CpG content contributes to tissue-resident macrophage enhancer selection

Tissue-resident macrophages acquire specialized identities through transcription factor networks operating in distinct chromatin environments. Early growth response 2 (EGR2) contributes both to alveolar macrophage identity and to interleukin (IL)-4-driven polarization of bone marrow-derived macrophages, yet the regulatory principles enabling its function across these contexts remain unclear. By integrating RNA-seq and ATAC-seq data from wild-type and Egr2-deficient macrophages, we show that macrophage identity is constrained by DNA methylation-dependent cis-regulatory landscapes. Alveolar macrophage-specific enhancers are predominantly CpG rich and hypomethylated, a feature shared with additional tissue-resident macrophage populations, whereas bone marrow-derived macrophage-accessible regulatory regions are largely CpG poor. Although IL-4 induces EGR2 together with KLF4 and DEC1 in bone marrow-derived macrophages, this transcription factor module fails to engage CpG-rich enhancers, indicating that the bone marrow-derived macrophage regulatory network lacks additional alveolar macrophage-specific components required for their activation. These findings identify CpG content as a determinant of enhancer competence and provide a mechanistic explanation for the context-dependent activity of EGR2 in macrophages, placing macrophage plasticity under the control of sequence-encoded epigenetic constraints.