Gene body methylation, gene length and gene expression. (A) Methylation levels across the bodies of genes in different expression ranks. The 0th rank represents all silent genes (RPKM = 0), while the expressed genes (RPKM > 0) were binned from 1 (least expressed) to 10 (most expressed) ranks. Genes were aligned at the transcription start sites (TSS, left dashed line) or the transcription termination sites (TTS, right dashed line), and average methylation levels for each 100-bp interval are plotted. (B) Distribution of gene body methylation levels across genes in different length intervals. Solid black and gray dashed lines denote the median and mean methylation levels for each group, respectively. Width of each shape at a given y value shows the relative frequency of genes present in that methylation level. (C) Distribution of gene body methylation levels across genes in different expression ranks. Genes were ranked as described in panel A, but expressed genes were divided into 20 bins.