Genome scanning by LTRs and emergence of new genes. (A) Transcription downstream from MuERV-L is apparent during ZGA, especially in two-cell embryos treated with aphidicolin (2Ca). Shown is a representative UCSC Genome Browser snapshot of an MuERV-L insertion expressed during ZGA. The gray horizontal lines represent five CPM. Stages: (GV) full-grown GV oocyte; (1C) one-cell (fertilized egg); (2C) two-cell; (4C) four-cell. (B) Cumulative display of transcription in 150-kb genomic flanks around the hundred MuERV-L elements most expressed during ZGA. (C–F) UCSC Genome Browser snapshots of selected genomic loci with mapped NGS data (Abe et al. 2015; Karlic et al. 2017). Gray dashed lines indicate CPMs. Positions of repetitive sequences (D–F) are indicated by gray rectangles in rows from the top: SINE, LINE, LTR, and DNA transposon elements. The conservation tracks (D,F) display homology with rat (top), rabbit, human, dog, and cow genomes. (C) A lncRNA gene with MuERV-L-derived 5′ exons and downstream exons from the genomic flank. (D) A new lncRNA gene formed by MaLR LTR insertions. The promoter and exon 1 come from an MTA solo LTR, exon 2 through exonization of an ORR1F solo LTR. (E) Examples of antisense pseudogene sequence rewiring yielding a lncRNA substrate for endosiRNAs where an MTB solo LTR was inserted into a locus already containing a pseudogene (Nme3) or a pseudogene (Dlgap5) was inserted into a locus already containing an MTA. (F) An example of a sense pseudogene (Speer4E pseudogene) rewiring yielding a CPAT positive transcript.
