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Epigenetics and h2b

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https://www.readbyqxmd.com/read/28209164/rnf40-regulates-gene-expression-in-an-epigenetic-context-dependent-manner
#1
Wanhua Xie, Sankari Nagarajan, Simon J Baumgart, Robyn Laura Kosinsky, Zeynab Najafova, Vijayalakshmi Kari, Magali Hennion, Daniela Indenbirken, Stefan Bonn, Adam Grundhoff, Florian Wegwitz, Ahmed Mansouri, Steven A Johnsen
BACKGROUND: Monoubiquitination of H2B (H2Bub1) is a largely enigmatic histone modification that has been linked to transcriptional elongation. Because of this association, it has been commonly assumed that H2Bub1 is an exclusively positively acting histone modification and that increased H2Bub1 occupancy correlates with increased gene expression. In contrast, depletion of the H2B ubiquitin ligases RNF20 or RNF40 alters the expression of only a subset of genes. RESULTS: Using conditional Rnf40 knockout mouse embryo fibroblasts, we show that genes occupied by low to moderate amounts of H2Bub1 are selectively regulated in response to Rnf40 deletion, whereas genes marked by high levels of H2Bub1 are mostly unaffected by Rnf40 loss...
February 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28180298/histone-h2b-monoubiquitination-is-a-critical-epigenetic-switch-for-the-regulation-of-autophagy
#2
Su Chen, Yuanya Jing, Xuan Kang, Lu Yang, Da-Liang Wang, Wei Zhang, Lei Zhang, Ping Chen, Jian-Feng Chang, Xiao-Mei Yang, Fang-Lin Sun
No abstract text is available yet for this article.
February 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28178526/crl4-dcaf8-ubiquitin-ligase-targets-histone-h3k79-and-promotes-h3k9-methylation-in-the-liver
#3
Gaofeng Li, Tong Ji, Jiang Chen, Yufei Fu, Lidan Hou, Yan Feng, Tingyue Zhang, Tianyu Song, Jie Zhao, Yoko Endo, Hui Lin, Xiujun Cai, Yong Cang
Transcription from chromosomes is regulated by posttranslational modifications to histones, such as methylation and ubiquitination. Monoubiquitination of histones H2A and H2B influences H3 methylation to reinforce the activation or repression of gene expression. Here, we provide evidence that H3 polyubiquitination represses transcription of fetal and cell-cycle genes in postnatal mouse liver by crosstalk with H3K9 methylation. We found that the CRL4 ubiquitin ligase targets H3 for polyubiquitination at K79 via the DCAF8 substrate receptor in hepatocytes...
February 7, 2017: Cell Reports
https://www.readbyqxmd.com/read/28108335/tryptase-catalyzed-core-histone-truncation-a%C3%A2-novel-epigenetic-regulatory-mechanism-in-mast-cells
#4
Fabio R Melo, Ola Wallerman, Aida Paivandy, Gabriela Calounova, Ann-Marie Gustafson, Benjamin R Sabari, Giuliano Zabucchi, C David Allis, Gunnar Pejler
BACKGROUND: Mast cells are key effector cells in allergic reactions. When activated to degranulate, they release a plethora of bioactive compounds from their secretory granules, including mast cell-restricted proteases such as tryptase. In a previous study, we showed that tryptase, in addition to its intragranular location, can be found within the nuclei of mast cells where it truncates core histones at their N-terminal ends. OBJECTIVE: Considering that the N-terminal portions of the core histones constitute sites for posttranslational modifications of major epigenetic impact, we evaluated whether histone truncation by tryptase could have an impact on epigenetic events in mast cells...
January 17, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/27993980/genetic-mosaics-and-time-lapse-imaging-identify-functions-of-histone-h3-3-residues-in-mouse-oocytes-and-embryos
#5
Liquan Zhou, Boris Baibakov, Bertram Canagarajah, Bo Xiong, Jurrien Dean
During development from oocyte to embryo, genetic programs in mouse germ cells are reshaped by chromatin remodeling to orchestrate the onset of development. Epigenetic modifications of specific amino acid residues of core histones and their isoforms can dramatically alter activation and suppression of gene expression. H3.3 is a histone H3 variant that plays essential roles in mouse oocytes and early embryos, but the functional role of individual amino acid residues has been unclear because of technical hurdles...
