Histone H3K4 demethylases are essential in development and differentiationThis paper is one of a selection of papers published in this Special Issue, entitled 28th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process

Epigenetic regulation of oligodendrocyte identity

The interplay of transcription factors and epigenetic modifiers, including histone modifications, DNA methylation and microRNAs during development is essential for the acquisition of specific cell fates. Here, we review the epigenetic "programming" of stem cells into oligodendrocytes, by analyzing three sequential stages of lineage progression. The first transition from pluripotent stem cells to neural precursors is characterized by repression of pluripotency genes and restriction of the lineage potential to the neural fate. The second transition from multipotential precursors to oligodendrocyte progenitors is associated with the progressive loss of plasticity and the repression of neuronal and astrocytic genes. The last step of differentiation of oligodendrocyte progenitors into myelin-forming cells is defined by a model of derepression of myelin genes.

Roles for common MLL/COMPASS subunits and the 19S proteasome in regulating CIITA pIV and MHC class II gene expression and promoter methylation

BACKGROUND

Studies indicate that the 19S proteasome contributes to chromatin reorganization, independent of the role the proteasome plays in protein degradation. We have previously shown that components of the 19S proteasome are crucial for regulating inducible histone activation events in mammalian cells. The 19S ATPase Sug1 binds to histone-remodeling enzymes, and in the absence of Sug1, a subset of activating epigenetic modifications including histone H3 acetylation, H3 lysine 4 trimethylation and H3 arginine 17 dimethylation are inhibited at cytokine-inducible major histocompatibilty complex (MHC)-II and class II transactivator (CIITA) promoters, implicating Sug1 in events required to initiate mammalian transcription.

RESULTS

Our previous studies indicate that H3 lysine 4 trimethylation at cytokine-inducible MHC-II and CIITA promoters is dependent on proteolytic-independent functions of 19S ATPases. In this report, we show that multiple common subunits of the mixed lineage leukemia (MLL)/complex of proteins associated with Set I (COMPASS) complexes bind to the inducible MHC-II and CIITA promoters; that overexpressing a single common MLL/COMPASS subunit significantly enhances promoter activity and MHC-II HLA-DRA expression; and that these common subunits are important for H3 lysine 4 trimethylation at MHC-II and CIITA promoters. In addition, we show that H3 lysine 27 trimethylation, which is inversely correlated with H3 lysine 4 trimethylation, is significantly elevated in the presence of diminished 19S ATPase Sug1.

CONCLUSION

Taken together, these experiments suggest that the 19S proteasome plays a crucial role in the initial reorganization of events enabling the relaxation of the repressive chromatin structure surrounding inducible promoters.

A moment's pause: putative nucleosome-based influences on MeCP2 regulation

There has been a hotbed of activity surrounding MeCP2 research in the past number of years. Despite better characterizing the functions and nature of this protein, it has become abundantly clear that MeCP2 is involved in far more complex activities than perhaps initially anticipated. Recent publications have shown that MeCP2 is dynamically post-translationally modified, and it is possible that these marks permit MeCP2 to inhabit very diverse chromatin environments. It is also of interest to consider how nucleosome composition differs in these varying chromatin regions, and how the chromatin template itself contributes to diversifying the regulatory roles of MeCP2. These will be critical points to examine when seeking to understand how MeCP2 behaviour differentiates in tissues other than the brain. By understanding the chromatin and (or) tissue context in which MeCP2 interacts, it may be possible to discern the specific etiology of diseases linked to MeCP2 dysfunction.

Proteomic analysis of bone tissues of patients with osteonecrosis of the femoral head

Osteonecrosis of the femoral head (ONFH) is a devastating disease that can result in a femoral head collapse. By proteomics analysis, we identified 1,967 proteins with two or more unique peptides from ONFH and from control bones with a false discovery rate of 4.8%. Using spectral counting, we identified 141 overexpressed and 56 underexpressed proteins comparing ONFH bones to the controls. GSEA (gene set enrichment analysis) revealed that proteins overexpressed in ONFH are enriched for gene sets related to multiple myeloma and adult T-cell lymphoma (ATL), and to JAK2-dependent genes. We confirmed the underexpression of CHST2 (isoform 1 of carbohydrate sulfotransferase 2), a key protein involved in biosynthesis of chondroitin sulfate proteoglycans, and the underexpression of GPCR26 (G-protein coupled receptor 26), a protein that mediates intracellular calcium mobilization, in ONFH bones compared to controls. Taken together, our data suggest that biosynthesis of chondroitin sulfate proteoglycans and cation transport and mobilization may be a key process involved in the pathogenesis of ONFH. Our analysis sheds new light on the understanding of the pathogenesis of ONFH.

Epigenetic mechanisms facilitating oligodendrocyte development, maturation, and aging

The process of oligodendrocyte differentiation is regulated by a dynamic interaction between a genetic and an epigenetic program. Recent studies, addressing nucleosomal histone modifications have considerably increased our knowledge regarding epigenetic regulation of gene expression during oligodendrocyte development and aging. These results have generated new hypotheses regarding the mechanisms underlying the decreased efficiency of endogenous remyelination in response to demyelinating injuries with increasing age. In this review, we present an overview of the epigenetic mechanisms regulating gene expression at specific stages of oligodendrocyte differentiation and maturation as well as the changes that occur with aging.

