- Domestication shaped the chromatin landscape of grain amaranth.Nature communications · 2025Article
- Responding to Stress: Diversity and Resilience of Grapevine in a Changing Climate Under the Perspective of Omics Research.International journal of molecular sciences · 2025Review
- Single-cell multi-modal chromatin profiles revealing epigenetic regulations of cells in hepatocellular carcinoma.Clinical and translational medicine · 2024Article
- Structural variant landscapes reveal convergent signatures of evolution in sheep and goats.Genome biology · 2024Article
- Multiome in the Same Cell Reveals the Impact of Osmotic Stress on Arabidopsis Root Tip Development at Single-Cell Level.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm.Nature communications · 2024Article
- Transcriptional and epigenetic decoding of the microglial aging process.Nature aging · 2023Article
- Unlocking the Secret to Higher Crop Yield: The Potential for Histone Modifications.Plants (Basel, Switzerland) · 2023Review
- Integrating ATAC-seq and RNA-seq Reveals the Dynamics of Chromatin Accessibility and Gene Expression in Apple Response to Drought.International journal of molecular sciences · 2022Article
- Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (International journal of molecular sciences · 2022Article
- Population-specific, recent positive selection signatures in cultivated Cucumis sativus L. (cucumber).G3 (Bethesda, Md.) · 2022Article
- Review
- Integrated metabolic, transcriptomic and chromatin accessibility analyses provide novel insights into the competition for anthocyanins and flavonols biosynthesis during fruit ripening in red apple.Frontiers in plant science · 2022Article
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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 > 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.
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