Genomic Characterization of Murine Monocytes Reveals C/EBPβ Transcription Factor Dependence of Ly6C- Cells
Alexander Mildner1, Jörg Schönheit2, Amir Giladi3
1Department of Immunology, Weizmann Institute of Science, 76100 Rehovot, Israel; Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
Abstract:
Monocytes are circulating, short-lived mononuclear phagocytes, which in mice and man comprise two main subpopulations. Murine Ly6C+ monocytes display developmental plasticity and are recruited to complement tissue-resident macrophages and dendritic cells on demand. Murine vascular Ly6C- monocytes patrol the endothelium, act as scavengers, and support vessel wall repair. Here we characterized population and single cell transcriptomes, as well as enhancer and promoter landscapes of the murine monocyte compartment. Single cell RNA-seq and transplantation experiments confirmed homeostatic default differentiation of Ly6C+ into Ly6C- monocytes. The main two subsets were homogeneous, but linked by a more heterogeneous differentiation intermediate. We show that monocyte differentiation occurred through de novo enhancer establishment and activation of pre-established (poised) enhancers. Generation of Ly6C- monocytes involved induction of the transcription factor C/EBPβ and C/EBPβ-deficient mice lacked Ly6C- monocytes. Mechanistically, C/EBPβ bound the Nr4a1 promoter and controlled expression of this established monocyte survival factor.
Insights
Murine monocytes differentiate from Ly6C+ to Ly6C- subsets via enhancer activation. Transcription factor C/EBPβ drives this process, crucial for Ly6C- monocyte generation and survival.
Area of Science:
- Immunology
- Cell Biology
- Transcriptomics
Background:
- Monocytes are critical immune cells with distinct subpopulations in mice and humans.
- Murine Ly6C+ monocytes are plastic and replenish tissue macrophages.
- Murine Ly6C- monocytes patrol vasculature and aid in repair.
Purpose of the Study:
- To characterize the murine monocyte compartment using transcriptomic and epigenetic analyses.
- To elucidate the differentiation pathways and regulatory mechanisms of monocyte subsets.
Main Methods:
- Single-cell RNA sequencing (scRNA-seq) of murine monocytes.
- Analysis of enhancer and promoter landscapes.
- Transplantation experiments.
- Gene knockout studies (C/EBPβ-deficient mice).
Main Results:
- Confirmed homeostatic differentiation of Ly6C+ into Ly6C- monocytes.
- Identified a heterogeneous differentiation intermediate between the main subsets.
- Demonstrated monocyte differentiation via de novo and poised enhancer activation.
- Showed C/EBPβ is essential for Ly6C- monocyte generation, binding the Nr4a1 promoter.
Conclusions:
- Monocyte differentiation involves dynamic enhancer regulation.
- C/EBPβ is a key transcription factor driving Ly6C- monocyte development.
- Understanding monocyte differentiation is vital for immune system research.
