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histone modification chromatin

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https://www.readbyqxmd.com/read/29330049/the-histone-demethylase-phf8-promotes-adult-acute-lymphoblastic-leukemia-through-interaction-with-the-mek-erk-signaling-pathway
#1
Yue Fu, Yaling Yang, Xiaoming Wang, Xiaolin Yin, Minran Zhou, Siqi Wang, Lin Yang, Tao Huang, Man Xu, Chunyan Chen
Adult acute lymphoblastic leukemia (ALL) is a malignant disorder of lymphoid progenitor cells that is associated with a high risk of relapse and poor prognosis. Thus, novel pathogenic mechanisms and therapeutic targets need to be explored. Histone methylation is one of the most significant chromatin post-translational modifications. Here, we show that the histone demethylase PHF8 is highly expressed in a large number of ALL clinical specimens and that PHF8 expression is associated with ALL progression. PHF8 knockdown inhibits proliferation and promotes the apoptosis of ALL cells in vitro as well as attenuates tumor growth in vivo...
January 9, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29326300/relationship-between-histone-modifications-and-transcription-factor-binding-is-protein-family-specific
#2
Beibei Xin, Remo Rohs
The very small fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies focusing on BSs within DNA regulatory regions found correlations between HM patterns and TF binding specificities. However, a mechanistic understanding of TF-DNA binding specificity determinants is still not available...
January 11, 2018: Genome Research
https://www.readbyqxmd.com/read/29325627/epigenetic-mechanisms-underlying-nervous-system-diseases
#3
Irfan A Qureshi, Mark F Mehler
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29325176/dynamic-motif-occupancy-dynamo-analysis-identifies-transcription-factors-and-their-binding-sites-driving-dynamic-biological-processes
#4
Zheng Kuang, Zhicheng Ji, Jef D Boeke, Hongkai Ji
Biological processes are usually associated with genome-wide remodeling of transcription driven by transcription factors (TFs). Identifying key TFs and their spatiotemporal binding patterns are indispensable to understanding how dynamic processes are programmed. However, most methods are designed to predict TF binding sites only. We present a computational method, dynamic motif occupancy analysis (DynaMO), to infer important TFs and their spatiotemporal binding activities in dynamic biological processes using chromatin profiling data from multiple biological conditions such as time-course histone modification ChIP-seq data...
January 9, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29322418/analysis-of-histone-modifications-in-acute-myeloid-leukaemia-using-chromatin-immunoprecipitation
#5
Benjamin J Shields, Andrew Keniry, Marnie E Blewitt, Matthew P McCormack
Chromatin Immunoprecipitation (ChIP) using antibodies specific for histone modifications is a powerful technique for assessing the epigenetic states of cell populations by either quantitative PCR (ChIP-PCR) or next generation sequencing analysis (ChIP-Seq). Here we describe the procedure for ChIP of histone marks in myeloid leukaemia cell lines and the subsequent purification of genomic DNA associated with repressive and activating histone modifications for further analysis. This procedure can be widely applied to a variety of histone marks to assess both activating and repressive modifications in the context of myeloid leukaemia...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29317660/microbiota-derived-short-chain-fatty-acids-promote-histone-crotonylation-in-the-colon-through-histone-deacetylases
#6
Rachel Fellows, Jérémy Denizot, Claudia Stellato, Alessandro Cuomo, Payal Jain, Elena Stoyanova, Szabina Balázsi, Zoltán Hajnády, Anke Liebert, Juri Kazakevych, Hector Blackburn, Renan Oliveira Corrêa, José Luís Fachi, Fabio Takeo Sato, Willian R Ribeiro, Caroline Marcantonio Ferreira, Hélène Perée, Mariangela Spagnuolo, Raphaël Mattiuz, Csaba Matolcsi, Joana Guedes, Jonathan Clark, Marc Veldhoen, Tiziana Bonaldi, Marco Aurélio Ramirez Vinolo, Patrick Varga-Weisz
The recently discovered histone post-translational modification crotonylation connects cellular metabolism to gene regulation. Its regulation and tissue-specific functions are poorly understood. We characterize histone crotonylation in intestinal epithelia and find that histone H3 crotonylation at lysine 18 is a surprisingly abundant modification in the small intestine crypt and colon, and is linked to gene regulation. We show that this modification is highly dynamic and regulated during the cell cycle. We identify class I histone deacetylases, HDAC1, HDAC2, and HDAC3, as major executors of histone decrotonylation...
