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Epigenetics & Chromatin

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https://www.readbyqxmd.com/read/28096900/ms_histonedb-a-manually-curated-resource-for-proteomic-analysis-of-human-and-mouse-histones
#1
Sara El Kennani, Annie Adrait, Alexey K Shaytan, Saadi Khochbin, Christophe Bruley, Anna R Panchenko, David Landsman, Delphine Pflieger, Jérôme Govin
BACKGROUND: Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry data relies on public databases which are either not exhaustive (Swiss-Prot) or contain many redundant entries (UniProtKB or NCBI). Currently, no protein database is ideally suited for the analysis of histones and the complex array of mammalian histone variants...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28035242/the-detailed-3d-multi-loop-aggregate-rosette-chromatin-architecture-and-functional-dynamic-organization-of-the-human-and-mouse-genomes
#2
Tobias A Knoch, Malte Wachsmuth, Nick Kepper, Michael Lesnussa, Anis Abuseiris, A M Ali Imam, Petros Kolovos, Jessica Zuin, Christel E M Kockx, Rutger W W Brouwer, Harmen J G van de Werken, Wilfred F J van IJcken, Kerstin S Wendt, Frank G Grosveld
BACKGROUND: The dynamic three-dimensional chromatin architecture of genomes and its co-evolutionary connection to its function-the storage, expression, and replication of genetic information-is still one of the central issues in biology. Here, we describe the much debated 3D architecture of the human and mouse genomes from the nucleosomal to the megabase pair level by a novel approach combining selective high-throughput high-resolution chromosomal interaction capture (T2C), polymer simulations, and scaling analysis of the 3D architecture and the DNA sequence...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28035241/dynamic-properties-of-independent-chromatin-domains-measured-by-correlation-spectroscopy-in-living-cells
#3
Malte Wachsmuth, Tobias A Knoch, Karsten Rippe
BACKGROUND: Genome organization into subchromosomal topologically associating domains (TADs) is linked to cell-type-specific gene expression programs. However, dynamic properties of such domains remain elusive, and it is unclear how domain plasticity modulates genomic accessibility for soluble factors. RESULTS: Here, we combine and compare a high-resolution topology analysis of interacting chromatin loci with fluorescence correlation spectroscopy measurements of domain dynamics in single living cells...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27980682/-gap-hunting-to-characterize-clustered-probe-signals-in-illumina-methylation-array-data
#4
Shan V Andrews, Christine Ladd-Acosta, Andrew P Feinberg, Kasper D Hansen, M Daniele Fallin
BACKGROUND: The Illumina 450k array has been widely used in epigenetic association studies. Current quality-control (QC) pipelines typically remove certain sets of probes, such as those containing a SNP or with multiple mapping locations. An additional set of potentially problematic probes are those with DNA methylation distributions characterized by two or more distinct clusters separated by gaps. Data-driven identification of such probes may offer additional insights for downstream analyses...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27980681/targeted-bisulfite-sequencing-of-the-dynamic-dna-methylome
#5
Michael J Ziller, Elena K Stamenova, Hongcang Gu, Andreas Gnirke, Alexander Meissner
BACKGROUND: The ability to measure DNA methylation precisely and efficiently continues to drive our understanding of this modification in development and disease. Whole genome bisulfite sequencing has the advantage of theoretically capturing all cytosines in the genome at single-nucleotide resolution, but it has a number of significant practical drawbacks that become amplified with increasing sample numbers. All other technologies capture only a fraction of the cytosines that show dynamic regulation across cell and tissue types...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27980680/hoxa-repression-is-mediated-by-nucleoporin-nup93-assisted-by-its-interactors-nup188-and-nup205
#6
Ajay S Labade, Krishanpal Karmodiya, Kundan Sengupta
BACKGROUND: The nuclear pore complex (NPC) mediates nuclear transport of RNA and proteins into and out of the nucleus. Certain nucleoporins have additional functions in chromatin organization and transcription regulation. Nup93 is a scaffold nucleoporin at the nuclear pore complex which is associated with human chromosomes 5, 7 and 16 and with the promoters of the HOXA gene as revealed by ChIP-on-chip studies using tiling microarrays for these chromosomes. However, the functional consequences of the association of Nup93 with HOXA is unknown...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27895716/widespread-recovery-of-methylation-at-gametic-imprints-in-hypomethylated-mouse-stem-cells-following-rescue-with-dnmt3a2
