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Epigenetics & Chromatin

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https://www.readbyqxmd.com/read/29329550/systematic-quantitative-analysis-of-h2a-and-h2b-variants-by-targeted-proteomics
#1
Sara El Kennani, Annie Adrait, Olga Permiakova, Anne-Marie Hesse, Côme Ialy-Radio, Myriam Ferro, Virginie Brun, Julie Cocquet, Jérôme Govin, Delphine Pflieger
BACKGROUND: Histones organize DNA into chromatin through a variety of processes. Among them, a vast diversity of histone variants can be incorporated into chromatin and finely modulate its organization and functionality. Classically, the study of histone variants has largely relied on antibody-based assays. However, antibodies have a limited efficiency to discriminate between highly similar histone variants. RESULTS: In this study, we established a mass spectrometry-based analysis to address this challenge...
January 12, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29310712/genome-wide-screening-of-dna-methylation-in-bovine-blastocysts-with-different-kinetics-of-development
#2
Jessica Ispada, Camila Bruna de Lima, Marc-André Sirard, Patrícia Kubo Fontes, Marcelo Fábio Gouveia Nogueira, Kelly Annes, Marcella Pecora Milazzotto
BACKGROUND: The timing of the first cell divisions may predict the developmental potential of an embryo, including its ability to establish pregnancy. Besides differences related to metabolism, stress, and survival, embryos with different speeds of development present distinct patterns of gene expression, mainly related to energy and lipid metabolism. As gene expression is regulated by epigenetic factors, and that includes DNA methylation patterns, in this study we compared the global DNA methylation profile of embryos with different kinetics of development in order to identify general pathways and regions that are most influenced by this phenotype...
January 8, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29273066/co-regulation-of-transcription-by-brg1-and-brm-two-mutually-exclusive-swi-snf-atpase-subunits
#3
Jesse R Raab, John S Runge, Camarie C Spear, Terry Magnuson
BACKGROUND: SWI/SNF is a large heterogeneous multi-subunit chromatin remodeling complex. It consists of multiple sets of mutually exclusive components. Understanding how loss of one sibling of a mutually exclusive pair affects the occupancy and function of the remaining complex is needed to understand how mutations in a particular subunit might affect tumor formation. Recently, we showed that the members of the ARID family of SWI/SNF subunits (ARID1A, ARID1B and ARID2) had complex transcriptional relationships including both antagonism and cooperativity...
December 22, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29273057/cenp-b-protects-centromere-chromatin-integrity-by-facilitating-histone-deposition-via-the-h3-3-specific-chaperone-daxx
#4
Viacheslav M Morozov, Serena Giovinazzi, Alexander M Ishov
BACKGROUND: The main chromatin unit, the nucleosome, can be modulated by the incorporation of histone variants that, in combination with posttranslational histones modifications, determine epigenetics properties of chromatin. Understanding the mechanism that creates a histone variants landscape at different genomic elements is expected to elevate our comprehension of chromatin assembly and function. The Daxx chaperone deposits transcription-associated histone H3.3 at centromeres, but mechanism of centromere-specific Daxx targeting remains unclear...
December 22, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29233176/uncoordinated-expression-of-dna-methylation-related-enzymes-in-human-cancer
#5
Jiao Liu, Xiuliang Cui, Jinhua Jiang, Dan Cao, Yufei He, Hongyang Wang
BACKGROUND: In addition to the important roles played by 5-methylcytosine (5mC), emerging evidence suggests that 5mC derivatives, such as 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), also exhibit regulatory functions in physiological and pathological processes. Four cytosine modifications (5mC, 5hmC, 5fC and 5caC) are produced and erased by a cyclic enzymatic cascade mediated by DNA methyltransferases (DNMTs), ten-eleven translocation (TET) family enzymes and thymine DNA glycosylase (TDG)...
December 12, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29221486/a-screening-system-to-identify-transcription-factors-that-induce-binding-site-directed-dna-demethylation
#6
Takahiro Suzuki, Shiori Maeda, Erina Furuhata, Yuri Shimizu, Hajime Nishimura, Mami Kishima, Harukazu Suzuki
BACKGROUND: DNA methylation is a fundamental epigenetic modification that is involved in many biological systems such as differentiation and disease. We and others recently showed that some transcription factors (TFs) are involved in the site-specific determination of DNA demethylation in a binding site-directed manner, although the reports of such TFs are limited. RESULTS: Here, we develop a screening system to identify TFs that induce binding site-directed DNA methylation changes...
December 8, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29216900/treatment-with-a-dna-methyltransferase-inhibitor-feminizes-zebrafish-and-induces-long-term-expression-changes-in-the-gonads
#7
Laia Ribas, Konstantinos Vanezis, Marco Antonio Imués, Francesc Piferrer
BACKGROUND: The role of epigenetic modifications such as DNA methylation during vertebrate sexual development is far from being clear. Using the zebrafish model, we tested the effects of one of the most common DNA methyltransferase (dnmt) inhibitor, 5-aza-2'-deoxycytidine (5-aza-dC), which is approved for the treatment of acute myeloid leukaemia and is under active investigation for the treatment of solid tumours. Several dose-response experiments were carried out during two periods, including not only the very first days of development (0-6 days post-fertilization, dpf), as done in previous studies, but also, and as a novelty, the period of gonadal development (10-30 dpf)...
