Fig. 4: Characterization of chromatin-associated RNAs in the 3D genome architecture. | Nature Communications

Fig. 4: Characterization of chromatin-associated RNAs in the 3D genome architecture.

From: Simultaneous profiling of chromatin-associated RNA at targeted DNA loci and RNA-RNA Interactions through TaDRIM-seq

Fig. 4

a Heatmap showing the top twenty chromatin-associated RNAs with the high connection frequency with genome, are widely recruited to multigenomic loci across the whole genome at 1 Mb resolution in CTCF TaDRIM-seq. b Circos plots of RNA-RNA interactions mediated by MALAT1 and NEAT1 lncRNA in TaDRIM-seq. Each line represents an RNA-RNA interaction. The outer circles show different chromosomes, and the inner circles indicate high-frequency contacts. c MALAT1 is colocalized with NEAT1, SMYD3, and GSE1 by RNA FISH in K562 cells. RNA FISH analysis also showed the co-localization of NEAT1, SMYD3, and GSE1. Scale bar, 2 μm. MALAT1/ NEAT1: n = 47 cells were examined; MALAT1/ SMYD3: n = 41 cells were examined; MALAT1/ GSE1: n = 42 cells were examined. d Model for 3D chromatin structure based on CTCF ChIA-PET and CTCF TaDRIM-seq data. Model 1: the RNA-DNA interactions of DNA ends (Basal) that are not involved in chromatin interactions. Model 2: RNA-DNA interactions of DNA ends (Anchor) that participate in the chromatin loop. Based on TaDRIM-seq technology, global RNA-RNA spatial interactions can be determined. e Boxplot showing the expression levels of basal genes from model 1 (n = 3927) and anchor genes from model 2 (n = 6064) in CTCF TaDRIM-seq, as well as intensities of H3K4me3 and RNAPII peaks in basal and anchor genes. H3K4me3 marker peaks are associated with basal genes (n = 15,358) and anchor genes (n = 7383), while RNAPII marker peaks are associated with basal genes (n = 5160) and anchor genes (n = 8743). In the box plot, the center line indicates the median, and the box represents the interquartile range (IQR). The whiskers extend to 1.5 times the IQR. P-values were evaluated using a one-sided Wilcoxon rank sum test. f Histogram showing the number of RNA-DNA interactions in models 1 and 2. Left: all RNA-DNA interactions in CTCF TaDRIM-seq. Right: MALAT1-chromatin interactions in CTCF TaDRIM-seq. g Screenshot showing genome-wide chromatin interactions involving MALAT1. h Connectivity network of RNA-chromatin interactions on chromosome 15 in K562 cells. Gray line: RNA-DNA interaction. DNA (green dots) belongs to Model 1, and DNA (blue dots) belongs to Model 2. RNA 1 (red-dot) is engaged in intermolecular RNA-RNA interactions, and RNA 2 (yellow-dot) is not involved in intermolecular RNA-RNA interactions. Source data are provided as a Source Data file.

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