Efficient regulation of VEGF expression by promoter-targeted lentiviral shRNAs based on epigenetic mechanism: a novel example of epigenetherapy

RATIONALE

We studied a possibility that shRNAs can lead to transcriptional gene activation at the promoter level via epigenetic mechanism.

OBJECTIVE

The purpose of this study was to test the effects on vascular endothelial growth factor (VEGF-A) expression by promoter targeted small hairpin RNAs (shRNAs) in vitro and in experimental animals in vivo using stable local lentiviral gene transfer.

METHODS AND RESULTS

One shRNA was identified which strongly increased VEGF-A expression in C166 endothelial cells at mRNA and protein level whereas another shRNA decreased VEGF-A expression. Quantitative chromatin immunoprecipitation analysis revealed that the repressing shRNA caused epigenetic changes, which increased nucleosome density within the promoter and transcription start site and led to repression of VEGF-A expression. Epigenetic changes caused by the activating shRNA were opposite to those caused by the repressing shRNA. These results were confirmed in vivo in an ischemic mouse hindlimb model after local gene transfer where VEGF-A upregulation achieved by promoter-targeted shRNA increased vascularity and blood flow.

CONCLUSIONS

We show that lentivirus-mediated delivery of shRNA molecules targeted to specific regions in the mVEGF-A promoter either induce or repress VEGF-A expression via epigenetic modulation. Thus, we describe a new approach of gene therapy, epigenetherapy, based on an epigenetic mechanism at the promoter level. Controlling transcription through manipulation of specific epigenetic marks provides a novel approach for the treatment of several diseases.

[Immunofluorescence patterns of histone H3 lysine 4 dimethylation on X chromosomes of different cloned cattle]

Using immunofluorescence staining, the patterns of histone H3 K4m2 of metaphase X chromosomes were measured in cloned cattle derived from FFB and FOV donor cells. The results demonstrated that the modification pattern of H3 K4m2 in the ear tissue of all clones was largely consistent with that of the donor cell line FFB and conventionally produced cattle, but different from that of the donor cell line FOV.

Mapping the epigenome--impact for toxicology

Recent advances in technological approaches for mapping and characterizing the epigenome are generating a wealth of new opportunities for exploring the relationship between epigenetic modifications, human disease and the therapeutic potential of pharmaceutical drugs. While the best examples for xenobiotic-induced epigenetic perturbations come from the field of non-genotoxic carcinogenesis, there is growing evidence for the relevance of epigenetic mechanisms associated with a wide range of disease areas and drug targets. The application of epigenomic profiling technologies to drug safety sciences has great potential for providing novel insights into the molecular basis of long-lasting cellular perturbations including increased susceptibility to disease and/or toxicity, memory of prior immune stimulation and/or drug exposure, and transgenerational effects.

Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation

Retinoblastoma protein (pRB) mediates cell-cycle withdrawal and differentiation by interacting with a variety of proteins. RB-Binding Protein 2 (RBP2) has been shown to be a key effector. We sought to determine transcriptional regulation by RBP2 genome-wide by using location analysis and gene expression profiling experiments. We describe that RBP2 shows high correlation with the presence of H3K4me3 and its target genes are separated into two functionally distinct classes: differentiation-independent and differentiation-dependent genes. The former class is enriched by genes that encode mitochondrial proteins, while the latter is represented by cell-cycle genes. We demonstrate the role of RBP2 in mitochondrial biogenesis, which involves regulation of H3K4me3-modified nucleosomes. Analysis of expression changes upon RBP2 depletion depicted genes with a signature of differentiation control, analogous to the changes seen upon reintroduction of pRB. We conclude that, during differentiation, RBP2 exerts inhibitory effects on multiple genes through direct interaction with their promoters.

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

We characterized the relationship of H3K4me1 and H3K4me3 at distal and proximal regulatory elements by comparing ChIP-seq profiles for these histone modifications and for two functionally different transcription factors: STAT1 in the immortalized HeLa S3 cell line, with and without interferon-gamma (IFNG) stimulation; and FOXA2 in mouse adult liver tissue. In unstimulated and stimulated HeLa cells, respectively, we determined approximately 270,000 and approximately 301,000 H3K4me1-enriched regions, and approximately 54,500 and approximately 76,100 H3K4me3-enriched regions. In mouse adult liver, we determined approximately 227,000 and approximately 34,800 H3K4me1 and H3K4me3 regions. Seventy-five percent of the approximately 70,300 STAT1 binding sites in stimulated HeLa cells and 87% of the approximately 11,000 FOXA2 sites in mouse liver were distal to known gene TSS; in both cell types, approximately 83% of these distal sites were associated with at least one of the two histone modifications, and H3K4me1 was associated with over 96% of marked distal sites. After filtering against predicted transcription start sites, 50% of approximately 26,800 marked distal IFNG-stimulated STAT1 binding sites, but 95% of approximately 5800 marked distal FOXA2 sites, were associated with H3K4me1 only. Results for HeLa cells generated additional insights into transcriptional regulation involving STAT1. STAT1 binding was associated with 25% of all H3K4me1 regions in stimulated HeLa cells, suggesting that a single transcription factor can interact with an unexpectedly large fraction of regulatory regions. Strikingly, for a large majority of the locations of stimulated STAT1 binding, the dominant H3K4me1/me3 combinations were established before activation, suggesting mechanisms independent of IFNG stimulation and high-affinity STAT1 binding.