Chrom-seq Identifies RNAs at Chromatin Marks [ChIP-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: To validate the function of lncRNA identified by chrom-seq, antisense oligonucleotides (ASOs) including ASOSETD5-AS1, ASOLINC00641 and ASO LINC00662 were transfected into HEK293T cells grown on the 6-well plates, respectively. ASO_NC was used for the negative control. Next, ChIP-seq of H3K9me3 and H3K27me3 was performed in cells depleted of these lncRNAs using antisense oligos (ASO).