January 9, 2018: Nature Communications
https://www.readbyqxmd.com/read/29314414/an-ortholog-of-curly-leaf-enhancer-of-zeste-like-1-is-required-for-proper-flowering-in-brachypodium-distachyon
#7
Aaron Lomax, Daniel P Woods, Yinxin Dong, Frédéric Bouché, Ying Rong, Kevin S Mayer, Xuehua Zhong, Richard M Amasino
Many plants require prolonged cold exposure to acquire the competence to flower. The process by which cold exposure results in competence is known as vernalization. In Arabidopsis thaliana, vernalization leads to the stable repression of the floral repressor FLOWERING LOCUS C via chromatin modification including an increase of trimethylation on lysine 27 of histone H3 (H3K27me3) by Polycomb Repressive Complex 2 (PRC2). Vernalization in pooids is associated with the stable induction of a floral promoter, VERNALIZATION 1...
January 4, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29313530/histone-h3-lysine-4-monomethylation-modulates-long-range-chromatin-interactions-at-enhancers
#8
Jian Yan, Shi-An A Chen, Andrea Local, Tristin Liu, Yunjiang Qiu, Kristel M Dorighi, Sebastian Preissl, Chloe M Rivera, Chaochen Wang, Zhen Ye, Kai Ge, Ming Hu, Joanna Wysocka, Bing Ren
Long-range chromatin interactions between enhancers and promoters are essential for transcription of many developmentally controlled genes in mammals and other metazoans. Currently, the exact mechanisms that connect distal enhancers to their specific target promoters remain to be fully elucidated. Here, we show that the enhancer-specific histone H3 lysine 4 monomethylation (H3K4me1) and the histone methyltransferases MLL3 and MLL4 (MLL3/4) play an active role in this process. We demonstrate that in differentiating mouse embryonic stem cells, MLL3/4-dependent deposition of H3K4me1 at enhancers correlates with increased levels of chromatin interactions, whereas loss of this histone modification leads to reduced levels of chromatin interactions and defects in gene activation during differentiation...
January 9, 2018: Cell Research
https://www.readbyqxmd.com/read/29310890/the-latest-twists-in-chromatin-remodeling
#9
REVIEW
Ralf Blossey, Helmut Schiessel
In its most restrictive interpretation, the notion of chromatin remodeling refers to the action of chromatin-remodeling enzymes on nucleosomes with the aim of displacing and removing them from the chromatin fiber (the effective polymer formed by a DNA molecule and proteins). This local modification of the fiber structure can have consequences for the initiation and repression of the transcription process, and when the remodeling process spreads along the fiber, it also results in long-range effects essential for fiber condensation...
January 5, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29305415/histone-modifier-gene-mutations-in-peripheral-t-cell-lymphoma-not-otherwise-specified
#10
Meng-Meng Ji, Yao-Hui Huang, Jin-Yan Huang, Zhao-Fu Wang, Di Fu, Han Liu, Feng Liu, Christophe Leboeuf, Li Wang, Jing Ye, Yi-Ming Lu, Anne Janin, Shu Cheng, Wei-Li Zhao
Due to heterogeneous morphological and immunophenotypic features, approximately 50% of peripheral T-cell lymphomas are unclassifiable and categorized as peripheral T-cell lymphomas, not otherwise specified, presenting aggressive disease course and poor clinical outcome. Identification of actionable biomarkers is urgently needed to develop better therapeutic strategies. Epigenetic alterations play a crucial role in tumor progression. Histone modifications, particularly methylation and acetylation, are generally involved in chromatin state regulation...
