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Epigenetics & Chromatin

SriGanesh Jammula, Diego Pasini
BACKGROUND: In epigenetic research, both the increasing ease of high-throughput sequencing and a greater interest in genome-wide studies have resulted in an exponential flooding of epigenetic-related data in public domain. This creates an opportunity for exploring data outside the limits of any specific query-centred study. Such data have to undergo standard primary analyses that are accessible with multiple well-stabilized programs. Further downstream analyses, such as genome-wide comparative, correlative and quantitative analyses, are critical in deciphering key biological features...
2016: Epigenetics & Chromatin
David H Taylor, Chelsea M McLean, Warren L Wu, Alex B Wang, Paul D Soloway
BACKGROUND: In mammals, tight regulation of cytosine methylation is required for embryonic development and cellular differentiation. The trans-acting DNA methyltransferases that catalyze this modification have been identified and characterized; however, these proteins lack sequence specificity, leaving the mechanism of targeting unknown. A cis-acting regulator within the Rasgrf1 imprinting control region (ICR) is necessary for establishment and maintenance of local imprinted methylation...
2016: Epigenetics & Chromatin
Tamara Y Erkina, Alexandre M Erkine
After more than three decades since the discovery of transcription activation domains (ADs) in gene-specific activators, the mechanism of their function remains enigmatic. The widely accepted model of direct recruitment by ADs of co-activators and basal transcriptional machinery components, however, is not always compatible with the short size yet very high degree of sequence randomness and intrinsic structural disorder of natural and synthetic ADs. In this review, we formulate the basis for an alternative and complementary model, whereby sequence randomness and intrinsic structural disorder of ADs are necessary for transient distorting interactions with promoter nucleosomes, triggering promoter nucleosome translocation and subsequently gene activation...
2016: Epigenetics & Chromatin
Stéphanie Käser-Pébernard, Catherine Pfefferli, Caroline Aschinger, Chantal Wicky
BACKGROUND: The nucleosome remodeling and deacetylase complex promotes cell fate decisions throughout embryonic development. Its core enzymatic subunit, the SNF2-like ATPase and Helicase Mi2, is well conserved throughout the eukaryotic kingdom and can be found in multiple and highly homologous copies in all vertebrates and some invertebrates. However, the reasons for such duplications and their implications for embryonic development are unknown. RESULTS: Here we studied the two C...
2016: Epigenetics & Chromatin
Philge Philip, Ann Boija, Roshan Vaid, Allison M Churcher, David J Meyers, Philip A Cole, Mattias Mannervik, Per Stenberg
[This corrects the article DOI: 10.1186/s13072-015-0042-4.].
2016: Epigenetics & Chromatin
Jian Sun, Yilin Zhao, Rebecca McGreal, Yamit Cohen-Tayar, Shira Rockowitz, Carola Wilczek, Ruth Ashery-Padan, David Shechter, Deyou Zheng, Ales Cvekl
BACKGROUND: Pax6 is a key regulator of the entire cascade of ocular lens formation through specific binding to promoters and enhancers of batteries of target genes. The promoters and enhancers communicate with each other through DNA looping mediated by multiple protein-DNA and protein-protein interactions and are marked by specific combinations of histone posttranslational modifications (PTMs). Enhancers are distinguished from bulk chromatin by specific modifications of core histone H3, including H3K4me1 and H3K27ac, while promoters show increased H3K4me3 PTM...
2016: Epigenetics & Chromatin
Anna Török, Philipp H Schiffer, Christine E Schnitzler, Kris Ford, James C Mullikin, Andreas D Baxevanis, Antony Bacic, Uri Frank, Sebastian G Gornik
BACKGROUND: Cnidarians are a group of early branching animals including corals, jellyfish and hydroids that are renowned for their high regenerative ability, growth plasticity and longevity. Because cnidarian genomes are conventional in terms of protein-coding genes, their remarkable features are likely a consequence of epigenetic regulation. To facilitate epigenetics research in cnidarians, we analysed the histone complement of the cnidarian model organism Hydractinia echinata using phylogenomics, proteomics, transcriptomics and mRNA in situ hybridisations...
2016: Epigenetics & Chromatin
Elena M Pugacheva, Evgeny Teplyakov, Qiongfang Wu, Jingjing Li, Cheng Chen, Chengcheng Meng, Jian Liu, Susan Robinson, Dmitry Loukinov, Abdelhalim Boukaba, Andrew Paul Hutchins, Victor Lobanenkov, Alexander Strunnikov
BACKGROUND: A common aberration in cancer is the activation of germline-specific proteins. The DNA-binding proteins among them could generate novel chromatin states, not found in normal cells. The germline-specific transcription factor BORIS/CTCFL, a paralog of chromatin architecture protein CTCF, is often erroneously activated in cancers and rewires the epigenome for the germline-like transcription program. Another common feature of malignancies is the changed expression and epigenetic states of genomic repeats, which could alter the transcription of neighboring genes and cause somatic mutations upon transposition...