#7
Avinash Thakur, Sarah-Jayne Mackin, Rachelle E Irwin, Karla M O'Neill, Gareth Pollin, Colum Walsh
BACKGROUND: Imprinted loci are paradigms of epigenetic regulation and are associated with a number of genetic disorders in human. A key characteristic of imprints is the presence of a gametic differentially methylated region (gDMR). Previous studies have indicated that DNA methylation lost from gDMRs could not be restored by DNMT1, or the de novo enzymes DNMT3A or 3B in stem cells, indicating that imprinted regions must instead undergo passage through the germline for reprogramming. However, previous studies were non-quantitative, were unclear on the requirement for DNMT3A/B and showed some inconsistencies...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27895715/protein-kinase-msk1-physically-and-functionally-interacts-with-the-kmt2a-mll1-methyltransferase-complex-and-contributes-to-the-regulation-of-multiple-target-genes
#8
Maaike Wiersma, Marianne Bussiere, John A Halsall, Nil Turan, Robert Slany, Bryan M Turner, Karl P Nightingale
BACKGROUND: The KMT2A/MLL1 lysine methyltransferase complex is an epigenetic regulator of selected developmental genes, in part through the SET domain-catalysed methylation of H3K4. It is essential for normal embryonic development and haematopoiesis and frequently mutated in cancer. The catalytic properties and targeting of KMT2A/MLL1 depend on the proteins with which it complexes and the post-translational protein modifications which some of these proteins put in place, though detailed mechanisms remain unclear...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27833660/insights-into-long-noncoding-rnas-of-naked-mole-rat-heterocephalus-glaber-and-their-potential-association-with-cancer-resistance
#9
Jian-Jun Jiang, Le-Hua Cheng, Huan Wu, Yong-Han He, Qing-Peng Kong
BACKGROUND: Long noncoding RNAs (lncRNAs) are a class of ubiquitous noncoding RNAs and have been found to act as tumor suppressors or oncogenes, which dramatically altered our understanding of cancer. Naked mole rat (NMR, Heterocephalus glaber) is an exceptionally long-lived and cancer-resistant rodent; however, whether lncRNAs play roles in cancer resistance in this seductive species remains unknown. RESULTS: In this study, we developed a pipeline and identified a total of 4422 lncRNAs across the NMR genome based on 12 published transcriptomes...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27833659/identification-of-activated-enhancers-and-linked-transcription-factors-in-breast-prostate-and-kidney-tumors-by-tracing-enhancer-networks-using-epigenetic-traits
#10
Suhn Kyong Rhie, Yu Guo, Yu Gyoung Tak, Lijing Yao, Hui Shen, Gerhard A Coetzee, Peter W Laird, Peggy J Farnham
BACKGROUND: Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach toward understanding the molecular events that lead to cancer is to characterize changes in transcriptional regulatory networks between normal and tumor tissue. Because enhancer activity is thought to be critical in regulating cell fate decisions, we have focused our studies on distal regulatory elements and transcription factors that bind to these elements...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27826357/systematic-comparison-of-monoclonal-versus-polyclonal-antibodies-for-mapping-histone-modifications-by-chip-seq
#11
Michele Busby, Catherine Xue, Catherine Li, Yossi Farjoun, Elizabeth Gienger, Ido Yofe, Adrianne Gladden, Charles B Epstein, Evan M Cornett, Scott B Rothbart, Chad Nusbaum, Alon Goren
BACKGROUND: The robustness of ChIP-seq datasets is highly dependent upon the antibodies used. Currently, polyclonal antibodies are the standard despite several limitations: They are non-renewable, vary in performance between lots and need to be validated with each new lot. In contrast, monoclonal antibody lots are renewable and provide consistent performance. To increase ChIP-seq standardization, we investigated whether monoclonal antibodies could replace polyclonal antibodies. We compared monoclonal antibodies that target five key histone modifications (H3K4me1, H3K4me3, H3K9me3, H3K27ac and H3K27me3) to their polyclonal counterparts in both human and mouse cells...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27822313/quantitative-analysis-of-chip-seq-data-uncovers-dynamic-and-sustained-h3k4me3-and-h3k27me3-modulation-in-cancer-cells-under-hypoxia
#12
Michiel E Adriaens, Peggy Prickaerts, Michelle Chan-Seng-Yue, Twan van den Beucken, Vivian E H Dahlmans, Lars M Eijssen, Timothy Beck, Bradly G Wouters, Jan Willem Voncken, Chris T A Evelo
