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histone modification chromatin

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https://www.readbyqxmd.com/read/28934504/accumulation-of-histone-variant-h3-3-with-age-is-associated-with-profound-changes-in-the-histone-methylation-landscape
#1
Andrey Tvardovskiy, Veit Schwämmle, Stefan J Kempf, Adelina Rogowska-Wrzesinska, Ole N Jensen
Deposition of replication-independent histone variant H3.3 into chromatin is essential for many biological processes, including development and reproduction. Unlike replication-dependent H3.1/2 isoforms, H3.3 is expressed throughout the cell cycle and becomes enriched in postmitotic cells with age. However, lifelong dynamics of H3 variant replacement and the impact of this process on chromatin organization remain largely undefined. Using quantitative middle-down proteomics we demonstrate that H3.3 accumulates to near saturation levels in the chromatin of various mouse somatic tissues by late adulthood...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28932910/a-histone-deacetylase-gene-slhda3-acts-as-a-negative-regulator-of-fruit-ripening-and-carotenoid-accumulation
#2
Jun-E Guo, Zongli Hu, Xiaohui Yu, Anzhou Li, Fenfen Li, Yunshu Wang, Shibing Tian, Guoping Chen
SlHDA3 functions as an inhibitor and regulates tomato fruit ripening and carotenoid accumulation. Post-translational modifications, including histones acetylation, play a pivotal role in the changes of chromatin structure dynamic modulation and gene activity. The regulation of histone acetylation is achieved by the action of histone acetyltransferases and deacetylases, which play crucial roles in the regulation of transcription activation. There is an increasing research focus on histone deacetylation in crops, but the role of histone deacetylase genes (HDACs) in tomato has not been elucidated...
September 20, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28932035/epigenetics-in-oral-squamous-cell-carcinoma
#3
REVIEW
K N Hema, T Smitha, H S Sheethal, S Angeline Mirnalini
Oral squamous cell carcinoma (OSCC) is the most common type of oral neoplasm, accounting for over 90% of all oral malignancies and 38% of head and neck tumors. Worldwide, OSCC is the eighth most common human cancer, with more than 500,000 new cases being diagnosed every year with a fairly onerous prognosis, encouraging further research on factors that might modify disease outcome. Genetic and/or environmental risk factors associated with the development of oral cancer have been sufficiently understood (smoking, alcohol, betel, diet, living habits, etc...
May 2017: Journal of Oral and Maxillofacial Pathology: JOMFP
https://www.readbyqxmd.com/read/28930539/transcriptional-regulation-of-p57-kip2-expression-during-development-differentiation-and-disease
#4
Marianna N Rossi, Oriella Andresini, Francesca Matteini, Rossella Maione
p57(kip2) is the most complex member of the CIP/KIP family of cyclin-dependent kinase inhibitors and plays a fundamental role in regulating cell cycle and differentiation during mammalian development. Consistently with a key role for p57(kip2) in the spatial and temporal control of cell proliferation, its expression is fine-tuned by multiple regulatory mechanisms, resulting in a tissue-, developmental phase- and cell type-specific pattern. Moreover, p57(kip2) is an imprinted gene, further supporting the importance of its proper expression dosage...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28926429/targeting-histone-acetylation-readers-and-writers-in-leukemia-and-cancer
#5
Christopher B Benton, Warren Fiskus, Kapil N Bhalla
Chromatin packaging of DNA provides a framework for transcriptional regulation. Modifications to DNA and histone proteins in nucleosomes lead to conformational changes, alterations in the recruitment of transcriptional complexes, and ultimately modulation of gene expression. We provide a focused review of control mechanisms that help modulate the activation and deactivation of gene transcription specifically through histone acetylation writers and readers in cancer. The chemistry of these modifications is subject to clinically actionable targeting, including state-of-the-art strategies to inhibit basic oncogenic mechanisms related to histone acetylation...
