Fig. 3

Oocyte methylome and correlation with transcriptome. a Visualization of the DNAme landscapes of FGOs and sperm using 2-kbp running genomic windows with a 1-kbp step. Quantification is absolute percentage of DNAme, with the x-axis set at 50 % methylation. b Distribution of 1-kbp genomic windows in FGOs and sperm according to their percentage of DNAme. c Distribution of genomic CpGs according to the following features: HyperDs and HypoDs, TSSs and CGIs, regions with intermediate methylation (25–75 %), regions with >50 % DNAme in DNMT knock-outs (Dnmts KO) and NGOs, and none of the above (Other). d Violin plot representation of DNAme of CpGs in FGOs in the entire genome (All) and in HyperDs and HypoDs (open circles represent the mean, dark circles the median, and black line the 1.5 × interquartile range). e Boxplot representation of the distribution of length, CpG density and GC content within HyperDs and HypoDs (lines represent the median and crosses the mean). f HyperDs ordered according to their increasing overlap with transcription in oocytes, based on the expressed reference genes (Ref. FPKM > 0.001), our transcriptome assembly, our assembly combined with read contigs, our assembly/contig combined with transcribed regions of partial DNAme (>25 %) in DNMT KOs and NGOs. g HypoDs ordered according to their increasing overlap with transcription in oocytes, based on the expressed reference genes (Ref. FPKM > 0.001), our transcriptome assembly, our assembly excluding genes with FPKM ≤ 0.5 alone or including also alternative TSSs. h Genomic location of CGIs and igDMRs in relation to expressed genes in the reference annotation and our oocyte transcriptome assembly