Developing and adult tissues use different cis-regulatory elements. Although DNA at some decommissioned embryonic enhancers is hypomethylated in adult cells, it is unknown whether this putative ...epigenetic memory is complete and recoverable. We find that, in adult mouse cells, hypomethylated CpG dinucleotides preserve a nearly complete archive of tissue-specific developmental enhancers. Sites that carry the active histone mark H3K4me1, and are therefore considered “primed,” are mainly cis elements that act late in organogenesis. In contrast, sites decommissioned early in development retain hypomethylated DNA as a singular property. In adult intestinal and blood cells, sustained absence of polycomb repressive complex 2 indirectly reactivates most—and only—hypomethylated developmental enhancers. Embryonic and fetal transcriptional programs re-emerge as a result, in reverse chronology to cis element inactivation during development. Thus, hypomethylated DNA in adult cells preserves a “fossil record” of tissue-specific developmental enhancers, stably marking decommissioned sites and enabling recovery of this epigenetic memory.
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•Hypomethylated DNA preserves nearly complete catalogs of developmental enhancers•Adult H3K4me1+H3K27ac− enhancers are not poised but remnants of fetal gene activity•TFs relieved of PRC2 repression selectively reactivate hypomethylated enhancers•Recommissioned enhancers drive tissue-specific fetal and embryonic gene activity
Although cells decommission embryonic enhancers by erasing histone marks, these regions retain hypomethylated DNA into adulthood, preserving an accurate archive of tissue-specific developmental cis elements. This epigenetic memory is recovered after prolonged absence of polycomb repressive complex 2, when transcription factors selectively reactivate hypomethylated developmental enhancers and their tissue-restricted target genes.
A growing body of data suggests the importance of epigenetic mechanisms in cancer. Polycomb repressive complex 2 (PRC2) has been implicated in self-renewal and cancer progression, and its components ...are overexpressed in many cancers. However, its role in cancer development and progression remains unclear. We used conditional alleles for the PRC2 components enhancer of zeste 2 (Ezh2) and embryonic ectoderm development (Eed) to characterize the role of PRC2 function in leukemia development and progression. Compared with wild-type leukemia, Ezh2-null MLL-AF9–mediated acute myeloid leukemia (AML) failed to accelerate upon secondary transplantation. However, Ezh2-null leukemias maintained self-renewal up to the third round of transplantation, indicating that Ezh2 is not strictly required for MLL-AF9 AML, but plays a role in leukemia progression. Genome-wide analyses of PRC2-mediated trimethylation of histone 3 demonstrated locus-specific persistence of H3K27me3 despite inactivation of Ezh2, suggesting partial compensation by Ezh1. In contrast, inactivation of the essential PRC2 gene, Eed, led to complete ablation of PRC2 function, which was incompatible with leukemia growth. Gene expression array analyses indicated more profound gene expression changes in Eed-null compared with Ezh2-null leukemic cells, including down-regulation of Myc target genes and up-regulation of PRC2 targets. Manipulating PRC2 function may be of therapeutic benefit in AML.
Changes of histone modification status at critical lineage-specifying gene loci in multipotent precursors can influence cell fate commitment. The contribution of these epigenetic mechanisms to ...natural killer (NK) cell lineage determination from common lymphoid precursors is not understood. Here we investigate the impact of histone methylation repressive marks (H3 Lys27 trimethylation; H3K27me3) on early NK cell differentiation. We demonstrate that selective loss of the histone-lysineN-methyltransferase Ezh2 (enhancer of zeste homolog 2) or inhibition of its enzymatic activity with smallmolecules unexpectedly increased generation of the IL-15 receptor (IL-15R) CD122⁺ NK precursors and mature NK progeny from both mouse and human hematopoietic stem and progenitor cells. Mechanistic studies revealed that enhanced NK cell expansion and cytotoxicity against tumor cells were associated with up-regulation of CD122 and the C-type lectin receptor NKG2D. Moreover, NKG2D deficiency diminished the positive effects of Ezh2 inhibitors on NK cell commitment. Identification of the contribution of Ezh2 to NK lineage specification and function reveals an epigenetic-based mechanism that regulates NK cell development and provides insight into the clinical application of Ezh2 inhibitors in NK-based cancer immunotherapies.
