Research Article

Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells

Science  12 Feb 2016:
Vol. 351, Issue 6274,
DOI: 10.1126/science.aad5510

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Genetic programming for self-renewal

Instead of repopulating themselves from tissue-resident stem cell pools like most types of differentiated cells, tissue macrophages maintain themselves by self-renewing. The underlying genetic programs that allow for this, however, are unknown. Soucie et al. now report that in macrophages at homeostasis, a pair of transcription factors (MafB and c-Maf) bind to and repress the enhancers of genes regulating self-renewal. When macrophages need to replenish their stocks, for example in response to injury, they transiently decrease MafB and c-Maf expression so they can self-renew. A parallel pathway also operates to control the self-renewal of embryonic stem cells.

Science, this issue p. 10.1126/science.aad5510

Structured Abstract

INTRODUCTION

In many organs of the body, differentiated cells are frequently lost and need to be replaced as part of normal homeostatic tissue maintenance or in response to injury. In most cases, this regeneration is assured by differentiation from tissue-specific stem cells. Together with a few other cell types, tissue macrophages represent a rare exception to this pathway, as they can be maintained independently of blood stem cells by local proliferation. Under certain conditions, mature macrophages can also be expanded and maintained long term in culture without transformation or loss of differentiation status. The gene regulatory mechanisms that allow such differentiated cells to self-renew while maintaining cell type–specific identity have so far remained unknown. Self-renewing macrophages provide a rare opportunity to study this question.

RATIONALE

Molecularly, cell identity can be defined by the genomic positions of gene regulatory enhancer elements. The cell type–specific signatures and activity status of such elements have been characterized by the analysis of specific histone modifications and the binding of regulatory proteins. To identify the regulatory mechanisms that enable macrophage self-renewal capacity to be integrated into the overall program of epigenetic macrophage identity, we have compared the enhancer repertoires of quiescent and self-renewing macrophages. Based on our previous observations that deletion of MafB and c-Maf transcription factors results in an extended self-renewal capacity of macrophages, we further investigated how the absence of Maf transcription factors affects the enhancers of specific self-renewal genes and how these mechanisms activate macrophage self-renewal under homeostatic and challenge conditions in vivo.

RESULTS

Compared to quiescent macrophages, self-renewing macrophages showed no appreciable difference with respect to genome-wide enhancer positions but displayed an increase in the activation status of many enhancers that were also bound by the lineage-specifying transcription factor PU.1 in both cell types. This finding suggests that these poised macrophage-specific enhancers became active in self-renewing macrophages. We found activated enhancers to be associated with a network of genes, centered on Myc and Klf2, that were up-regulated and functionally important for self-renewal in these cells. The same genes were also required for embryonic stem (ES) cell self-renewal but were associated with a distinct, ES cell–specific set of enhancers. We observed that activated self-renewal–associated macrophage enhancers were directly repressed by MafB binding. The loss of MafB and c-Maf expression relieved this repression and led to activation of the self-renewal gene network in MafB and cMaf knockout macrophages, as well as in alveolar macrophages that express constitutively low levels of these transcription factors. In vivo single-cell analysis further revealed that, both in the steady state and in response to immune stimulation, proliferating resident macrophages could access this network by transient down-regulation of Maf transcription factors.

CONCLUSION

Our results demonstrate that self-renewal in macrophages involves down-regulation of MafB and cMaf, as well as concomitant activation of a self-renewal gene network shared with ES cells but controlled from cell type–specific enhancers. Macrophage enhancers associated with self-renewal genes are already present in quiescent cells and can become activated when direct repression by Maf transcription factors is relieved. Our findings provide a general molecular rationale for the compatibility of self-renewal and differentiated cell functions and may also be more generally relevant for the direct activation of self-renewal activity in other differentiated cell types with therapeutic potential.

The self-renewal potential of both ES cells and differentiated macrophages is dependent on a shared network of self-renewal genes (left) that are controlled by distinct lineage-specific enhancers (right). In quiescent macrophages, the transcription factor MafB binds and represses these enhancers. The loss of MafB expression results in enhancer activation and enables macrophage self-renewal. At bottom left, red arrows indicate activation; blue bars represent inhibition. Circle size is a function of the number of times the target is affected by other regulators. Embedded Image, macrophage; E, enhancer; P, promoter.

ILLUSTRATION: SERENA BIELLI

Abstract

Differentiated macrophages can self-renew in tissues and expand long term in culture, but the gene regulatory mechanisms that accomplish self-renewal in the differentiated state have remained unknown. Here we show that in mice, the transcription factors MafB and c-Maf repress a macrophage-specific enhancer repertoire associated with a gene network that controls self-renewal. Single-cell analysis revealed that, in vivo, proliferating resident macrophages can access this network by transient down-regulation of Maf transcription factors. The network also controls embryonic stem cell self-renewal but is associated with distinct embryonic stem cell–specific enhancers. This indicates that distinct lineage-specific enhancer platforms regulate a shared network of genes that control self-renewal potential in both stem and mature cells.

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