Fig. 5: Cell-type-specific RNA–chromatin interaction patterns. | Nature Communications

Fig. 5: Cell-type-specific RNA–chromatin interaction patterns.

From: RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

Fig. 5: Cell-type-specific RNA–chromatin interaction patterns.The alternative text for this image may have been generated using AI.

a For each gene, the Jaccard distance between the genome-wide RNA–DNA binding profiles in mESCs and mOPCs is compared with the difference in capture rate (proxy for gene expression) between the two cell types. b Distribution of the log2 ratios of RADICL-seq mESC to mOPC DNA normalized tag counts for targeted gene promoter regions, which are defined as ±2 kb around the TSS. Cell-type-specific marker gene positions are highlighted for both mESCs (red) and mOPCs (blue). Counts were normalized by library size. c RADICL-seq counts of unique genomic targets per interacting RNA in mESCs vs. mOPCs. d, e Circos plots depicting Neat1 genomic interactions in mESCs and mOPCs, respectively. f, g Circos plots depicting Fgfr2 genomic interactions in mESCs and mOPCs, respectively. Each line represents the interaction between the genic transcript and the contacted genomic bin, while its color indicates log2 of the RADICL-seq count. The chromosome of origin of the RNA under investigation is shown enlarged (gray shading) on the left portion of each circos plot. All panels were generated using significant total datasets.

Back to article page