BACKGROUND: A comprehensive assessment of the epigenetic dynamics in cancer cells is the key to understanding the molecular mechanisms underlying cancer and to improving cancer diagnostics, prognostics and treatment. By combining genome-wide ChIP-seq epigenomics and microarray transcriptomics, we studied the effects of oxygen deprivation and subsequent reoxygenation on histone 3 trimethylation of lysine 4 (H3K4me3) and lysine 27 (H3K27me3) in a breast cancer cell line, serving as a model for abnormal oxygenation in solid tumors...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27800026/hypoxia-increases-genome-wide-bivalent-epigenetic-marking-by-specific-gain-of-h3k27me3
#13
Peggy Prickaerts, Michiel E Adriaens, Twan van den Beucken, Elizabeth Koch, Ludwig Dubois, Vivian E H Dahlmans, Caroline Gits, Chris T A Evelo, Michelle Chan-Seng-Yue, Bradly G Wouters, Jan Willem Voncken
BACKGROUND: Trimethylation at histone H3 lysine 4 (H3K4me3) and lysine 27 (H3K27me3) controls gene activity during development and differentiation. Whether H3K4me3 and H3K27me3 changes dynamically in response to altered microenvironmental conditions, including low-oxygen conditions commonly present in solid tumors, is relatively unknown. Demethylation of H3K4me3 and H3K27me3 is mediated by oxygen and 2-oxoglutarate dioxygenases enzymes, suggesting that oxygen deprivation (hypoxia) may influence histone trimethylation...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27800025/histone-macroh2a1-2-promotes-metabolic-health-and-leanness-by-inhibiting-adipogenesis
#14
Valerio Pazienza, Concetta Panebianco, Francesca Rappa, Domenico Memoli, Michela Borghesan, Sara Cannito, Asami Oji, Giuseppe Mazza, Domenico Tamburrino, Giuseppe Fusai, Rosario Barone, Giulia Bolasco, Francesc Villarroya, Joan Villarroya, Kiyotaka Hatsuzawa, Francesco Cappello, Roberta Tarallo, Tomoko Nakanishi, Manlio Vinciguerra
BACKGROUND: Obesity has tremendous impact on the health systems. Its epigenetic bases are unclear. MacroH2A1 is a variant of histone H2A, present in two alternatively exon-spliced isoforms macroH2A1.1 and macroH2A1.2, regulating cell plasticity and proliferation, during pluripotency and tumorigenesis. Their role in adipose tissue plasticity is unknown. RESULTS: Here, we show evidence that macroH2A1.1 protein levels in the visceral adipose tissue of obese humans positively correlate with BMI, while macroH2A1...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27795737/expression-and-epigenomic-landscape-of-the-sex-chromosomes-in-mouse-post-meiotic-male-germ-cells
#15
Charlotte Moretti, Daniel Vaiman, Frederic Tores, Julie Cocquet
BACKGROUND: During meiosis, the X and Y chromosomes are transcriptionally silenced. The persistence of repressive chromatin marks on the sex chromatin after meiosis initially led to the assumption that XY gene silencing persists to some extent in spermatids. Considering the many reports of XY-linked genes expressed and needed in the post-meiotic phase of mouse spermatogenesis, it is still unclear whether or not the mouse sex chromatin is a repressive or permissive environment, after meiosis...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27777629/an-h4k16-histone-acetyltransferase-mediates-decondensation-of-the-x-chromosome-in-c-elegans-males
#16
Alyssa C Lau, Kevin P Zhu, Elizabeth A Brouhard, Michael B Davis, Györgyi Csankovszki
BACKGROUND: In C. elegans, in order to equalize gene expression between the sexes and balance X and autosomal expression, two steps are believed to be required. First, an unknown mechanism is hypothesized to upregulate the X chromosome in both sexes. This mechanism balances the X to autosomal expression in males, but creates X overexpression in hermaphrodites. Therefore, to restore the balance, hermaphrodites downregulate gene expression twofold on both X chromosomes. While many studies have focused on X chromosome downregulation, the mechanism of X upregulation is not known...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27777628/high-throughput-assessment-of-context-dependent-effects-of-chromatin-proteins
#17
Laura Brueckner, Joris van Arensbergen, Waseem Akhtar, Ludo Pagie, Bas van Steensel
BACKGROUND: Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporters with Gal4-mediated tethering. We applied the assay to Drosophila heterochromatin protein 1a (HP1a), which is mostly known as a repressive protein but has also been linked to transcriptional activation...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27708717/epimine-a-computational-program-for-mining-epigenomic-data
#18
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
https://www.readbyqxmd.com/read/27688812/imprinted-dna-methylation-reconstituted-at-a-non-imprinted-locus
#19
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
https://www.readbyqxmd.com/read/27679670/nucleosome-distortion-as-a-possible-mechanism-of-transcription-activation-domain-function
#20
REVIEW
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
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