The study of RNA molecules in our cells has revealed much about how genes are regulated and how different parts of the genome communicate with each other. Eukaryotic genomes (the DNA found in the nucleus of cells) are transcribed into many different types of RNA, which play crucial roles in controlling gene expression. Some of these RNAs are located near the DNA they came from, while others travel across the genome, influencing different regions. These RNAs that are associated with chromatin (the material DNA is made of) are called chromatin-associated RNAs, or caRNAs. While scientists have uncovered some functions for these caRNAs in gene regulation and genome organization, studying them has been a challenge due to their complexity.

In a recent breakthrough, researchers at the Huazhong Agricultural University have developed a new technique called TaDRIM-seq (Targeted DNA-RNA Interaction Mapping sequencing), which allows scientists to explore caRNAs more effectively. This method uses a clever combination of protein tagging and proximity ligation (a way to bring molecules closer together so they can be studied) to track caRNAs across different regions of the genome. One of the key advantages of TaDRIM-seq is that it requires fewer cells to gather the same amount of data compared to older methods, and it is faster and easier to use.

The TaDRIM-seq technique

a TaDRIM-seq schematic. b Genome browser tracks showing the distribution of DNA from H3K4me3 and CTCF TaDRIM-seq data in K562 cells; H3K4me3 TaDRIM-seq in 293T cells and Arabidopsis; and H3, H3K4me3, and H3K27me3 TaDRIM-seq data in rice. c Strand orientation of TaDRIM-seq sense and antisense RNA. Left: CTCF TaDRIM-seq RNA. Rigth: H3K9ac TaDRIM-seq RNA. d Number of RNAs identified on CTCF-marked genomic loci using TaDRIM-seq, RedChIP, and fRIP-seq in K562 cells. e Scatterplot showing RNA-DNA interactions by CTCF TaDRIM-seq compared with CTCF RedChIP in K562. Pearson correlation coefficient: r = 0.82. f Examples of RNA-chromatin interactions within the region chr1: 5,811,994-12,441,569, located within the broader region chr1: 1-19,209,288, were identified using CTCF TaDRIM-seq and RedChIP data. Each line represents an RNA-DNA interaction that is divided into RNA ends and DNA ends. Bottom: scatterplot showing the RNA-DNA interactions mediated by protein-coding RNA from RERE gene in chr1: 8,297,864–9,467,625. Source data are provided as a Source Data file.

TaDRIM-seq has shown remarkable results in both plant and mammalian cells. In their experiments, the researchers discovered that caRNAs are highly concentrated at specific DNA regions known to play a role in shaping the genome’s 3D structure, like chromatin loops. They also found that RNA interactions within the genome change throughout the day in rice plants, shedding light on how the timing of these interactions might affect gene regulation.

This technique opens up new opportunities for understanding how the genome is organized, how genes are turned on and off, and how RNA and DNA work together to shape the function of our cells. By revealing these previously hidden RNA-DNA and RNA-RNA interactions, TaDRIM-seq could lead to a better understanding of disease mechanisms and new strategies for genetic research.

Availability – The TaDRIM-seq RNA-RNA interaction analysis code is now available on GitHub (https://github.com/304243504/HiR)