Chrom-seq Identifies RNAs at Chromatin Marks [Chrom-seq]

Chromatin marks are associated with transcriptional regulatory activities. Here, We developed a method termed Chrom-seq to efficiently capture RNAs associated with various chromatin marks in living cells. Chrom-seq jointly applies highly specific chromatin-mark reader with APEX2 which catalyzes the oxidation of biotin-aniline to label the adjacent RNAs for isolation by streptavidin-coated beads. Using the readers of mCBX7/dPC, mCBX1 and mTAF3, we detected RNA species significantly associated with H3K27me3, H3K9me3 and H3K4me3, respectively. Chrom-seq provides an antibody-free approach to systematically map RNAs at chromatin marks with potential regulatory roles in different epigenetic events. Overall design: Chrom-seq leverages highly specific reader protein to bring the engineered ascorbate peroxidase APEX2 close to the modified chromatin. Upon exposure to H2O2, APEX2 catalyzes oxidation of surrounding biotin-aniline (Btn-An) which then reacts with guanosines in adjacent RNA molecules to form a covalent adduct, facilitating subsequent purification of tagged RNAs with streptavidin-conjugated beads for identification by sequencing.