January 5, 2018: Haematologica
https://www.readbyqxmd.com/read/29305015/alternative-splicing-in-genetic-diseases-improved-diagnosis-and-novel-treatment-options
#11
Atze J Bergsma, Erik van der Wal, Mike Broeders, Ans T van der Ploeg, W W M Pim Pijnappel
Alternative splicing is an important mechanism to regulate gene expression and to expand the repertoire of gene products in order to accommodate an increase in complexity of multicellular organisms. It needs to be precisely regulated, which is achieved via RNA structure, splicing factors, transcriptional regulation, and chromatin. Changes in any of these factors can lead to disease. These may include the core spliceosome, splicing enhancer/repressor sequences and their interacting proteins, the speed of transcription by RNA polymerase II, and histone modifications...
2018: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/29304373/genomic-dna-methylation-signatures-enable-concurrent-diagnosis-and-clinical-genetic-variant-classification-in-neurodevelopmental-syndromes
#12
Erfan Aref-Eshghi, David I Rodenhiser, Laila C Schenkel, Hanxin Lin, Cindy Skinner, Peter Ainsworth, Guillaume Paré, Rebecca L Hood, Dennis E Bulman, Kristin D Kernohan, Kym M Boycott, Philippe M Campeau, Charles Schwartz, Bekim Sadikovic
Pediatric developmental syndromes present with systemic, complex, and often overlapping clinical features that are not infrequently a consequence of Mendelian inheritance of mutations in genes involved in DNA methylation, establishment of histone modifications, and chromatin remodeling (the "epigenetic machinery"). The mechanistic cross-talk between histone modification and DNA methylation suggests that these syndromes might be expected to display specific DNA methylation signatures that are a reflection of those primary errors associated with chromatin dysregulation...
January 4, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29304334/beyond-the-histone-code-a-physical-map-of-chromatin-states
#13
Iva A Tchasovnikarova, Robert E Kingston
Post-translational modifications of histones are widely used to discriminate between different types of chromatin. In a recent issue of Molecular Cell, Becker et al. (2017) delineate chromatin states based on physical properties, thereby expanding our understanding of chromatin function.
January 4, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29301971/intracranial-aneurysm-associated-single-nucleotide-polymorphisms-alter-regulatory-dna-in-the-human-circle-of-willis
#14
Melanie D Laarman, Marit W Vermunt, Rachel Kleinloog, Jelkje J de Boer-Bergsma, Netherlands Brain Bank, Gabriël J E Rinkel, Menno P Creyghton, Michal Mokry, Jeroen Bakkers, Ynte M Ruigrok
BACKGROUND AND PURPOSE: Genome-wide association studies significantly link intracranial aneurysm (IA) to single-nucleotide polymorphisms (SNPs) in 6 genomic loci. To gain insight into the relevance of these IA-associated SNPs, we aimed to identify regulatory regions and analyze overall gene expression in the human circle of Willis (CoW), on which these aneurysms develop. METHODS: We performed chromatin immunoprecipitation and sequencing for histone modifications H3K4me1 and H3K27ac to identify regulatory regions, including distal enhancers and active promoters, in postmortem specimens of the human CoW...
January 4, 2018: Stroke; a Journal of Cerebral Circulation
https://www.readbyqxmd.com/read/29301935/-inhibition-of-histone-h3k27-demethylase-selectively-modulates-inflammatory-phenotypes-of-natural-killer-cells
#15
Adam Cribbs, Edward S Hookway, Graham Wells, Morten Lindow, Susanna Obad, Henrik Oerum, Rab K Prinjha, Nick Athanasou, Aneka Sowman, Martin Philpott, Henry Penn, Kalle Soderstrom, Marc Feldmann, Udo Oppermann
Natural killer (NK) cells are innate lymphocytes, important in immune surveillance and elimination of stressed, transformed, or virus-infected cells. They critically shape the inflammatory cytokine environment to orchestrate interactions of cells of the innate and adaptive immune systems. Some studies have reported that NK cell activation and cytokine secretion are controlled epigenetically, but have yielded only limited insight into the mechanisms. Using chemical screening with small-molecule inhibitors of chromatin methylation and acetylation, further validated by knockdown approaches, we here identified Jumonji-type histone H3K27 demethylases as key regulators of cytokine production in human NK cell subsets...
