H3K4me3 and H3K9me3 histone modification profiles of uterine stromal cells from young and aged mouse females

Epigenetic profiling of uterine stromal cells (UtSCs) was performed for the active and repressive histone modifications H3K4me3 and H3K9me3, respectively. We find that UtSCs from aged females are epigenetically distinct, as determined by genomic enrichment profiling for H3K4me3 and H3K9me3, respectively. We find that many pregnancy hormone-inducible genes exhibit a profound lack of promoter-associated H3K4me3 in aged UtSCs, implying that a significant enrichment of active histone marks prior to gene stimulation is required to enable the elicitation of a rapid transcriptional response. Overall design: Uterine stromal cells (UtSCs) were isolated from C57BL/6Babr females aged 8-12 weeks (“Young”) and 43-54 weeks (“Aged”) at E3.5 of pregnancy. Up until this point, all females were virgin. 200,00 UtSCs were processed for chromatin immunoprecipitation (ChIP) with antibodies against histone modifications H3K4me3 and H3K9me3. 10% of chromatin prior to ChIP was kept as Input. Input and ChIP DNA was used for library build with the NEBNext Ultra II DNA library prep kit (Illumina E7645). Indexed libraries were pooled and sequenced on an Illumina HiSeq2500 sequencer, using a 50bp paired-end protocol. Raw fastq data were mapped to the Mus musculus GRCm38 genome assembly using Bowtie2.