Epigenetics refers to the mechanisms that regulate gene expression at the transcriptional and post-transcriptional level, often in response to signals from the environment. Epigenetic pathways are involved in a myriad of complex cellular processes that have far-reaching impacts on organisms and populations. Chromatin, small RNAs, and their spatial organisation into membraneless condensates (often termed “granules”) are all involved in epigenetic processes, however the interplay between them is still poorly understood.
From a pulldown experiment designed to search for readers of H3K23me3, we have identified two genes of interest in Caenorhabditis elegans that we believe are involved in germline epigenetic processes. Based off their structural features as observed using AlphaFold predictions, we have named these previously uncharacterised genes lotr-2 and tdrd-3. We are investigating how knockouts of these genes affect animals at the epigenomic, transcriptomic and phenotypic levels to gain an understanding of their overall function.
lotr-2 encodes for a LOTUS and Tudor domain-containing protein. Mutants display perturbations in germ granule formation and disruption in genetic pathways related to somatic development. tdrd-3 is an ortholog of the mammalian Tdrd3, which encodes for another Tudor domain-containing protein with large intrinsically disordered regions (IDRs). We have observed endogenously tagged TDRD-3 localising to cytoplasmic stress granules in the germline. RNAseq of tdrd-3 mutants reveals strong downregulation of sperm-related genes, however these mutants do not display an obvious fertility defect in standard broodsize assays.
Both lotr-2 and tdrd-3 were initially identified by us in a screen for chromatin interactors, however we have also observed evidence for them functioning outside the nucleus in perinuclear or cytoplasmic granules, which are often involved in post-transcriptional regulation. Through our ongoing work to characterise these genes, we are contributing to detangling the complex network of interactions between various molecular signals which coordinate epigenetic responses.