Stage-specific epigenetic regulation of CD4 expression by coordinated enhancer elements during T cell development

Priya D Issuree,Paul Zappile,Hai-Hui Xue,Christy Au,Dan R Littman,Richard M Myers,Jane A Skok,Ramya Raviram,Kenneth Day

doi:10.1038/s41467-018-05834-w

Abstract

The inheritance of gene expression patterns is dependent on epigenetic regulation, but the establishment and maintenance of epigenetic landscapes during T cell differentiation are incompletely understood. Here we show that two stage-specific Cd4 cis-elements, the previously characterized enhancer E4p and a novel enhancer E4m, coordinately promote Cd4 transcription in mature thymic MHC-II-specific T cells, in part through the canonical Wnt pathway. Specifically, E4p licenses E4m to orchestrate DNA demethylation by TET1 and TET3, which in turn poises the Cd4 locus for transcription in peripheral T cells. Cd4 locus demethylation is important for subsequent Cd4 transcription in activated peripheral T cells wherein these cis-elements become dispensable. By contrast, in developing thymocytes the loss of TET1/3 does not affect Cd4 transcription, highlighting an uncoupled event between transcription and epigenetic modifications. Together our findings reveal an important function for thymic cis-elements in governing gene expression in the periphery via a heritable epigenetic mechanism.

Highlights

The inheritance of gene expression patterns is dependent on epigenetic regulation, but the establishment and maintenance of epigenetic landscapes during T cell differentiation are incompletely understood
It remains unclear whether gene body methylation changes are required for appropriate transcription of Cd4 in CD4 SP T cells during maturation in the thymus or whether methylation changes are a result of transcriptional activity mediated by cis -elements and have subsequent critical functions related to heritable transmission of gene states
We found that TET1 and TET3 mediate locus demethylation of Cd4, likely through the activity of E4m and E4p during thymocyte maturation, but that methylation changes do not impede transcription in non-dividing cells and are instead critical for establishing heritable expression states in dividing cells

Summary

Introduction

The inheritance of gene expression patterns is dependent on epigenetic regulation, but the establishment and maintenance of epigenetic landscapes during T cell differentiation are incompletely understood. Germline deletion of the core 432 bp E4p element abrogates CD4 upregulation at the DN4 to DP transition, but a reduced number of MHC-II-specific thymocytes can be selected in Cd4E4PΔ/E4PΔ mice, in part due to upregulation of a moderate amount of CD4 during positive selection signaling, suggesting potential regulation by another ciselement in a stage-specific manner[7] This view is supported by the finding that E4p deletion in proliferating mature CD4+ T cells has no effect on maintenance of Cd4 expression. Lack of demethylation in the absence of TET1/3 did not result in a major Cd4 transcriptional defect in the thymus, but led instead to gradual loss of its expression during proliferation of mature T cells, suggesting that thymic demethylation is required for establishment of stable CD4 expression in dividing mature CD4+ T cells. The enhancers that regulate Cd4 expression perform multiple functions, including direct support of transcriptional activity, and regulation of the gene’s methylation state and entrainment of cis-elements that sustain expression after the cells exit the thymus

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Conclusion