DNA-RNA immunoprecipitation followed by DNA sequencing (DRIP-seq)

To understand the role of the histone H3K9 methyltransferase, Clr4, essential for heterochromatin assembly on DNA-RNA hybrid formation, we prepared DNA-RNA hybrids from Schizosaccharomyces pombe of the wild-type and the clr4 deletion strains using S9.6 antibodies, which specifically binds DNA:RNA hybrids. We carried out the next generation short-read sequencing of DNA-RNA hybrids without reverse transcription of RNA strands.