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Table 2 Overabundance of methylated repeats upstream of the transcription starting site of differentially and non-differentially methylated genes compared to non-methylated genes in Chrysemys picta hatchlings

From: MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination

Number (#) and percentage (%) of methylated repeats Number of gene bodies with methylated repeats at three distances of start codon
1 kb 5 kb 10 kb
Among all 17,646 methylated genes 16,791 (95.1%) 17,030 (96.5%) 17,202 (97.5%)
Among all 433 non-methylated genes 29 (6.7%) 90 (20.8%) 161 (37%)
Among the 2086 male-hypermethylated genes 1650 (79%) 1656 (79.3%) 1662 (79.7%)
Among the 2414 female-hypermethylated genes 1949 (80.7%) 1959 (81.1%) 1961 (81.2%)
Among the 840 methylated genes of interest (Additional file 1: Table S1, Additional file 1: Table S2, Additional file 1: Table S3, Additional file 1: Table S4, Additional file 1: Table S5, Additional file 1: Table S6, Additional file 1: Table S7, Additional file 1: Table S8) 822 (97.8%) 828 (98.6%) 831 (98.9%)
Male-hypermethylated repeat windows located near male-hypermethylated genes 681/946 (72%) 706/973 (72.6%) 718/989 (72.6%)
Female-hypermethylated repeat windows located near female-hypermethylated genes 801/1032 (77.6%) 816/1050 (77.7%) 825/1064 (77.5%)
  1. Repeats were overrepresented upstream of all methylated regions examined (Chi-square test P < 0.00001 in all cases) but not upstream of non-methylated genes