Fig. 3: Transcription is closely associated with the local presence of a triangle chromatin domain. | Nature Communications

Fig. 3: Transcription is closely associated with the local presence of a triangle chromatin domain.

From: Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL

Fig. 3: Transcription is closely associated with the local presence of a triangle chromatin domain.The alternative text for this image may have been generated using AI.

a Asymmetrical heatmap showing chromatin interactions in Hi–C (left lower corner) and Micro-C-XL at 200-bp resolution (upper right corner). Tracks showing PCG annotations, TE annotations, chromatin states, multiple epigenetic modifications (e.g., H3K14ac, H3K36me3, H3K4me3, H3K9me2, H3K27me1, and H3K27me3), Pol II occupancy, and RNA expression are presented under chromatin interactions heatmap. Vertical dashed lines are displayed on maps and tracks to facilitate chromatin organization, gene transcription, and gene arrangement analyses. Three gene arrangements, including divergent (blue arrow), convergent (red arrow), and tandem (black arrow) gene pairs, are presented at the top of the map. b Similar to a, with the addition of tRNA gene annotations and Pol III occupancy data. One dashed line was added, showing the location of a tRNA gene. c Aggregated analysis of chromatin interactions over three types of gene arrangements. Ideograms showing arrangements are presented at the top of each heatmap. d Aggregated analysis of chromatin interactions using transcription start sites (TSSs) from nine types of genes with increasing expression levels (greater expression is indicated by greater red intensity, except in first class [i.e., silenced genes]). e Aggregated analysis of chromatin interactions using gene bodies from nine types of genes with increased expression levels, using ideograms presented in (d). Enrichment scores are relative to a random background.

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