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

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.

Allele‐specific expression and chromatin accessibility contribute to heterosis in tea plants (Camellia sinensis)

“…Although ATAC-seq technology has demonstrated its power in resolving ACRs and associated TF binding sites (Lu et al, 2019;Reynoso et al, 2019;Sijacic et al, 2018), its role in plant heterosis formation remains unclear. Consistent with previous studies in other plants (Dai et al, 2022;Schwope et al, 2021), chromatin accessibility was found to be positively correlated with gene expression in tea plants. Interestingly, the total number and length of ACRs in tea hybrids were markedly larger than those in both parents, which may confer stronger transcriptional activity of the genes in tea hybrids.…”

“…The number of ACRs and the total sequence length of the hybrids were significantly larger than those of the parents, indicating more robust chromatin accessibility of the hybrid genomes. By comparing the ATAC-seq data of multiple plant genomes reported previously (Lu et al, 2019;Schwope et al, 2021;Zhou et al, 2021), the genome proportion of ACRs in tea plants was much lower than that of plants with smaller genomes such as Spirodela polyrhiza, Arabidopsis thaliana, Eutrema salsugineum and Vitis vinifera, but higher than that of Hordeum vulgare (Figure 4b). We further examined the distribution of ACRs in the tea plant genome and classified them as gACRs (genic ACRs in exons, introns and UTRs), pACRs (proximal ACRs within 2 kb upstream of the TSS and 2 kb downstream of the TTS) and dACRs (distal ACRs in the intergenic).…”

Integrating ATAC-seq and RNA-seq Reveals the Dynamics of Chromatin Accessibility and Gene Expression in Apple Response to Drought

“…This approach has high sensitivity and specificity and requires few cells. ATAC-seq has been widely applied in many plants to predict cis-acting elements and chromatin accessibility [ 16 , 17 , 18 ]. Additionally, ATAC-seq has been used to assess changes in chromatin accessibility during stress responses in different plants.…”

Population-specific, recent positive selection signatures in cultivated Cucumis sativus L. (cucumber)

“…2 ). In the East Asian population, we found 7 SNPs leading to the change of amino acids and 72 SNPs localized at potential promoters of genes (defined as the 2-kb region upstream of the transcription start site) ( Schwope et al 2021 ). In Eurasian, 19 missense variants and 761 SNPs located in promoter regions were observed.…”