Fig. 1

LTR12/ERV9 elements are expressed in early embryonic development and contribute new TSS to genes expressed before and after ZGA. A Number of detected LTR-driven transpochimeric gene transcripts (TcGTs) in a de novo transcriptome assembly of human embryonic development RNA-seq [88]. Number represents the transcripts found (TSS overlapping with LTR, minimum 1 read spanning junction), heatmap color represents -log10(padj). The p-value was computed through a hypergeometric test and adjusted for multiple testing. B Number of detected LTR-driven TcGTs in a de novo transcriptome assembly of a subset of tissues from the GTex dataset [50], method same as in (A). C Z-score clusters of expression of all detected LTR12C loci over human embryonic development stages [88]. 2 clusters were formed. Red lines = LTR12C loci with at least one detected TcGT at any stage of development in (A). Grey lines = LTR12C loci without known TcGTs. Thick black line: mean expression value across replicates for each sample. D Transcription factors from ENCODE with ChIP-seq peaks overlapping LTR12C loci with minimum overlap of 1 bp. *: p<0.05, **: p<0.01, ***: p<0.001, Fisher hypergeometric test, adjusted for multiple testing. E Multiple sequence alignment of all LTR12 family members (Aliview colors for DNA bases, grey = gap) with conserved NFY motif highlighted