February 1, 2017: Development
https://www.readbyqxmd.com/read/27935863/a-ruthenium-anticancer-compound-interacts-with-histones-and-impacts-differently-on-epigenetic-and-death-pathways-compared-to-cisplatin
#6
Cynthia Licona, Marie-Elodie Spaety, Antonelle Capuozzo, Moussa Ali, Rita Santamaria, Olivier Armant, Francois Delalande, Alain Van Dorsselaer, Sarah Cianferani, John Spencer, Michel Pfeffer, Georg Mellitzer, Christian Gaiddon
Ruthenium complexes are considered as potential replacements for platinum compounds in oncotherapy. Their clinical development is handicapped by a lack of consensus on their mode of action. In this study, we identify three histones (H3.1, H2A, H2B) as possible targets for an anticancer redox organoruthenium compound (RDC11). Using purified histones, we confirmed an interaction between the ruthenium complex and histones that impacted on histone complex formation. A comparative study of the ruthenium complex versus cisplatin showed differential epigenetic modifications on histone H3 that correlated with differential expression of histone deacetylase (HDAC) genes...
January 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/27926813/perturbation-of-h3k27me3-associated-epigenetic-processes-increases-agrobacterium-mediated-transformation
#7
Hidekazu Iwakawa, Benjamin C Carter, Brett C Bishop, Joe Ogas, Stanton B Gelvin
Agrobacterium-mediated transformation is a core technology for basic plant science and agricultural biotechnology. Improving transformation frequency is a major goal for plant transgenesis. We previously showed that T-DNA insertions in some histone genes decreased transformation susceptibility, whereas overexpression of several Arabidopsis H2A and H4 isoforms increased transformation. Overexpression of several histone H2B and H3 isoforms had little effect on transformation frequency. However, overexpression of histone H3-11 (HTR11) enhanced transformation...
January 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/27922451/direct-screening-for-chromatin-status-on-dna-barcodes-in-yeast-delineates-the-regulome-of-h3k79-methylation-by-dot1
#8
Hanneke Vlaming, Thom M Molenaar, Tibor van Welsem, Deepani W Poramba-Liyanage, Desiree E Smith, Arno Velds, Liesbeth Hoekman, Tessy Korthout, Sjoerd Hendriks, A F Maarten Altelaar, Fred van Leeuwen
Given the frequent misregulation of chromatin in cancer, it is important to understand the cellular mechanisms that regulate chromatin structure. However, systematic screening for epigenetic regulators is challenging and often relies on laborious assays or indirect reporter read-outs. Here we describe a strategy, Epi-ID, to directly assess chromatin status in thousands of mutants. In Epi-ID, chromatin status on DNA barcodes is interrogated by chromatin immunoprecipitation followed by deep sequencing, allowing for quantitative comparison of many mutants in parallel...
6, 2016: ELife
https://www.readbyqxmd.com/read/27890612/in%C3%A2-vitro-reconstitution-and-biochemical-analyses-of-the-schizosaccharomyces-pombe-nucleosome
#9
Masako Koyama, Wataru Nagakura, Hiroki Tanaka, Tomoya Kujirai, Yuji Chikashige, Tokuko Haraguchi, Yasushi Hiraoka, Hitoshi Kurumizaka
Schizosaccharomyces pombe, which has a small genome but shares many physiological functions with higher eukaryotes, is a useful single-cell, model eukaryotic organism. In particular, many features concerning chromatin structure and dynamics, including heterochromatin, centromeres, telomeres, and DNA replication origins, are well conserved between S. pombe and higher eukaryotes. However, the S. pombe nucleosome, the fundamental structural unit of chromatin, has not been reconstituted in vitro. In the present study, we established the method to purify S...
