Fig. 1: Identification of human and mouse maternal igDMRs embedded within lineage-specific LITs.

a Venn diagram showing the intersection of known maternal igDMRs in mouse and human, along with the subset of igDMRs in each species embedded within a LIT. For each LIT-associated igDMR, the family of the LTR in which transcription initiates in oocytes is shown on the right. The presence of each LTR family in relevant mammalian lineages is color-coded as in Supplementary Fig. 1c. b List of imprinted genes/igDMRs associated with LITs. Maternal igDMRs unique to mouse (4) or human (17) are shown, along with DNAme levels (heat map) for each igDMR in syntenic regions in the gametes, blastocyst, placenta and adult tissues in human and mouse. The retrogene retro-Coro1c is absent in the syntenic human region on chromosome 6p22.3 (No orthologue). ZNF396 does not have a syntenic CGI in mice (No synteny). CT: cytotrophoblast; PBMC: peripheral blood mononuclear cell. c, d Screenshots of the human and mouse RHOBTB3/Rhobtb3 and SCIN/Scin loci, including locations of annotated genes, LTR retrotransposons, and regions of syntenic homology. The relevant CGI, igDMR, and upstream LTR in human are highlighted in green, blue, and red respectively. For each species, RNA-seq data from GVOs are shown, along with assembled transcripts, including LITs and their 5′ LTR exons (red) for the human genes. DNAme levels in gametes, blastocyst, placenta, and liver are shown across each locus in both species. For the human DNAme data, profiles from female 11-week primordial germs cells are also shown (11W PGC) and oocyte DNAme is from a mixture of GVO and MII oocytes. Details of all the datasets used in this study are presented in Supplementary Data 1.