Genomic distribution of 5fC in comparison to 5hmC and 5mC. (a) Average enrichment (log2 of read count in pull down/read count in input) of 5fC, 5hmC, and 5mC in different genomic regions. 5fC and 5hmC followed similar distributions with high enrichments in CGIs, promoters and exons. Error bars are the mean of each replicate. (b) Distribution of 5fC, 5hmC and 5mC in the 5' UTR of retrotransposon elements LINE1 and in IAP LTR. Error bars are the mean of each replicate. (c) Genes were classified into CGI- and non-CGI-containing promoters and the normalized read count (reads per kilobase per million mapped reads (RPKM)) averaged across all genes. The profile of genes with CGI promoters showed high levels of 5hmC and 5fC close to the transcription start site (TSS), while an opposite trend was observed for 5mC. In contrast, genes with non-CGI promoters showed low levels of all three cytosine modifications in the promoter. The levels increased slightly near transcription initiation sites and then stayed constant throughout the gene body.