2016: Epigenetics & Chromatin
Hongfeng Chen, Jason J Workman, Brian D Strahl, R Nicholas Laribee
BACKGROUND: How cells respond and adapt to environmental changes, such as nutrient flux, remains poorly understood. Evolutionarily conserved nutrient signaling cascades can regulate chromatin to contribute to genome regulation and cell adaptation, yet how they do so is only now beginning to be elucidated. In this study, we provide evidence in yeast that the conserved nutrient regulated target of rapamycin complex 1 (TORC1) pathway, and the histone H3N-terminus at lysine 37 (H3K37), function collaboratively to restrict specific chromatin-binding high mobility group box (HMGB) proteins to the nucleus to maintain cellular homeostasis and viability...
2016: Epigenetics & Chromatin
Stefan Wallner, Christopher Schröder, Elsa Leitão, Tea Berulava, Claudia Haak, Daniela Beißer, Sven Rahmann, Andreas S Richter, Thomas Manke, Ulrike Bönisch, Laura Arrigoni, Sebastian Fröhler, Filippos Klironomos, Wei Chen, Nikolaus Rajewsky, Fabian Müller, Peter Ebert, Thomas Lengauer, Matthias Barann, Philip Rosenstiel, Gilles Gasparoni, Karl Nordström, Jörn Walter, Benedikt Brors, Gideon Zipprich, Bärbel Felder, Ludger Klein-Hitpass, Corinna Attenberger, Gerd Schmitz, Bernhard Horsthemke
BACKGROUND: Monocyte-to-macrophage differentiation involves major biochemical and structural changes. In order to elucidate the role of gene regulatory changes during this process, we used high-throughput sequencing to analyze the complete transcriptome and epigenome of human monocytes that were differentiated in vitro by addition of colony-stimulating factor 1 in serum-free medium. RESULTS: Numerous mRNAs and miRNAs were significantly up- or down-regulated. More than 100 discrete DNA regions, most often far away from transcription start sites, were rapidly demethylated by the ten eleven translocation enzymes, became nucleosome-free and gained histone marks indicative of active enhancers...
2016: Epigenetics & Chromatin
Shih-Ying Tsai, Yuh-Long Chang, Krishna B S Swamy, Ruei-Lin Chiang, Der-Hwa Huang
BACKGROUND: Genome-wide studies in higher eukaryotes have revealed the presence of paused RNA polymerase II (RNA-Pol) at about 30-50 bp downstream of the transcription start site of genes involved in developmental control, cell proliferation and intercellular signaling. Promoter-proximal pausing is believed to represent a critical step in transcriptional regulation. GAGA sequence motifs have frequently been found in the upstream region of paused genes in Drosophila, implicating a prevalent binding factor, GAF, in transcriptional pausing...
2016: Epigenetics & Chromatin
Kostas A Triantaphyllopoulos, Ioannis Ikonomopoulos, Andrew J Bannister
Epigenetic inheritance plays a crucial role in many biological processes, such as gene expression in early embryo development, imprinting and the silencing of transposons. It has recently been established that epigenetic effects can be inherited from one generation to the next. Here, we review examples of epigenetic mechanisms governing animal phenotype and behaviour, and we discuss the importance of these findings in respect to animal studies, and livestock in general. Epigenetic parameters orchestrating transgenerational effects, as well as heritable disorders, and the often-overlooked areas of livestock immunity and stress, are also discussed...
2016: Epigenetics & Chromatin
Niran Hadad, Dustin R Masser, Sreemathi Logan, Benjamin Wronowski, Colleen A Mangold, Nicholas Clark, Laura Otalora, Archana Unnikrishnan, Matthew M Ford, Cory B Giles, Jonathan D Wren, Arlan Richardson, William E Sonntag, David R Stanford, Willard Freeman
BACKGROUND: Changes to the epigenome with aging, and DNA modifications in particular, have been proposed as a central regulator of the aging process, a predictor of mortality, and a contributor to the pathogenesis of age-related diseases. In the central nervous system, control of learning and memory, neurogenesis, and plasticity require changes in cytosine methylation and hydroxymethylation. Although genome-wide decreases in methylation with aging are often reported as scientific dogma, primary research reports describe decreases, increases, or lack of change in methylation and hydroxymethylation and their principle regulators, DNA methyltransferases and ten-eleven translocation dioxygenases in the hippocampus...
