Fig. 1: RADICL-seq method for the identification of RNA–chromatin interactions. | Nature Communications

Fig. 1: RADICL-seq method for the identification of RNA–chromatin interactions.

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

Fig. 1

a Schematic representation of the RADICL-seq protocol. Top: sequence of enzymatic reactions occurring in fixed nuclei after partial lysis of the nuclear membrane. The adduct formed by genomic DNA (black), RNA (red), and proteins (blue circles) is subjected to controlled DNase I digestion and chromatin preparation. After RNase H digestion, an adapter (dark blue) containing an internally biotinylated residue (black dot) bridges the RNA and DNA molecules that lie in close proximity. Bottom: sequence of enzymatic reactions performed in solution. After reversal of crosslinks, the RNA–DNA chimera is converted into a fully double-stranded DNA (dsDNA) molecule and digested by the EcoP15I enzyme to a designated length (adpr, adapter). After ligation of the sequencing linkers (yellow) and biotin pull-down, the library is PCR amplified and high-throughput sequenced. b Reproducibility of the RNA–DNA interaction frequencies across replicates, assessed by counting the occurrences of genic transcripts and 25-kb genomic bin pairs. c RNA and d DNA tag origins. The inner pie charts represent a broader classification into intergenic and genic (annotated genes), while the outer circles show a finer classification of the genic portion. e, f Comparison between (e) nuclear and (f) cytosolic RNA-seq tag counts and RADICL-seq genic transcript counts. The former are normalized to tags per million (TPM), while the latter are normalized to reads per kilobase (RPK). The linear regression lines are shown in red. g Density of the normalized counts of DNA reads detected by RADICL-seq around ATAC-seq (blue), DHS-seq (green), and H3K9me3 ChIP-seq (red) peaks; dashed lines represent the density profiles of aggregated signal from random genomic reads equal in number and size to the real peaks.

Back to article page