The trimethylation of Lys 36 residue on H3 (H3K36me3) is a signature histone mark for gene expression in the C.elegans germline. Its genome distribution is mediated specifically by MES-4 and MET-1 histone methyltransferases. This modification regulates several events related to transcription, including promoting splicing, suppressing cryptic transcription initiation, and suppressing DNA damage. H3K36me3 is likely linked to these downstream pathways by epigenetic "readers", proteins that bind a specific epigenetic mark and regulate downstream pathways in response. However, H3K36me3 reader proteins in the C.elegans germline are poorly characterized. We explored the possibility that Oocyte-Excluded Factor 1 (OEF-1), a germline-specific factor discovered in our lab (McManus and Reinke, 2017), might function as a reader of H3K36me3. OEF-1 has a role in germline progression, binds preferentially to autosomal genes, and co-localizes with H3K36me3. To study the functional relationship between OEF-1 and H3K36me3, we developed a computational pipeline comprehensive of ChIP-seq and RNA-seq experiments, which we then analyzed. ChIP-seq data for H3K27me3 and H3K36me3 in
oef-1 mutants and wild-type adults were obtained from purified germ nuclei, and binding profiles were then further analyzed. RNA-seq was performed from dissected gonads from
oef-1 mutant and wild-type young adults and analyzed for gene expression and splicing differences. From the ChIP-seq data, we found a strong correlation between OEF-1 and H3K36me3 binding profiles. From the RNA-seq data, we found that, even though the loss of OEF-1 has minimal effect on transcript abundance, it greatly increases the frequency of retained introns predominantly at the level of autosomal germline-specific genes. Thus, our data to date implicates OEF-1 in a role in promoting splicing fidelity in the C.elegans germ line, potentially by its association with H3K36me3 at germline-expressed genes.