SCoTCH-seq reveals that 5-hydroxymethylcytosine encodes regulatory information across DNA strands

In mammalian genomes, cytosine modifications form a layer of regulatory information alongside the genetic code. Decoding this information is crucial to our understanding of biology and disease. Established sequencing methods cannot simultaneously resolve cytosine's three most common forms—cytosine (C), 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC)—across both strands of the DNA double helix. Thus, how epigenetic information is distributed in DNA remains unclear. We present an accurate and quantitative, base-resolution approach to sequence genomes, together with mC and hmC, in both strands of the same DNA fragment. We show that different forms of cytosine combine across the double helix at CpG sites to form discrete information states in the mouse epigenome. These CpG states have distinct genomic distributions—including at promoters, enhancers, and gene bodies—and have different relationships with transcription. We show that while all possible forms of hydroxymethylation occur, hmC is predominantly asymmetric and that different forms of asymmetric hmC are not equivalent. Our findings demonstrate that 5-hydroxymethylcytosine combines with different cytosine variants across the DNA double helix to form distinct states of regulatory information. Overall design: Simultaneous hydroxymethylation and methylation profiling on double-stranded DNA extracted from mouse embryonic stem cells (E14) by high throughput sequencing (custom library prep). Data were obtained from two independent replicates and samples included spike-in controls (Lambda, pUC19 and custom synthetic oligonucleotide duplexes) to assess the accuracy of methylation and hydroxymethylation calls.