January 22, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27832544/in-vitro-assay-to-study-histone-ubiquitination-during-transcriptional-regulation
#10
Jogender Tushir-Singh, Sanchita Bhatnagar
In mammals, gene expression is largely controlled at the transcriptional level. In response to environmental or intrinsic signaling, gene expression is often fine-tuned by epigenetic modifications, including DNA methylation and histone modifications. One such histone modification is ubiquitination that predominately occurs in mono-ubiquitinated forms on histone H2A and H2B. We recently identified and characterized a novel E3 ligase called TRIM37 that ubiquitinates H2A. This study highlights the consequence of aberrant histone ubiquitination at the promoters of tumor suppressor genes in breast cancer...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27825936/new-insights-into-the-molecular-mechanisms-of-chemical-carcinogenesis-in-vivo-adduction-of-histone-h2b-by-a-reactive-metabolite-of-the-chemical-carcinogen-furan
#11
João Nunes, Inês L Martins, Catarina Charneira, Igor P Pogribny, Aline de Conti, Frederick A Beland, M Matilde Marques, Cristina C Jacob, Alexandra M M Antunes
Furan is a rodent hepatocarcinogen ubiquitously found in the environment and heat-processed foods. Furan undergoes cytochrome P450 2E1-catalyzed bioactivation to cis-2-butene-1,4-dial (BDA), which has been shown to form an electrophilic conjugate (GSH-BDA) with glutathione. Both BDA and GSH-BDA yield covalent adducts with lysine residues in proteins. Dose- and time-dependent epigenetic histone alterations have been observed in furan-treated rats. While the covalent modification of histones by chemical carcinogens has long been proposed, histone-carcinogen adducts have eluded detection in vivo...
December 15, 2016: Toxicology Letters
https://www.readbyqxmd.com/read/27789696/histone-h2b-monoubiquitination-is-a-critical-epigenetic-switch-for-the-regulation-of-autophagy
#12
Su Chen, Yuanya Jing, Xuan Kang, Lu Yang, Da-Liang Wang, Wei Zhang, Lei Zhang, Ping Chen, Jian-Feng Chang, Xiao-Mei Yang, Fang-Lin Sun
Autophagy is an evolutionarily conserved cellular process that primarily participates in lysosome-mediated protein degradation. Although autophagy is a cytoplasmic event, how epigenetic pathways are involved in the regulation of autophagy remains incompletely understood. Here, we found that H2B monoubiquitination (H2Bub1) is down-regulated in cells under starvation conditions and that the decrease in H2Bub1 results in the activation of autophagy. We also identified that the deubiquitinase USP44 is responsible for the starvation-induced decrease in H2Bub1...
October 26, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27665728/structural-and-histone-binding-ability-characterization-of-the-arb2-domain-of-a-histone-deacetylase-hda1-from-saccharomyces-cerevisiae
#13
Hui Shen, Yuwei Zhu, Chongyuan Wang, Hui Yan, Maikun Teng, Xu Li
Hda1 is the catalytic core component of the H2B- and H3- specific histone deacetylase (HDAC) complex from Saccharomyces cerevisiae, which is involved in the epigenetic repression and plays a crucial role in transcriptional regulation and developmental events. Though the N-terminal catalytic HDAC domain of Hda1 is well characterized, the function of the C-terminal ARB2 domain remains unknown. In this study, we determine the crystal structure of the ARB2 domain from S. cerevisiae Hda1 at a resolution of 2.7 Å...
September 26, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27602058/the-cnidarian-hydractinia-echinata-employs-canonical-and-highly-adapted-histones-to-pack-its-dna
#14
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
https://www.readbyqxmd.com/read/27582499/histone-h2ak119-and-h2bk120-monoubiquitination-modulate-set7-9-and-suv39h1-in-type-1-diabetes-induced-renal-fibrosis
#15
Santosh Kumar Goru, Almesh Kadakol, Anuradha Pandey, Vajir Malek, Nisha Sharma, Anil Bhanudas Gaikwad
Hyperglycaemia-induced expression of extracellular matrix (ECM) components plays a major role in the development diabetic nephropathy (DN). The epigenetic mechanisms that modulate ECM gene expression in DN remain unclear. Therefore, we examined the role of histone H2A and H2B mono-ubiquitination on epigenetic chromatin marks such as histone H3 lysine dimethylation (H3K4Me2, H3K9Me2 and H3K79Me2) in type 1 diabetic rat kidney. Hyperglycaemia increased collagen deposition and Col1a1 gene expression. In whole kidney of diabetic animals, both H2AK119 mono-ubiquitination (H2AK119Ub) and H2BK120 mono-ubiquitination (H2BK120Ub) were found to be increased whereas, in glomeruli of diabetic animals expression of both H2AK119Ub and H2BK120Ub were reduced...
