Fig. 3.

LTR-initiated transcription impacts species-specific gene transcription and gene body DNAme in oocytes. a Pearson correlation between mouse, rat, and human oocyte transcript levels over 11,186 syntenic Ensembl annotated genes. ^aC57BL/6, ^bCast/Ei, ^cSprague Dawley, ^dWistar Han. b Number of annotated Ensembl genes with one or more overlapping LIT(s). s: sense overlap, splicing into a genic exon and >10% contribution to all of the gene’s isoforms, as antisense overlap. c Comparison of gene transcription between mouse and rat GVOs (gray). Highlighted are genes with an LTR-driven isoform that contributes to at least 10% of the gene transcripts in mouse (red), rat (blue), or in both species (black). d Comparison of gene transcription between mouse and human GVOs (gray). Highlighted are genes with an LTR-driven isoform that contributes to at least 10% of the gene transcripts in mouse (red), human (blue), or in both species (black). e Screenshot of the Bmp5/BMP5 locus. In mouse oocytes, transcription initiates from an intragenic MTA element, and gene body H3K36me3 and DNAme are observed only downstream of the MTA. Note that the ortholog is not transcribed in rat or human oocytes. f Screenshot of the Sirt2/SIRT2 locus. In rat oocytes, transcription initiates in an upstream RLTR31B2 element, and DNAme downstream of this alternative promoter encompasses the canonical Sirt2 promoter. In both mouse and human oocytes, the orthologous gene is transcribed from the canonical (hypomethylated) promoter. g Screenshot of the Zfp90/ZFP90 locus. A human-specific isoform initiates in an LTR12C upstream of the canonical CGI promoter, which is hypermethylated exclusively in human oocytes. Zfp90 is transcribed from the canonical TSS in mouse and rat oocytes. h Screenshot of the Th locus showing an unannotated isoform that initiates in an RMER19A LTR- upstream of the canonical promoter exclusively in mouse and rat oocytes. DNAme extends downstream of the RMER19A TSS in both species, coincident with H3K36me3 in mouse, and encompasses the annotated Th TSS. Mouse and human WGBS datasets analyzed from refs. ^12,16 and human RNA-seq data from ref. ¹⁷