Set1 targets gene with essential identity and tumor suppressing functions in planarian stem cells. Mnase-ChIP was used to validate a wide histone H3K4me3 peak width signature.

Previous publications have reported the significance of a wide histone H3K4me3 signature at essential genes in many organisms and cell types. Most of these published datasets were produced using cross-linking ChIP-seq, in which the chromatin was chemically cross-linked using formadehyde and then mechanically sheared with sonication. Here we use Mnase-ChIP, a non-cross-linking method that fractionates chromatin using the enzyme micrococcal nuclease, to show that this wide H3K4me3 signature is not a technical artifact of cross-linking ChIP. Overall design: ChIP-seq was done using an Mnase-based method of chromatin fractionation prior to IP with an antibody to histone H3 K4me3. The experiment was performed using isolated S.mediterannea stem cells (X1 cells) mixed with Drosophila S2 cells; 800K planarian X1 cells were mixed with 9.8M S2 cells, processed for Mnase-ChIP, and the ChIP DNA sequenced with their corresponding input DNA.