January 4, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29298422/winged-eye-induces-transdetermination-of-drosophila-imaginal-disc-by-acting-in-concert-with-a-histone-methyltransferase-su-var-3-9
#16
Keita Masuko, Naoyuki Fuse, Kanae Komaba, Tomonori Katsuyama, Rumi Nakajima, Hirofumi Furuhashi, Shoichiro Kurata
Drosophila imaginal disc cells exhibit a remarkable ability to convert cell fates in response to various perturbations, a phenomenon called transdetermination (TD). We previously identified winged eye (wge) as a factor that induces eye-to-wing TD upon overexpression in eye imaginal discs, but the molecular mechanisms underlying TD have remained largely unclear. Here, we found that wge induces various histone modifications and enhances the methylation of Lys9 on histone H3 (H3K9), a feature of heterochromatin...
January 2, 2018: Cell Reports
https://www.readbyqxmd.com/read/29288791/chromatin-modifications-of-htert-gene-in-htert-immortalized-human-mesenchymal-stem-cells-upon-exposure-to-radiation
#17
Nedime Serakinci, Pınar Mega Tiber, Oya Orun
Regulation of telomerase activity is thought to participate in the cellular response to ionizing radiation. Epigenetic mechanisms play a role in this regulation, as well as other mechanisms such as transcription, phosphorylation, etc. Here, we investigated chromatin modifications in telomerase promoter upon exposure to ionizing radiation in human mesenchymal stem cells (hMSC) and telomerase-immortalized hMSCs (hMSC-telo1) together with a hMSC-telo1 cell line in which TRF2 expression was partially repressed (siTRF2 hMSC-telo1)...
December 27, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/29288744/metabolic-suppression-in-the-pelagic-crab-pleuroncodes-planipes-in-oxygen-minimum-zones
#18
Brad A Seibel, Bryan E Luu, Shannon N Tessier, Trisha Towanda, Kenneth B Storey
The pelagic red crab, Pleuroncodes planipes, is abundant throughout the Eastern Tropical Pacific in both benthic and pelagic environments to depths of several hundred meters. The oxygen minimum zones in this region reaches oxygen levels as low as 0.1kPa at depths within the crabs vertical range. Crabs maintain aerobic metabolism to a critical PO2 of ~0.27±0.2kPa (10°C), in part by increasing ventilation as oxygen declines. At subcritical oxygen levels, they enhance anaerobic ATP production slightly as indicated by modest increases in lactate levels...
December 27, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/29288231/sulforaphane-modifies-histone-h3-unpacks-chromatin-and-primes-defense
#19
Britta Schillheim, Irina Jansen, Stephani Baum, Carsten Bolm, Alexander Beesley, Uwe Conrath
Modern crop production calls for agrochemicals that prime plants for enhanced defense. Reliable test systems for spotting priming-inducing chemistry, however, are rare. We developed an assay for the high-throughput search for compounds that prime microbial pattern-induced secretion of antimicrobial furanocoumarins (phytoalexins) in cultured parsley cells. The screen produced 1-isothiocyanato-4-methylsulfinylbutane (sulforaphane; SFN), a secondary metabolite in many crucifers, as a novel defense priming compound...
December 29, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29286469/generation-of-native-chromatin-immunoprecipitation-sequencing-libraries-for-nucleosome-density-analysis
#20
Alireza Lorzadeh, Rodrigo Lopez Gutierrez, Linda Jackson, Michelle Moksa, Martin Hirst
We present a modified native chromatin immunoprecipitation sequencing (ChIP-seq) experimental protocol compatible with a Gaussian mixture distribution based analysis methodology (nucleosome density ChIP-seq; ndChIP-seq) that enables the generation of combined measurements of micrococcal nuclease (MNase) accessibility with histone modification genome-wide. Nucleosome position and local density, and the posttranslational modification of their histone subunits, act in concert to regulate local transcription states...
December 12, 2017: Journal of Visualized Experiments: JoVE
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