December 8, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29212533/subtracting-the-sequence-bias-from-partially-digested-mnase-seq-data-reveals-a-general-contribution-of-tfiis-to-nucleosome-positioning
#8
Gabriel Gutiérrez, Gonzalo Millán-Zambrano, Daniel A Medina, Antonio Jordán-Pla, José E Pérez-Ortín, Xenia Peñate, Sebastián Chávez
BACKGROUND: TFIIS stimulates RNA cleavage by RNA polymerase II and promotes the resolution of backtracking events. TFIIS acts in the chromatin context, but its contribution to the chromatin landscape has not yet been investigated. Co-transcriptional chromatin alterations include subtle changes in nucleosome positioning, like those expected to be elicited by TFIIS, which are elusive to detect. The most popular method to map nucleosomes involves intensive chromatin digestion by micrococcal nuclease (MNase)...
December 7, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29208012/pho-dynamically-interacts-with-spt5-to-facilitate-transcriptional-switches-at-the-hsp70-locus
#9
Allwyn Pereira, Renato Paro
BACKGROUND: Numerous target genes of the Polycomb group (PcG) are transiently activated by a stimulus and subsequently repressed. However, mechanisms by which PcG proteins regulate such target genes remain elusive. RESULTS: We employed the heat shock-responsive hsp70 locus in Drosophila to study the chromatin dynamics of PRC1 and its interplay with known regulators of the locus before, during and after heat shock. We detected mutually exclusive binding patterns for HSF and PRC1 at the hsp70 locus...
December 6, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29191233/functional-dissection-of-drosophila-melanogaster-suur-protein-influence-on-h3k27me3-profile
#10
Olga V Posukh, Daniil A Maksimov, Petr P Laktionov, Dmitry E Koryakov, Stepan N Belyakin
BACKGROUND: In eukaryotes, heterochromatin replicates late in S phase of the cell cycle and contains specific covalent modifications of histones. SuUR mutation found in Drosophila makes heterochromatin replicate earlier than in wild type and reduces the level of repressive histone modifications. SUUR protein was shown to be associated with moving replication forks, apparently through the interaction with PCNA. The biological process underlying the effects of SUUR on replication and composition of heterochromatin remains unknown...
December 1, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29179736/phylogenetic-analysis-of-the-core-histone-doublet-and-dna-topo-ii-genes-of-marseilleviridae-evidence-of-proto-eukaryotic-provenance
#11
Albert J Erives
BACKGROUND: While the genomes of eukaryotes and Archaea both encode the histone-fold domain, only eukaryotes encode the core histone paralogs H2A, H2B, H3, and H4. With DNA, these core histones assemble into the nucleosomal octamer underlying eukaryotic chromatin. Importantly, core histones for H2A and H3 are maintained as neofunctionalized paralogs adapted for general bulk chromatin (canonical H2 and H3) or specialized chromatin (H2A.Z enriched at gene promoters and cenH3s enriched at centromeres)...
November 28, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29126443/ubiquitin-c-terminal-hydrolase-isozyme-l1-is-associated-with-shelterin-complex-at-interstitial-telomeric-sites
#12
Aleksandar Ilic, Sumin Lu, Vikram Bhatia, Farhana Begum, Thomas Klonisch, Prasoon Agarwal, Wayne Xu, James R Davie
BACKGROUND: Ubiquitin C-terminal hydrolase isozyme L1 (UCHL1) is primarily expressed in neuronal cells and neuroendocrine cells and has been associated with various diseases, including many cancers. It is a multifunctional protein involved in deubiquitination, ubiquitination and ubiquitin homeostasis, but its specific roles are disputed and still generally undetermined. RESULTS: Herein, we demonstrate that UCHL1 is associated with genomic DNA in certain prostate cancer cell lines, including DU 145 cells derived from a brain metastatic site, and in HEK293T embryonic kidney cells with a neuronal lineage...
November 10, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29126440/chromatin-organization-changes-during-the-establishment-and-maintenance-of-the-postmitotic-state
#13
Yiqin Ma, Laura Buttitta
BACKGROUND: Genome organization changes during development as cells differentiate. Chromatin motion becomes increasingly constrained and heterochromatin clusters as cells become restricted in their developmental potential. These changes coincide with slowing of the cell cycle, which can also influence chromatin organization and dynamics. Terminal differentiation is often coupled with permanent exit from the cell cycle, and existing data suggest a close relationship between a repressive chromatin structure and silencing of the cell cycle in postmitotic cells...
