2.5 dpc Uterus Chip-Seq of Kdm4a mice

Purpose: ChipSeq allows us to identify binding sites of target proteins of interest in the genome, helping create a global profile for the same. Kdm4a is a H3K9me3 histone demethylase that acts to prevent spurious accumulation of this repressive mark at H3K4me3 positive transcription start sites. To complement transcriptome data from Kdm4a mice, we performed Chip-Seq on 2.5dpc mouse uterus of 8-10 week old littermate control and Kdm4a knockout mice for Kdm4a, H3K9me3 and H3K4me3. This would help us check which of the target genes with changed gene expression was due to the direct change in histone lanscape in absence of Kdm4a. Overall design: Wildtype and Kdm4a knockout mice were set up for natural timed mating. At 2.5 dpc, we harvested pre-receptive uterus from mice after confirming the presence of embryos by flushing the oviduct. The uteri were subsequently cross-linked with 1% paraformaldehyde, homogenized mechanically and chromatin extracted and sheared by sonication. 1mg for Kdm4a and 100 uG for histone IPs were used as input. ChipSeq Libraries were then constructed using Illumina from eluates using 2ng of IP-ed DNA as input material. The profiles are compared between wildtype and Kdm4a knockout conditions.