Fig. 4: Phylogenetic relationship between LTR, LIT, and maternal DNAme at mouse-specific igDMRs.

a The presence or absence of a LIT overlapping the CGI at Cdh15, Slc38a4, and Impact are indicated with closed boxes and dashes, respectively. X: species in which the LTR is absent. b Screenshots of Slc38a4/SLC38A4 and Impact/IMPACT loci showing GVO RNA-seq data (and the associated de novo Cufflinks transcript assembly), DNAme profiles in NGO, GVO and sperm, and H3K4me3, PolII, and H3K36me3 ChIP-seq tracks for mouse GVO. Highlighted are the upstream initiating LTR (red), CGI promoter (green), and mouse igDMR (blue). The syntenic region in human is also shown, including GVO RNA-seq and DNAme from oocytes and sperm. A 5′ RACE gene model initiating within the MTC element at the Impact locus is included in the right panel¹⁴. c Scatter plot of oocyte H3K4me3 and transcription levels for all mouse MT2A elements, with those acting as transcription start sites in oocytes highlighted in blue. The remaining transcribed elements reflect exonization events. The MT2A element initiating the LIT at Slc38a4 (red) is amongst the most active elements of this family. d Histogram of the distribution of mouse MT2A LTRs as a function of divergence from the consensus sequence. The LTR driving expression at Slc38a4 is amongst the most highly diverged.