Dissecting the dynamic changes of 5-hydroxymethylcytosine in T-cell development and differentiation

Significance 5-Hydroxymethylcytosine (5hmC) is an epigenetic DNA modification produced through the enzymatic activity of TET proteins. Here we present the first genome-wide mapping of 5hmC in T cells during sequential steps of lineage commitment in the thymus and the periphery (thymic DP, CD4 SP, and CD8 SP cells; peripheral naive CD8 and CD4 T cells; and in vitro-differentiated Th1 and Th2 cells). We show that 5hmC is enriched at gene bodies and cell type-specific enhancers, that its levels in the gene body correlate strongly with gene expression and histone modifications, and that its levels change dynamically during the course of T-cell development and differentiation. Our analysis will facilitate increased understanding of the role of 5hmC in T-cell development and differentiation. The discovery of Ten Eleven Translocation proteins, enzymes that oxidize 5-methylcytosine (5mC) in DNA, has revealed novel mechanisms for the regulation of DNA methylation. We have mapped 5-hydroxymethylcytosine (5hmC) at different stages of T-cell development in the thymus and T-cell differentiation in the periphery. We show that 5hmC is enriched in the gene body of highly expressed genes at all developmental stages and that its presence correlates positively with gene expression. Further emphasizing the connection with gene expression, we find that 5hmC is enriched in active thymus-specific enhancers and that genes encoding key transcriptional regulators display high intragenic 5hmC levels in precursor cells at those developmental stages where they exert a positive effect. Our data constitute a valuable resource that will facilitate detailed analysis of the role of 5hmC in T-cell development and differentiation.

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