RADICL-Seq Maps RNA–Chromatin Interactions

Scientists have developed a new method that allows scientists to better understand how RNA interacts with chromatin—the organized complex of proteins and the genome. The method, which the researchers called RADICL-seq, was presented in a paper that was published yesterday in Nature Communications.

“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 senior author Piero Carninci of RIKEN.

Previous work has found that there are large numbers of long non-protein coding RNAs in the mammalian genome that interact with the DNA. Many of these RNAs are found in the cell nucleus and are attached to chromatin. However, it has still not been 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: RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq). RADICL-seq maps genome-wide RNA–chromatin interactions in intact nuclei, allowing researchers to identify distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and it 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 that are expressed preferentially in certain cell types. The first, NEAT1, is associated with a mysterious structure known as paraspeckles that is 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, NEAT1 acts almost exclusively on genomic regions of chromosome 19, from which it itself derives, whereas in oligodendrocyte progenitor 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.

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