Fig. 7. Activity of LTR elements during bovine preimplantation development.

a Open chromatin enrichment of LTR elements with increased accessibility in 4-cell, 8-cell, and/or morula-stage embryos, and VST expression of the same LTR elements; three replicates per stage. b ATAC-seq and RNA-seq read coverage at a highly expressed ERV1-2 repeat sequence. ATAC-seq tracks show coverage from 30 million reads per library; RNA-seq tracks show combined coverage from three replicates. TF motifs predicted from JASPAR binding motifs MA0039.3 (KLF4) and MA0712.1 (OTX2), respectively. c Average normalized ATAC-seq (FPKM) and (d) RNA-seq signal (RPKM) at MLT1A0 repeats overlapped by 8-cell intergenic open chromatin harboring DUXA motifs, predicted based on JASPAR motif MA0468.1. e Co-option of an accessible MLT1A0 element with a DUXA binding motif as an alternative promoter upstream of the C1D locus. RNA-seq data from Graf et al.³². Source data are provided as a Source Data file.