2016: Epigenetics & Chromatin
Tamas Aranyi, Daniel Stockholm, Roseline Yao, Catherine Poinsignon, Thibaut Wiart, Guillaume Corre, Nizar Touleimat, Jörg Tost, Anne Galy, Andràs Paldi
BACKGROUND: Lentiviral vectors (LV) are widely used for various gene transfer or gene therapy applications. The effects of LV on target cells are expected to be limited to gene delivery. Yet, human hematopoietic CD34+ cells respond to functional LVs as well as several types of non-integrating LVs by genome-wide DNA methylation changes. RESULTS: A new algorithm for the analysis of 450K Illumina data showed that these changes were marked by de novo methylation. The same 4126 cytosines located in islands corresponding to 1059 genes were systematically methylated...
2016: Epigenetics & Chromatin
Juan Du, Amy Leung, Candi Trac, Michael Lee, Brian W Parks, Aldons J Lusis, Rama Natarajan, Dustin E Schones
BACKGROUND: Functional regulatory regions in eukaryotic genomes are characterized by the disruption of nucleosomes leading to accessible chromatin. The modulation of chromatin accessibility is one of the key mediators of transcriptional regulation, and variation in chromatin accessibility across individuals has been linked to complex traits and disease susceptibility. While mechanisms responsible for chromatin variation across individuals have been investigated, the overwhelming majority of chromatin variation remains unexplained...
2016: Epigenetics & Chromatin
Sara Fneich, André Théron, Céline Cosseau, Anne Rognon, Benoit Aliaga, Jérôme Buard, David Duval, Nathalie Arancibia, Jérôme Boissier, David Roquis, Guillaume Mitta, Christoph Grunau
BACKGROUND: Adaptive evolution is not possible without the generation of phenotypic variants. The origin of these variations has been a central topic in evolutionary biology. Up to now, it was commonly accepted that standing genetic variation is the only cause of phenotypic variants. However, epigenetic information is emerging as a complementary source of heritable phenotypic variation that contributes to evolution. The relative importance of genetics and epigenetics in generating heritable phenotypic variation is nevertheless a matter of debate...
2016: Epigenetics & Chromatin
Wai-Shin Yong, Fei-Man Hsu, Pao-Yang Chen
DNA methylation is an epigenetic modification that plays an important role in regulating gene expression and therefore a broad range of biological processes and diseases. DNA methylation is tissue-specific, dynamic, sequence-context-dependent and trans-generationally heritable, and these complex patterns of methylation highlight the significance of profiling DNA methylation to answer biological questions. In this review, we surveyed major methylation assays, along with comparisons and biological examples, to provide an overview of DNA methylation profiling techniques...
2016: Epigenetics & Chromatin
Elodie Portales-Casamar, Alexandre A Lussier, Meaghan J Jones, Julia L MacIsaac, Rachel D Edgar, Sarah M Mah, Amina Barhdadi, Sylvie Provost, Louis-Philippe Lemieux-Perreault, Max S Cynader, Albert E Chudley, Marie-Pierre Dubé, James N Reynolds, Paul Pavlidis, Michael S Kobor
BACKGROUND: Prenatal alcohol exposure is the leading preventable cause of behavioral and cognitive deficits, which may affect between 2 and 5 % of children in North America. While the underlying mechanisms of alcohol's effects on development remain relatively unknown, emerging evidence implicates epigenetic mechanisms in mediating the range of symptoms observed in children with fetal alcohol spectrum disorder (FASD). Thus, we investigated the effects of prenatal alcohol exposure on genome-wide DNA methylation in the NeuroDevNet FASD cohort, the largest cohort of human FASD samples to date...
2016: Epigenetics & Chromatin
Lacey J Luense, Xiaoshi Wang, Samantha B Schon, Angela H Weller, Enrique Lin Shiao, Jessica M Bryant, Marisa S Bartolomei, Christos Coutifaris, Benjamin A Garcia, Shelley L Berger
BACKGROUND: During the process of spermatogenesis, male germ cells undergo dramatic chromatin reorganization, whereby most histones are replaced by protamines, as part of the pathway to compact the genome into the small nuclear volume of the sperm head. Remarkably, approximately 90 % (human) to 95 % (mouse) of histones are evicted during the process. An intriguing hypothesis is that post-translational modifications (PTMs) decorating histones play a critical role in epigenetic regulation of spermatogenesis and embryonic development following fertilization...
2016: Epigenetics & Chromatin
Melissa T Manners, Adam Ertel, Yuzhen Tian, Seena K Ajit
BACKGROUND: Methyl-CpG-binding protein 2 (MeCP2), a protein with affinity for methylated cytosines, is crucial for neuronal development and function. MeCP2 regulates gene expression through activation, repression and chromatin remodeling. Mutations in MeCP2 cause Rett syndrome, and these patients display impaired nociception. We observed an increase in MeCP2 expression in mouse dorsal root ganglia (DRG) after peripheral nerve injury. The functional implication of increased MeCP2 is largely unknown...
2016: Epigenetics & Chromatin
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