November 10, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29115969/correction-to-nua4-histone-acetyltransferase-activity-is-required-for-h4-acetylation-on-a-dosage-compensated-monosomic-chromosome-that-confers-resistance-to-fungal-toxins
#14
Hironao Wakabayashi, Christopher Tucker, Gabor Bethlendy, Anatoliy Kravets, Stephen L Welle, Michael Bulger, Jeffrey J Hayes, Elena Rustchenko
After the publication of this work [1], it was noticed that an initial was missing from the author name: Jeffrey Hayes. His name should be written as: Jeffrey J. Hayes.
November 7, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29084613/h2a-o-glcnacylation-at-serine-40-functions-genomic-protection-in-association-with-acetylated-h2az-or-%C3%AE-h2ax
#15
Koji Hayakawa, Mitsuko Hirosawa, Ruiko Tani, Chikako Yoneda, Satoshi Tanaka, Kunio Shiota
BACKGROUND: We have previously reported a novel O-GlcNAc modification at serine 40 (S40) of H2A (H2AS40Gc). S40-type H2A isoforms susceptible to O-GlcNAcylation are evolutionarily new and restricted to the viviparous animals; however, the biological function of H2AS40Gc is largely unknown. H2A isoforms are consisted of S40 and alanine 40 (A40) type and this residue on H2A is located in the L1 of the globular domain, which is also known as a variable portion that distinguishes between the canonical and non-canonical H2A variants...
October 30, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29061172/nua4-histone-acetyltransferase-activity-is-required-for-h4-acetylation-on-a-dosage-compensated-monosomic-chromosome-that-confers-resistance-to-fungal-toxins
#16
Hironao Wakabayashi, Christopher Tucker, Gabor Bethlendy, Anatoliy Kravets, Stephen L Welle, Michael Bulger, Jeffrey Hayes, Elena Rustchenko
BACKGROUND: The major human fungal pathogen Candida albicans possesses a diploid genome, but responds to growth in challenging environments by employing chromosome aneuploidy as an adaptation mechanism. For example, we have shown that C. albicans adapts to growth on the toxic sugar L-sorbose by transitioning to a state in which one chromosome (chromosome 5, Ch5) becomes monosomic. Moreover, analysis showed that while expression of many genes on the monosomic Ch5 is altered in accordance with the chromosome ploidy, expression of a large fraction of genes is increased to the normal diploid level, presumably compensating for gene dose...
October 23, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29061167/genome-wide-profiling-of-transcribed-enhancers-during-macrophage-activation
#17
Elena Denisenko, Reto Guler, Musa M Mhlanga, Harukazu Suzuki, Frank Brombacher, Sebastian Schmeier
BACKGROUND: Macrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M(IFN-γ) and M(IL-4/IL-13) are well known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for transcriptional activation of gene expression. RESULTS: Using cap analysis of gene expression and epigenetic data, we identify on large-scale transcribed enhancers in bone marrow-derived mouse macrophages, their time kinetics, and target protein-coding genes...
October 23, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29047414/histone-isoform-h2a1h-promotes-attainment-of-distinct-physiological-states-by-altering-chromatin-dynamics
#18
Saikat Bhattacharya, Divya Reddy, Vinod Jani, Nikhil Gadewal, Sanket Shah, Raja Reddy, Kakoli Bose, Uddhavesh Sonavane, Rajendra Joshi, Sanjay Gupta
BACKGROUND: The distinct functional effects of the replication-dependent histone H2A isoforms have been demonstrated; however, the mechanistic basis of the non-redundancy remains unclear. Here, we have investigated the specific functional contribution of the histone H2A isoform H2A1H, which differs from another isoform H2A2A3 in the identity of only three amino acids. RESULTS: H2A1H exhibits varied expression levels in different normal tissues and human cancer cell lines (H2A1C in humans)...
October 18, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29037228/neuroepigenetic-mechanisms-in-disease
#19
REVIEW
Michael A Christopher, Stephanie M Kyle, David J Katz
Epigenetics allows for the inheritance of information in cellular lineages during differentiation, independent of changes to the underlying genetic sequence. This raises the question of whether epigenetic mechanisms also function in post-mitotic neurons. During the long life of the neuron, fluctuations in gene expression allow the cell to pass through stages of differentiation, modulate synaptic activity in response to environmental cues, and fortify the cell through age-related neuroprotective pathways. Emerging evidence suggests that epigenetic mechanisms such as DNA methylation and histone modification permit these dynamic changes in gene expression throughout the life of a neuron...
October 16, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28982377/environmental-epigenetics-in-zebrafish
#20
REVIEW
Vincenzo Cavalieri, Giovanni Spinelli
It is widely accepted that the epigenome can act as the link between environmental cues, both external and internal, to the organism and phenotype by converting the environmental stimuli to phenotypic responses through changes in gene transcription outcomes. Environmental stress endured by individual organisms can also enforce epigenetic variations in offspring that had never experienced it directly, which is termed transgenerational inheritance. To date, research in the environmental epigenetics discipline has used a wide range of both model and non-model organisms to elucidate the various epigenetic mechanisms underlying the adaptive response to environmental stimuli...
October 5, 2017: Epigenetics & Chromatin
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