Earlier work has shown that the transcription factor C/EBPα induced a transdifferentiation of committed lymphoid precursors into macrophages in a process requiring endogenous PU.1. Here we have ...examined the effects of PU.1 and C/EBPα on fibroblasts, a cell type distantly related to blood cells and akin to myoblasts, adipocytes, osteoblasts, and chondroblasts. The combination of the two factors, as well as PU.1 and C/EBPβ, induced the up-regulation of macrophage/hematopoietic cell surface markers in a large proportion of NIH 3T3 cells. They also up-regulated these markers in mouse embryo- and adult skin-derived fibroblasts. Based on cell morphology, activation of macrophage-associated genes, and extinction of fibroblast-associated genes, cell lines containing an attenuated form of PU.1 and C/EBPα acquired a macrophage-like phenotype. The lines also display macrophage functions: They phagocytose small particles and bacteria, mount a partial inflammatory response, and exhibit strict CSF-1 dependence for growth. The myeloid conversion is primarily induced by PU.1, with C/EBPα acting as a modulator of macrophage-specific gene expression. Our data suggest that it might become possible to induce the transdifferentiation of skin-derived fibroblasts into cell types desirable for tissue regeneration.
Polycomb repressive complex 2 (PRC2) plays crucial roles in transcriptional regulation and stem cell development. However, the context-specific functions associated with alternative subunits remain ...largely unexplored. Here we show that the related enzymatic subunits EZH1 and EZH2 undergo an expression switch during blood cell development. An erythroid-specific enhancer mediates transcriptional activation of EZH1, and a switch from GATA2 to GATA1 controls the developmental EZH1/2 switch by differential association with EZH1 enhancers. We further examine the in vivo stoichiometry of the PRC2 complexes by quantitative proteomics and reveal the existence of an EZH1-SUZ12 subcomplex lacking EED. EZH1 together with SUZ12 form a non-canonical PRC2 complex, occupy active chromatin, and positively regulate gene expression. Loss of EZH2 expression leads to repositioning of EZH1 to EZH2 targets. Thus, the lineage- and developmental stage-specific regulation of PRC2 subunit composition leads to a switch from canonical silencing to non-canonical functions during blood stem cell specification.
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•During blood cell development there is a switch from EZH2 to EZH1 expression•GATA switch regulates EZH2 to EZH1 switch through lineage-specific EZH1 enhancers•EZH1 and SUZ12 form a non-canonical PRC2 complex in transcriptional activation•Alternative PRC2 subunit composition confers a switch to non-canonical functions
Xu et al. show that the developmental switch of lineage-specifying GATA factors controls an expression switch of EZH2 to EZH1 during blood cell differentiation. EZH1 and SUZ12 assemble a non-canonical complex independent of EED and positively regulate gene expression. Thus, the alternative PRC2 subunit composition confers non-canonical functions during development.
Deeply buried sandstone reservoirs are characterized by their wide pore-throat distributions and varied storage and percolation capacities. An integrated analysis comprising casting thin section, ...scanning electron microscopy, X-ray computed tomography (micro-CT), high-pressure mercury intrusion (HPMI), and constant-rate mercury intrusion (CRMI) is performed on thirteen samples from the Jurassic Sangonghe Formation in the Junggar Basin to investigate the pore structures and their influence on the storage and percolation capacities. HPMI, CRMI, and micro-CT are combined to determine the full-range pore size distributions (FPSDs), which have multimodal distributions between 2.77 nm and 500 μm with three broad peaks. The right peak, ranging from 100 to 500 μm, is associated with residual and dissolution intergranular pores. The middle peak is mainly composed of dissolution intergranular and intragranular pores with radii between 10 and 100 μm. The left peak exhibited fluctuations and is characterized by dissolution intragranular and intercrystalline pores with radii of 37 nm–10 μm. According to the pore types, sizes, and proportions in the FPSD, the pores are classified as intercrystalline nanopores (<1 μm), intragranular micro-small pores (1–10 μm), mixed intergranular and intragranular mesopores (10–100 μm), and intergranular macropores (>100 μm). A storage capacity evaluation combining the classifications and FPSD indicates that the macropores and nanopores primarily contribute to porosity, albeit with contrasting influences on the storage capacity. The contents of macropores determine the storage capacity of a deeply buried sandstone reservoir, while the negative effects of nanopores become predominant with decreasing porosity. A percolation capacity evaluation on the basis of CRMI results suggests that the permeability contribution is dominated by nanopores in tight sandstone, controlled by micro-small pores in low-permeability sandstone, and dominated by mesopores in conventional sandstone. Mesopores always play a favorable role in percolation. However, the negative impacts of nanopores should be considered in low-permeability and tight sandstone. Micro-small pores have a negative influence on the permeability of conventional sandstone, but are favorable for the fluid percolation of most low-permeability and tight sandstone reservoirs. A new empirical equation indicates that r10 of the FPSD is the suitable as the proper pore-throat radius for the permeability estimation of deeply buried sandstone reservoirs.
