Regulation of DNA methylation dictates Cd4 expression during the development of helper and cytotoxic T cell lineages

Abstract

During development, progenitor cells with binary potential give rise to daughter cells that have distinct functions. Heritable epigenetic mechanisms then lock in gene expression programs that define lineage identity. Cd4 regulation in helper and cytotoxic T cells exemplifies this process, with enhancer- and silencer-regulated establishment of epigenetic memories for stable gene expression and repression, respectively. Using a genetic screen, we identified the DNA methylation machinery as essential for maintaining Cd4 silencing in the cytotoxic lineage. Further, we found a requirement for the proximal enhancer in mediating removal of Cd4 DNA methylation marks, allowing for stable expression in T helper cells. These findings suggest that stage-specific methylation and demethylation events in Cd4 regulate its heritable expression in response to the distinct signals that dictate lineage choice during T cell development.

What Happens in the Thymus Does Not Stay in the Thymus: How T Cells Recycle the CD4+–CD8+ Lineage Commitment Transcriptional Circuitry To Control Their Function

“…Epigenetic gene silencing largely relies on two processes: methylation of DNA itself (at position 5 of cytosine [5 mC] typically within palindromic CpG dinucleotide pairs) (62, 63) and post-transcriptional modifications of histones, the core proteins permitting assemblage of eukaryotic chromatin into nucleosomes (64). While there is currently no reported evidence that histone modifications contribute to Cd4 silencing, DNA methylation has recently been shown to be a key player (65). CpG methylation, initiated by DNA methyl transferases Dnmt3a and Dnmt3b, and transmitted during cell division by Dnmt1, is thought to promote gene silencing either by direct inhibition of transcription factor binding or by recruiting methyl CpG-binding proteins associated with transcription repression complexes (66).…”

“…Importantly, the symmetry of CpG motifs allows their methylation to be ‘copied’ by Dnmt1 to newly synthesized strands during DNA replication, thereby ensuring truly epigenetic inheritance of this mark. Indeed, the Cd4 locus is hypermethylated in CD8 + T cells and hypomethylated in CD4 + T cells (65). Hypermethylation of the Cd4 locus is established early at the DN3 stage and maintained through the DP stage to CD8 SP, in a silencer-dependent manner.…”

“…However, in mature CD8 + T cells, hypermethylation is silencer independent and remains stable throughout cell division. Furthermore, Dnmt1 (redundantly with Dnmt3a and Dnmt3b) is necessary to maintain Cd4 silencing during cell division (65). Thus, DNA methylation is critical to Cd4 silencing in CD8 + T cells.…”

Tagging Methyl-CpG-Binding Domain Proteins Reveals Different Spatiotemporal Expression and Supports Distinct Functions

“…Precise temporal control of methylation and demethylation is essential for the development and differentiation of both T cells [64] and intestinal epithelial crypt cells [65], indicating that MBD2 may contribute to the interpretation of DNA methylation in these tissues. For example, MBD2 has a role in T-cell development that is partially dependent on the methylation status of critical genes such as Foxp3 [50,66], but also has a role in the innate immune system to indirectly affect T-cell activation and differentiation [49].…”

Cell-Intrinsic Barriers of T Cell-Based Immunotherapy

“…A recent study reported that a stable DNA-methylation program at the proximal enhancer of the cd4 locus (CD4) is essential to enforce cd4 gene silencing in CD8 + T cells, whereas CD4 + T cells lack this program, suggesting an important role of epigenetic programming in securing cell-identity during T-cell development [49]. Genome-wide DNA-methylation profiling of naïve and effector virus-specific CD8 + T cells during acute LCMV infection have revealed that many promoters and putative regulatory cis-elements of effector genes become demethylated during effector T-cell differentiation, along with differential methylation programming at naïve/effector-specific transcription factor binding sites [47].…”