August 31, 2016: Biochemical Journal
https://www.readbyqxmd.com/read/27551260/astrocyte-reactivity-following-blast-exposure-involves-aberrant-histone-acetylation
#16
Zachary S Bailey, Michael B Grinter, Pamela J VandeVord
Blast induced neurotrauma (BINT) is a prevalent injury within military and civilian populations. The injury is characterized by persistent inflammation at the cellular level which manifests as a multitude of cognitive and functional impairments. Epigenetic regulation of transcription offers an important control mechanism for gene expression and cellular function which may underlie chronic inflammation and result in neurodegeneration. We hypothesize that altered histone acetylation patterns may be involved in blast induced inflammation and the chronic activation of glial cells...
2016: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/27487198/single-molecule-observation-reveals-spontaneous-protein-dynamics-in-the-nucleosome
#17
Jongseong Kim, Sijie Wei, Jaehyoun Lee, Hongjun Yue, Tae-Hee Lee
Structural dynamics of a protein molecule is often critical to its function. Single-molecule methods provide efficient ways to investigate protein dynamics, although it is very challenging to achieve a millisecond or higher temporal resolution. Here we report spontaneous structural dynamics of the histone protein core in the nucleosome based on a single-molecule method that can reveal submillisecond dynamics by combining maximum likelihood estimation and fluorescence correlation spectroscopy. The nucleosome, comprising ∼147 bp DNA and an octameric histone protein core consisting of H2A, H2B, H3, and H4, is the fundamental packing unit of the eukaryotic genome...
September 1, 2016: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/27439608/epigenetic-role-of-nuclear-s6k1-in-early-adipogenesis
#18
Sang Ah Yi, Jihoon Han, Jeung-Whan Han
S6K1 is a key regulator of cell growth, cell size, and metabolism. Although the role of cytosolic S6K1 in cellular processes is well established, the function of S6K1 in the nucleus remains poorly understood. Our recent study has revealed that S6K1 is translocated into the nucleus upon adipogenic stimulus where it directly binds to and phosphorylates H2B at serine 36. Such phosphorylation promotes EZH2 recruitment and subsequent histone H3K27 trimethylation on the promoter of its target genes including Wnt6, Wnt10a, and Wnt10b, leading to repression of their expression...
August 2016: BMB Reports
https://www.readbyqxmd.com/read/27399157/transcriptomic-alterations-in-daphnia-magna-embryos-from-mothers-exposed-to-hypoxia
#19
Keng-Po Lai, Jing-Woei Li, Christine Ying-Shan Chan, Ting-Fung Chan, Karen Wing-Yee Yuen, Jill Man-Ying Chiu
Hypoxia occurs when dissolved oxygen (DO) falls below 2.8mgL(-1) in aquatic environments. It can cause trans-generational effects not only in fish, but also in the water fleas Daphnia. In this study, transcriptome sequencing analysis was employed to identify transcriptomic alterations induced by hypoxia in embryos of Daphnia magna, with an aim to investigate the mechanism underlying the trans-generational effects caused by hypoxia in Daphnia. The embryos (F1) were collected from adults (F0) that were previously exposed to hypoxia (or normoxia) for their whole life...
August 2016: Aquatic Toxicology
https://www.readbyqxmd.com/read/27352023/the-hdaci-panobinostat-shows-growth-inhibition-both-in-vitro-and-in-a-bioluminescent-orthotopic-surgical-xenograft-model-of-ovarian-cancer
#20
Øystein Helland, Mihaela Popa, Katharina Bischof, Bjørn Tore Gjertsen, Emmet McCormack, Line Bjørge
BACKGROUND: In most epithelial ovarian carcinomas (EOC), epigenetic changes are evident, and overexpression of histone deacetylases (HDACs) represents an important manifestation. In this study, we wanted to evaluate the effects of the novel HDAC inhibitor (HDACi) panobinostat, both alone and in combination with carboplatin, on ovarian cancer cell lines and in a murine bioluminescent orthotopic surgical xenograft model for EOC. METHODS: The effects of panobinostat, both alone and in combination with carboplatin, on proliferation and apoptosis in ovarian cancer cell lines, were evaluated using colony and WST-1 assays, Hoechst staining and flow cytometry analysis...
2016: PloS One
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