Li, X. et al. Nat. Biotechnol. http://dx.doi.org/10.1038/nbt.3968 (2017).
To understand how genomes are regulated, one needs to have a comprehensive picture of all the proteins and RNAs that bind DNA. Li et al. sought to profile the RNA–chromatin interactome with a method they called GRID-seq (in situ global RNA interactions with DNA by deep sequencing). They first stabilized the RNAs on chromatin with a double-fixation step, and then they isolated the nuclei and digested the DNA before attaching a bivalent linker that binds the single-stranded RNA as well as the double-stranded DNA and can be purified via its biotin label. The authors apply GRID-seq to fly, mouse and human cells and draw a connectivity map of RNAs bound to active promoters and enhancers.
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Profiling chromatin-bound RNAs. Nat Methods 14, 1031 (2017). https://doi.org/10.1038/nmeth.4475
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DOI: https://doi.org/10.1038/nmeth.4475