The Yin and Yang of Chromatin Dynamics In Stem Cell Fate Selection

Abstract

Adult organisms rely on tissue stem cells for maintenance and repair. During homeostasis, the concerted action of local niche signals and epigenetic regulators establish stable gene expression patterns to ensure that stem cells are not lost over time. However, stem cells also provide host tissues with a remarkable plasticity to respond to perturbations. How adult stem cells choose and acquire new fates is unknown, but the genome-wide mapping of epigenetic landscapes suggests a critical role for chromatin remodeling in these processes. Here, we explore the emerging role of chromatin modifiers and pioneer transcription factors in adult stem cell fate decisions and plasticity, which ensure that selective lineage choices are only made when environmentally cued.

Keywords: adult stem cells; cell identity; chromatin dynamics; fate selection; plasticity; super-enhancer.

Figure 1. Dynamic chromatin remodeling during stem cell lineage commitment

(A) In adult stem cells, differentiation-associated gene promoters are frequently silenced by the concerted action of Polycomb-repressive complexes (PRC) and DNA methyltransferases (DNMT3A/B). The PRC2 component EZH2 deposits the silencing mark H3K27me3, which can be recognized by the PRC1 moiety CBX. This facilitates PRC1 recruitment and allows for RING1A/B mediated deposition of H2AK119ub, which further leads to chromatin compaction. DNMT3A/B can methylate CpG islands at promoters and contribute to gene silencing, while histone deacetylases (HDACs) remove active chromatin marks (e.g. H3K27ac). This ultimately results in condensed chromatin and potent repression of gene expression. (B) Upon stem cell lineage commitment, dynamic chromatin remodeling is required to induce a program of differentiation. TET enzymes remove 5mCpG through iterative oxidation, whereas histone demethylases (e.g. JMJD3) eliminate repressive chromatin marks (e.g. H3K27me3). On the other hand, histone methyltransferases (HMTs) establish a permissive chromatin environment, for example by deposition of the H3K4me1 (at enhancers) or H3K4me3 (at promoters) marks. Upon external niche stimuli, pioneer factors engage their target sites in silent chromatin, and recruit histone acetyl transferases (p300/CBP, which deposit H3K27ac) as well as other transcription factors. Although the temporal order of chromatin remodeling is unclear, transcription factors at enhancers can eventually be recognized by the Mediator co-activator complex, which recruits RNA Polymerase II to gene promoters, resulting in de-repression of gene activity and the induction of stem cell differentiation.

Figure I. Super-enhancer epicenters confer tissue-, lineage- and temporal-specificity. (within Box 2)

(A) Hair follicle stem cell super-enhancers consist of clusters of active enhancers with exceptionally high density of H3K27ac (ChIP-seq) and transcriptional activators (adapted from [81]). Red box highlights one of the hair follicle stem cell super-enhancer epicenters. The schematic illustrates that epicenters are short (<2kb) DNA segments, densely bound by multiple cell-stage specific transcription factors and co-activators. In hair follicle stem cells, SOX9 acts as pioneer factor, which recruits other transcription factors, Mediator (MED1) and histone acetyltransferases (p300, CBP). Active enhancers are also depleted of 5mC (through TET enzymes) and display high levels of H3K4me1 (through histone methyltransferases, HMTs). (B) Co-occupancy (ChIP-seq) of hair follicle stem cell transcription factors and Mediator subunit MED1 occurs within super-enhancer epicenters (left, adapted from [81]). To test whether epicenters faithfully drive reporter gene expression in vivo (green fluorescent protein, eGFP, coupled with a minimal SV40 promoter under the control of the epicenter), high-titer lentivirus (LV, middle) was injected into the amniotic cavity of E9.5 mouse embryos. This results in stable integration of the reporter construct into skin progenitor chromatin and propagation into adult mice. The immunofluorescence image (right) marks the nuclei of the skin in blue (DAPI), the hair follicle stem cells in red (keratin 24), and a subset of stem cells that received the viral reporter. Note absence of eGFP in other skin cells (see also [81]). These findings illustrate that epicenters of quiescent hair follicle stem cells are only active in these cells, highlighting the cell-stage specificity of these special open chromatin domains.