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1,3,4-Oxadiazole derivatives are among the most studied anticancer drugs. Previous studies have analyzed the action of different 1,3,4-oxadiazole derivatives and their effects on cancer cells. This study investigated the characterization of two new compounds named 6 and 14 on HeLa and PC-3 cancer cell lines. Based on the previously obtained IC50, cell cycle effects were monitored by flow cytometry. RNA sequencing (RNAseq) was performed to identify differentially expressed genes, followed by functional annotation using gene ontology (GO), KEGG signaling pathway enrichment, and protein–protein interaction (PPI) network analyses. The tubulin polymerization assay was used to analyze the interaction of both compounds with tubulin. The results showed that 6 and 14 strongly inhibited the proliferation of cancer cells by arresting them in the G2/M phase of the cell cycle. Transcriptome analysis showed that exposure of HeLa and PC-3 cells to the compounds caused a marked reprograming of gene expression. Functional enrichment analysis indicated that differentially expressed genes were significantly enriched throughout the cell cycle and cancer-related biological processes. Furthermore, PPI network, hub gene, and CMap analyses revealed that compounds 14 and 6 shared target genes with established microtubule inhibitors, indicating points of similarity between the two molecules and microtubule inhibitors in terms of the mechanism of action. They were also able to influence the polymerization process of tubulin, suggesting the potential of these new compounds to be used as efficient chemotherapeutic agents.

Summary How regeneration cues are converted into the epigenetic information that controls gene expression in adult stem cells is currently unknown. We identified an inflammation-activated signaling in muscle stem (satellite) cells, by which the polycomb repressive complex 2 (PRC2) represses Pax7 expression during muscle regeneration. TNF-activated p38α kinase promotes the interaction between YY1 and PRC2, via threonine 372 phosphorylation of EZH2, the enzymatic subunit of the complex, leading to the formation of repressive chromatin on Pax7 promoter. TNF-α antibodies stimulate satellite cell proliferation in regenerating muscles of dystrophic or normal mice. Genetic knockdown or pharmacological inhibition of the enzymatic components of the p38/PRC2 signaling—p38α and EZH2—invariably promote Pax7 expression and expansion of satellite cells that retain their differentiation potential upon signaling resumption. Genetic knockdown of Pax7 impaired satellite cell proliferation in response to p38 inhibition, thereby establishing the biological link between p38/PRC2 signaling to Pax7 and satellite cell decision to proliferate or differentiate.

The Second German-Catalan Workshop on Epigenetics and Cancer was held in Barcelona on November 19–21, 2014. The workshop brought together, for the second time, scientists from 2 German and 2 Catalan research institutions: the DKFZ, from Heidelberg, the CRCME, from Freiburg, and the IMPPC and PEBC/IDIBELL, both from Barcelona. The German-Catalan Workshops are intended to establish the framework for building a Research School to foster collaborations between researchers from the different institutions. Exchange programs for graduate students are among the activities of the future School. The topics presented and discussed in 33 talks were diverse and included work on DNA methylation, histone modifications, chromatin biology, characterization of imprinted regions in human tissues, non-coding RNAs, and epigenetic drug discovery. Among novel developments from the previous Workshop are the report of the epigenetics angle of the Warburg effect and the long-range trans-acting interaction of DNA methylation and of nucleosome remodeling. A shift in the view on DNA methylation became apparent by the realization of the intertwined interplay between hyper- and hypo-methylation in differentiation and cancer.

