Paternal reprogramming-escape histone H3K4me3 marks located within promoters of RNA splicing genes

Abstract Motivation Exposure of mouse embryos to atrazine decreased histone tri-methylation at lysine 4 (H3K4me3) and increased expression of alternatively spliced RNA in the third generation. Specificity protein (SP) family motifs were enriched in the promoters of genes encoding differentially expressed alternative transcripts. Results H3K4me3 chromatin immunoprecipitation sequencing (ChIP-seq) of mouse sperm, preimplantation embryo development and male gonad primordial germ cells (PGCs) were analysed to identify the paternal reprogramming-escape H3K4me3 regions (RERs). In total, 251 RERs selected harbour H3K4me3 marks in sperm, with signals occurring in the paternal genome during early development and in male gonad PGCs, and 179 genes had RERs within 1 kb of transcription start sites (TSSs). These genes were significantly enriched in the gene ontology term ‘RNA splicing’, and SP1/SP2/SP3 motifs were enriched in RER-associated H3K4me3 peaks. Overall, the H3K4me3 marks within TSSs of RNA splicing genes survived two rounds of the epigenetic reprogramming process. Supplementary information Supplementary data are available at Bioinformatics online.