| Experiment Id | GSE124215 | Name | Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues [RNA-Seq] |
| Experiment Type | RNA-Seq | Study Type | WT vs. Mutant |
| Source | GEO | Curation Date | 2022-12-09 |
| description | Background: Genomic imprinting is an epigenetic phenomenon that allows a subset of genes to be expressed mono-allelically based on parent-of-origin, and is typically regulated by differential DNA methylation inherited from gametes. Imprinting is pervasive in murine extra-embryonic lineages and, uniquely, the imprinting of several genes has been found to be conferred non-canonically through maternally-inherited repressive histone modification H3K27me3. However, the underlying regulatory mechanisms of non-canonical imprinting in post-implantation development remain unexplored. Results: We identify imprinted regions in post-implantation epiblast and extra-embryonic ectoderm (ExE) by assaying allelic histone modifications (H3K4me3, H3K36me3, H3K27me3), gene expression and DNA methylation in reciprocal C57BL/6 and CAST hybrid embryos. We distinguish loci with DNA methylation- dependent (canonical) and independent (non-canonical) imprinting by assaying hybrid embryos with ablated maternally-inherited DNA methylation. We find that non-canonical imprints are localized to endogenous retrovirus-K (ERVK) long terminal repeats (LTRs), which act as imprinted promoters specifically in extra-embryonic lineages. Transcribed ERVK LTRs are CpG-rich and located in close proximity to gene promoters, and imprinting status is determined by their epigenetic patterning in the oocyte. Finally, we show that oocyte-derived H3K27me3 associates with non-canonical imprints is not maintained beyond pre-implantation development, and is replaced by secondary imprinted DNA methylation on the maternal allele in post-implantation ExE, while being completely silenced by bi-allelic DNA methylation in epiblast. Conclusions: This study reveals distinct epigenetic mechanisms regulating non-canonical imprinted gene expression between embryonic and extra-embryonic development, and identifies an integral role for ERVK LTR repetitive elements. To evaluate the allelic regulation of histone modifications in the embryo, we assayed H3K4me3, H3K36me3 and H3K27me3 using ultra low-input ChIP-seq (Hanna et al. 2018) and post-bisulfite adaptor tagging (PBAT) in reciprocal hybrid (C57BL6/Babr x CAST/Ei) embryonic day (E) 6.5 epiblast and extra-embryonic ectoderm (ExE). We additionally profiled these epigenetic marks in E6.5 embryos derived from females with a double conditional knockout for Dnmt3a and Dnmt3b in oocytes (matDKO), driven by Zp3-cre. Consequently, these matDKO embryos will inherit no maternal DNA methylation, but are able to sufficiently establish DNA methylation post-fertilisation. Allelic gene expression was evaluated in E7.5 epiblast and ExE of all hybrid crosses. |