•HPMI, CRMI and Micro-CT are combined to obtain the full-range pore size distribution.•A new pore classification is proposed for deeply buried sandstone reservoirs.•Nanopore and macropore are considered main controlling factors for storage capacity.•Nanopore, micro-small pore and mesopore serve as main throats for fluid percolation.•A permeability estimation model is proposed by determining proper pore-throat radius.
Epigenetic marks are crucial for organogenesis, but their role in heart development is poorly understood. Polycomb repressive complex 2 (PRC2) trimethylates histone H3 at lysine 27, which establishes ...H3K27me3 repressive epigenetic marks that promote tissue-specific differentiation by silencing ectopic gene programs.
We studied the function of PRC2 in murine heart development using a tissue-restricted conditional inactivation strategy.
Inactivation of the PRC2 subunit Ezh2 by Nkx2-5(Cre) (Ezh2(NK)) caused lethal congenital heart malformations, namely, compact myocardial hypoplasia, hypertrabeculation, and ventricular septal defect. Candidate and genome-wide RNA expression profiling and chromatin immunoprecipitation analyses of Ezh2(NK) heart identified genes directly repressed by EZH2. Among these were the potent cell cycle inhibitors Ink4a/b (inhibitors of cyclin-dependent kinase 4 A and B), the upregulation of which was associated with decreased cardiomyocyte proliferation in Ezh2(NK). EZH2-repressed genes were enriched for transcriptional regulators of noncardiomyocyte expression programs such as Pax6, Isl1, and Six1. EZH2 was also required for proper spatiotemporal regulation of cardiac gene expression, because Hcn4, Mlc2a, and Bmp10 were inappropriately upregulated in ventricular RNA. PRC2 was also required later in heart development, as indicated by cardiomyocyte-restricted TNT-Cre inactivation of the PRC2 subunit Eed. However, Ezh2 inactivation by TNT-Cre did not cause an overt phenotype, likely because of functional redundancy with Ezh1. Thus, early Ezh2 inactivation by Nk2-5(Cre) caused later disruption of cardiomyocyte gene expression and heart development.
Our study reveals a previously undescribed role of EZH2 in regulating heart formation and shows that perturbation of the epigenetic landscape early in cardiogenesis has sustained disruptive effects at later developmental stages.
In proliferating cells, where most Polycomb repressive complex 2 (PRC2) studies have been performed, gene repression is associated with PRC2 trimethylation of H3K27 (H3K27me3). However, it is ...uncertain whether PRC2 writing of H3K27me3 is mechanistically required for gene silencing. Here, we studied PRC2 function in postnatal mouse cardiomyocytes, where the paucity of cell division obviates bulk H3K27me3 rewriting after each cell cycle. EED (embryonic ectoderm development) inactivation in the postnatal heart (Eed
) caused lethal dilated cardiomyopathy. Surprisingly, gene upregulation in Eed
was not coupled with loss of H3K27me3. Rather, the activating histone mark H3K27ac increased. EED interacted with histone deacetylases (HDACs) and enhanced their catalytic activity. HDAC overexpression normalized Eed
heart function and expression of derepressed genes. Our results uncovered a non-canonical, H3K27me3-independent EED repressive mechanism that is essential for normal heart function. Our results further illustrate that organ dysfunction due to epigenetic dysregulation can be corrected by epigenetic rewiring.
Polycomb repressive complex 2 (PRC2) controls maintenance and lineage determination of stem cells by suppressing genes that regulate cellular differentiation and tissue development. However, the role ...of PRC2 in lineage-committed somatic cells is mostly unknown. Here we show that Eed deficiency in chondrocytes causes severe kyphosis and a growth defect with decreased chondrocyte proliferation, accelerated hypertrophic differentiation and cell death with reduced Hif1a expression. Eed deficiency also causes induction of multiple signalling pathways in chondrocytes. Wnt signalling overactivation is responsible for the accelerated hypertrophic differentiation and kyphosis, whereas the overactivation of TGF-β signalling is responsible for the reduced proliferation and growth defect. Thus, our study demonstrates that PRC2 has an important regulatory role in lineage-committed tissue cells by suppressing overactivation of multiple signalling pathways.
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