Whole-genome analysis of 5-hydroxymethylcytosines and 5-methylcytosines at base resolution in human brain
5-hydroxymethylcytosines (5hmC) is particularly abundant in mammalian brain with little-known functions. Here we present the first genome-wide and single-base-resolution maps of 5hmC and 5mC in human brain by combined application of TAB-Seq and MethylC-Seq. We report that the majority of modified cytosines are hydroxymethylated in adult human brain, a significant proportion of which are highly-hydroxymethylated with enrichment in active genic regions and distal-regulatory elements. 5hmC is more enriched in poised than active enhancers, and CpG island shores and enhancers show comparable 5hmC profiles. Notably, 5hmC spikes were identified at the 5’ splicing sites, suggesting a link between 5hmC and splicing. Additionally, we identified a transcription-correlated 5hmC bias towards to sense strand and a 5mC bias towards antisense strand of gene bodies, and a bias towards C-rich sequences surrounding the 5hmC sites. Our data imply multiple roles for 5hmC in alternative splicing and gene regulation in addition to be an intermediate of DNA demethylation in human brain. Overall design: Examination of hydroxymethylomes of 1 adult and 1 fetal brain tissue of frontal lobe, as well as 1 methylome of the same adult. We performed both WGBS and TAB-seq for the adult brain, but only TAB-seq for the fetal brain. So the formats of the two .txt files are a little different. Both files have header lines, which may help you understand their formats. Columns of "GSE46710_Ad_Front.hmC_sites_FDR_0.01.txt.gz": 1. Chromosome 2. Position: 0-based coordinate of the cytosine on the chromosome. 3. Strand: on which strand of the reference genome does the cytosine locates. 4. Context: CG/CHG/CHH 5. Depth(C+T)_from_MethylC-Seq: the sequencing depth (sum of cytosines and thymines) on this site of WGBS. 6. Non-converted_C_from_MethylC-Seq: the number of cytosines on this site of WGBS. 7. Modification_level_from_MethylC-Seq(%): the quotient in percentage of Non-converted_C_from_MethylC-Seq divided by Depth(C+T)_from_MethylC-Seq. 8. Depth(C+T)_from_TAB-Seq: the sequencing depth (sum of cytosines and thymines) on this site of TAB-seq. 9. Non-converted_C_from_TAB-Seq: the number of cytosines on this site of TAB-seq. 10. Modification_level_from_TAB-Seq(%): the quotient in percentage of Non-converted_C_from_TAB-Seq divided by Depth(C+T)_from_TAB-Seq, "NA" if it is not called as an hmC. 11. Calling_hmC_site(1-passed;0-failed): given that the FDR is smaller than 0.01, whether the cytosine should be called as an hmC.