Recently, numerous interdisciplinary approaches that include integration of bioinformatics, epigenetics, and molecular and cellular biology have started to shed light on the complex dynamics that regulate cellular processes such as cell “stemness,” reprogramming, and differentiation. From the sequencing of the first complete genomes to the recent high-throughput genomic and proteomic approaches, a huge amount of information has been generated to improve our understanding of how the eukaryotic genome works to activate and coordinate specific programs of gene expression. The focus of this review is to provide an overview of the epigenetic regulatory mechanisms controlling crucial cellular fate decisions, in particular during differentiation and reprogramming. A special emphasis has been given to skeletal myogenesis, as it provides an amenable model for in vitro and in vivo studies. Y. Ito et al. in “A system approach and skeletal myogenesis” provide an overview of the most common approaches currently used to address transcriptional regulation. They discuss deep sequencing and microarray-based methods, cell-based high throughput assays, and the generation of in situ gene expression databases as potent tools to dissect complex networks of gene expression. Using skeletal muscle as a paradigm, they highlight the main discoveries obtained through the different methods and underline the advantages of an integrated approach to obtain a full picture of cellular differentiation. An increasing number of studies suggest an epigenetic component in the development of many human diseases. In the review article “Epigenetic alterations in muscular disorders,” Dr. C. Lanzuolo discusses how altered epigenetic mechanisms contribute to human pathology and in particular to the development and progression of neuromuscular disorders. Muscular dystrophies arise from either mutations of proteins that play a role in the integrity of the sarcolemma—the plasma membrane that wraps the myofibers in skeletal muscles—or are due to a dysfunction within the cell nucleus. Dr. C. Lanzuolo focuses on the so-called nuclear muscular dystrophies and she analyzes the possible contribution of an important group of epigenetic modifiers, the polycomb-group (PcG) complexes, to the pathogenesis of these diseases. The dissection of the aberrant epigenetic profiles associated to several human pathologies has contributed to the design of experimental therapies with epigenetic drugs. The review “Tackling skeletal muscle cells epigenome in the next-generation sequencing era” by R. Fittipaldi and G. Caretti points to the significance of genome-wide study of the epigenetic modifications and the transcription factors that are activated during skeletal muscle differentiation. The authors discuss on the new genome-wide technologies to monitor the epigenetic landscape that characterizes myoblast-to-myotube transition in order to obtain innovative information on molecular mechanisms orchestrating biological processes, such myogenic differentiation. The fine regulation of a myogenic gene such as myogenin is discussed in “Turning on myogenin in muscle: A paradigm for understanding mechanisms of tissue-specific gene expression” by H. Faralli and F. J. Dilworth. Transcription factors, cofactors, and epigenetic modifications contribute to regulate muscle-specific gene expression during development. In particular, the authors highlight the fact that a tissue-specific factors such as MyoD cooperate with more ubiquitously expressed proteins (Six4, Mef2, and Pbx1) to establish a transcriptionally permissive environment to ensure proper spatiotemporal myogenin expression. The current challenge of epigenetics is how to analyse and extract biological knowledge from the large volumes of data produced with new high-throughput technologies. In this regard, the paper of S. Althammer et al., “Predictive models of gene regulation from high-throughput epigenomics data” describes a computational framework using integrative tools and machine learning algorithms that facilitate the systematic analysis of high-throughput sequencing epigenetic data for integrative studies. Their analysis shows a different epigenetic code of expression for intron-less and intron-containing genes, with more prominent differences for genes with low GC content (LGC) in their promoter, showing for instance that at the promoter regions of LGC intron-less genes, H3K36me3 and H3K4me1 are the most informative marks while in polyadenylation sites of expressed genes, the H3K36me3 signal is much weaker than in intron-containing genes. Based on epigenetic data, their model predicts very strongly gene expression between two conditions; therefore, this approach can be applied to study gene expression in different developmental stages, disease states, or treatments. Of tremendous relevance for its therapeutic potential, is the possibility to manipulate cell identity. In the review titled “The stability of the induced epigenetic programs”, M. J. Barrero discusses the epigenetic changes that occur during differentiation and the way back upon cellular reprogramming emphasizing on the thin regulation of pluripotent and lineage-specific genes expression to ensure a correct differentiation during development and in adult life. “The epigenetic regulation of B lymphocyte differentiation, transdifferentiation, and reprogramming” by B. Barneda-Zahonero et al. reviews the hierarchical network of transcription factors that mediate the epigenetic signature regulating the transcriptome during B cell development. B lymphocytes are highly specialized terminally differentiated cells responsible for generating high-affinity antibodies, providing the humoral immunity against pathogens. Every day the human body generates millions of B lymphocytes from precursor hematopoietic stem cells by a differentiation process that is a tightly regulated. This multistep differentiation process, vital to immunity, combines the successive expression of specific transcriptional factors and associated epigenetic changes to restrict the developmental potential of lymphoid progenitors to the B cell pathway by repressing B-lineage-inappropriate genes, while simultaneously promoting B cell development by activating B-lymphoid-specific genes. Lucia Latella Daniela Palacios Sonia Forcales Pier Lorenzo Puri

During muscle regeneration, the mechanism integrating environmental cues at the chromatin of muscle progenitors is unknown. We show that inflammation-activated MKK6-p38 and insulin growth factor 1 (IGF1)-induced PI3K/AKT pathways converge on the chromatin of muscle genes to target distinct components of the muscle transcriptosome. p38 alpha/beta kinases recruit the SWI/SNF chromatin-remodeling complex; AKT1 and 2 promote the association of MyoD with p300 and PCAF acetyltransferases, via direct phosphorylation of p300. Pharmacological or genetic interference with either pathway led to partial assembly of discrete chromatin-bound complexes, which reflected two reversible and distinct cellular phenotypes. Remarkably, PI3K/AKT blockade was permissive for chromatin recruitment of MEF2-SWI/SNF complex, whose remodeling activity was compromised in the absence of MyoD and acetyltransferases. The functional interdependence between p38 and IGF1/PI3K/AKT pathways was further established by the evidence that blockade of AKT chromatin targets was sufficient to prevent the activation of the myogenic program triggered by deliberate activation of p38 signaling.

The balance between acetylation and deacetylation of histone and nonhistone proteins controls gene expression in a variety of cellular processes, with transcription being activated by acetyltransferases and silenced by deacetylases. We report here the formation and enzymatic characterization of a complex between the acetyltransferase p300 and histone deacetylases. The C/H3 region of p300 was found to co-purify deacetylase activity from nuclear cell extracts. A prototype of class I histone deacetylases, HDAC1, interacts with p300 C/H3 domain in vitro and in vivo. The p300-binding protein E1A competes with HDAC1 for C/H3 binding; and, like E1A, HDAC1 overexpression interferes with either activation of Gal4p300 fusion protein or p300-dependent co-activation of two C/H3-binding proteins, MyoD and p53. The exposure to deacetylase inhibitors could reverse the dominant-negative effect of a C/H3 fragment insulated from the rest of the molecule, on MyoD- and p53-dependent transcription, whereas inhibition by E1A was resistant to trichostatin A. These data support the hypothesis that association between acetyltransferases and deacetylases can control the expression of genes implicated in cellular growth and differentiation, and suggest that the dominant-negative effect of the p300 C/H3 fragment relies on deacetylase recruitment.