New RNA mapping technique shows how RNA interacts with chromatin in the genome

A group led by scientists from the RIKEN Center for Integrative Medical Sciences (IMS) in Japan have developed a new method, RADICL-seq, which allows scientists to better understand how RNA interacts with the genome through chromatin—the structure in which the genome is organized.

There have been many changes in our understanding of the function of RNA in biology. Decades ago, it was generally believed that RNA functioned merely as an intermediary for the translation of DNA into proteins. However, the decoding of the human genome in the early 2000s led to the realization that a large amount of RNA—known as “junk” at the time—did not code proteins. Subsequent work on large-scale genomic projects such as ENCODE and RIKEN-led FANTOM found that there were large numbers of long non-protein coding RNAs in the mammalian genome, which interact with the DNA. Many of these RNAs are found in the cell nucleus, and are attached to chromatin, the structure used to tightly fold the DNA. However, it is still not clear exactly what RNAs interact with which regions of the DNA in different cells.

To achieve a better understanding of these interactions, and to determine whether RNA is actually a part of the chromatin structure, the scientists developed a new technology, which they called RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), which maps genome-wide RNA-chromatin interactions in intact nuclei. This technology, published in Nature Communications, allows researchers to identify distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and emphasizes the role of transcription in the establishment of chromatin structure.

To test the validity of the method, the scientists looked at two non-coding RNAs which are known to be expressed preferentially in certain cell types. The first, known at NEAT1, may be involved in the structure as it is associated with a mysterious structure known as paraspeckles found in mammalian cell nuclei. The second, Fgfr2, is involved in embryonic development and tissue repair, especially for bone and blood vessels. They found that in mouse embryonic stem cells—an early type of cell—that NEAT1 acts almost exclusively on genomic regions of chromosome 19, from which it itself derives from, whereas in oligodendrocyte progenitor cells—a later type of developmental cell that can differentiate into brain cells—it interacts with a broad range of genomic regions on other chromosomes as well. Fgfr2, by contrast, mostly interacts with genomic regions on its own chromosome.

RADICL-seq method for the identification of RNA–chromatin interactions

rna-seq

a Schematic representation of the RADICL-seq protocol. 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. ef Comparison between (e) nuclear and (f) cytosolic RNA-seq tag counts and RADICL-seq genic transcript counts. 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.

“This study is a first step toward understanding how the interplay between RNA and chromatin ensures proper genome function. Our data indicate that RNAs may exert more widespread effects on gene regulation and chromatin organization than previously thought,” says Alessandro Bonetti, one of the corresponding authors of the study.

“The broad, genome-wide applications of this technology will help us to understand the fundamental role of non-coding RNA as a regulator of genome activity, which could lead to future applications and therapies” says Piero Carninci, one of the senior authors of the study.

Bonetti et al. (2020) RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions. Nat Commun [Epub ahead of print]. [article]

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