TET2- and TDG-mediated changes are required for the acquisition of distinct histone modifications in divergent terminal differentiation of myeloid cells

Abstract

The plasticity of myeloid cells is illustrated by a diversity of functions including their role as effectors of innate immunity as macrophages (MACs) and bone remodelling as osteoclasts (OCs). TET2, a methylcytosine dioxygenase highly expressed in these cells and frequently mutated in myeloid leukemias, may be a key contributor to this plasticity. Through transcriptomic and epigenomic analyses, we investigated 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and gene expression changes in two divergent terminal myeloid differentiation processes, namely MAC and OC differentiation. MACs and OCs undergo highly similar 5hmC and 5mC changes, despite their wide differences in gene expression. Many TET2- and thymine-DNA glycosylase (TDG)-dependent 5mC and 5hmC changes directly activate the common terminal myeloid differentiation programme. However, the acquisition of differential features between MACs and OCs also depends on TET2/TDG. In fact, 5mC oxidation precedes differential histone modification changes between MACs and OCs. TET2 and TDG downregulation impairs the acquisition of such differential histone modification and expression patterns at MAC-/OC-specific genes. We prove that the histone H3K4 methyltransferase SETD1A is differentially recruited between MACs and OCs in a TET2-dependent manner. We demonstrate a novel role of these enzymes in the establishment of specific elements of identity and function in terminal myeloid differentiation.

5-Hydroxymethylcytosine (5hmC), or How to Identify Your Favorite Cell

“…This is the case for Tet2 (and to a lesser degree Tet3), which is consistently reported in murine models [39,40,43,[45][46][47]49] and human cells [37,38,42,[50][51][52]. Of note, the role of Tet2 in mast cell differentiation described above [40] is partially independent of 5hmC, as rescuing mast cell developmental changes upon Tet2 knockout was only possible by the re-expression of Tet2 independently of its catalytic activity, which assumes that Tet2 possibly interacts with other complexes (something similar has been shown between TET1 and the SIN3A co-repressor complex [53]).…”

“…Despite this global reduction, 5hmC remains enriched at particular loci, matching the distribution shown by earlier studies (i.e., promoters and gene bodies). In addition, 5hmC enrichment has been described in enhancers [19,36,[38][39][40][41] and lineage-specific TF binding sites [42,43]. In line with this, 5hmC changes are overrepresented in highly transcribed genes.…”

TET Enzymes and 5hmC in Adaptive and Innate Immune Systems

“…During monocyte to OC or to MAC differentiation, the transcription factor PU.1 was found to associate with both hypo- and hypermethylated regions and to directly bind to TET2 as well as to the DNA methyltransferase DNMT3B (20). TET2 functioned together with thymine-DNA glycosylase (TDG), and to a lesser extent with activation-induced deaminase (AID), to hydroxymethylate and demethylate DNA, facilitating the establishment of cell-type-specific gene expression programs (83). The same study also showed that TET2 was responsible for recruiting the histone H3K4 methyltransferase SETD1A, and for increasing H3K4me3 modification at cell-type specific genes examined (83).…”

“…TET2 functioned together with thymine-DNA glycosylase (TDG), and to a lesser extent with activation-induced deaminase (AID), to hydroxymethylate and demethylate DNA, facilitating the establishment of cell-type-specific gene expression programs (83). The same study also showed that TET2 was responsible for recruiting the histone H3K4 methyltransferase SETD1A, and for increasing H3K4me3 modification at cell-type specific genes examined (83).…”

Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci

“…Five hundred nanograms of BS-converted DNA was hybridized on Infinium MethylationEPIC Bead Chip array (Illumina, Inc., San Diego, CA, USA) following manufacturer's instructions to assess DNA methylation of 850,000 selected CpGs that cover 99% of annotated RefSeq genes. Fluorescence of probes was detected by BeadArray Reader (Illumina, Inc.), and image processing and data extraction were performed as previously described [34]. Downstream data processing and normalization were performed using the R statistical language.…”