Fig. 2
Gene expression and DNA methylation along the porcine RB1 and KBTBD6 loci. A The 65-kb region containing the RB1 locus between 19.275 Mb (19,275,000) and 19.34 Mb (19,340,000) based on NCBI RefSeq annotation. RNA-seq read coverages of the RB1 transcripts in PA and CN embryos are presented in values of TPM. Mean methylation ratios based on WGBS are followed by mean methylation differences (PA-CN). B A close view of the 2nd intron area of the RB1 gene and methylation status. C The 192-kb region containing the KBTBD6 locus between 25.59 Mb (25,590,000) and 25.782 Mb (25,782,000). RNA-seq read coverages of KBTBD6 and surrounding transcripts in TPM, and mean methylation ratios based on WGBS. D and E Zoomed-in views of promoter regions of the KBTBD7 and KBTBD6 genes. R, DMR (FDR < 0.05) in red. Also, the DMR (hypermethylated in PA) is overlaid with red histogram lines in PA-CN. Red vertical bars in the ideogram, chromosomal locations; I, CpG island; GC%, GC content; black arrows, transcriptional direction; brown boxes, protein-coding transcripts (tall, translated region; short, untranslated region); purple boxes, noncoding transcripts; PA1–2, individual PA embryos; CN1–2, individual CN embryos; PA, mean methylation ratio for PA embryos; CN, mean methylation ratio for CN embryos