September 2017: Cancer Journal
https://www.readbyqxmd.com/read/28925386/5-hydroxymethylcytosine-signatures-in-circulating-cell-free-dna-as-diagnostic-biomarkers-for-human-cancers
#6
Wenshuai Li, Xu Zhang, Xingyu Lu, Lei You, Yanqun Song, Zhongguang Luo, Jun Zhang, Ji Nie, Wanwei Zheng, Diannan Xu, Yaping Wang, Yuanqiang Dong, Shulin Yu, Jun Hong, Jianping Shi, Hankun Hao, Fen Luo, Luchun Hua, Peng Wang, Xiaoping Qian, Fang Yuan, Lianhuan Wei, Ming Cui, Taiping Zhang, Quan Liao, Menghua Dai, Ziwen Liu, Ge Chen, Katherine Meckel, Sarbani Adhikari, Guifang Jia, Marc B Bissonnette, Xinxiang Zhang, Yupei Zhao, Wei Zhang, Chuan He, Jie Liu
DNA modifications such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are epigenetic marks known to affect global gene expression in mammals. Given their prevalence in the human genome, close correlation with gene expression and high chemical stability, these DNA epigenetic marks could serve as ideal biomarkers for cancer diagnosis. Taking advantage of a highly sensitive and selective chemical labeling technology, we report here the genome-wide profiling of 5hmC in circulating cell-free DNA (cfDNA) and in genomic DNA (gDNA) of paired tumor and adjacent tissues collected from a cohort of 260 patients recently diagnosed with colorectal, gastric, pancreatic, liver or thyroid cancer and normal tissues from 90 healthy individuals...
September 19, 2017: Cell Research
https://www.readbyqxmd.com/read/28923849/bivalent-epigenetic-control-of-oncofetal-gene-expression-in-cancer
#7
Sayyed K Zaidi, Seth E Frietze, Jonathan A Gordon, Jessica L Heath, Terri Messier, Deli Hong, Joseph R Boyd, Mingu Kang, Anthony N Imbalzano, Jane B Lian, Janet L Stein, Gary S Stein
Multiple mechanisms of epigenetic control that include DNA methylation, histone modification, non-coding RNAs, and mitotic gene bookmarking play pivotal roles in stringent gene regulation during lineage commitment and maintenance. Experimental evidence indicates that bivalent chromatin domains, i.e., regions of genome that are marked by both H3K4me3 (activating) and H3K27me3 (repressive) histone modifications, are a key property of pluripotent stem cells. Bivalency of developmental genes during the G1 phase of the pluripotent stem cell cycle contributes to cell fate decisions...
September 18, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28921466/roles-of-hdacs-in-the-responses-of-innate-immune-cells-and-as-targets-in-inflammatory-diseases
#8
Yiqun Hu, Bandar Ali Suliman
Histone deacetylases (HDACs) are an emerging class of molecules involved in the epigenetic regulation of innate immune responses through Toll-like receptor (TLR) and interferon (IFN) signaling pathways. HDACs are also key drivers of inflammatory diseases via epigenetic regulation through chromatin DNA and histone modification by methylation and acetylation, among other mechanisms, which control innate immune cell gene expression. Importantly, these epigenetic changes are reversible, and HDACs may also be targeted by small-molecule HDAC inhibitors, which have been used in clinical settings for cancer therapy...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28920961/germline-mutations-affecting-the-histone-h4-core-cause-a-developmental-syndrome-by-altering-dna-damage-response-and-cell-cycle-control
#9
Federico Tessadori, Jacques C Giltay, Jane A Hurst, Maarten P Massink, Karen Duran, Harmjan R Vos, Robert M van Es, Richard H Scott, Koen L I van Gassen, Jeroen Bakkers, Gijs van Haaften
Covalent modifications of histones have an established role as chromatin effectors, as they control processes such as DNA replication and transcription, and repair or regulate nucleosomal structure. Loss of modifications on histone N tails, whether due to mutations in genes belonging to histone-modifying complexes or mutations directly affecting the histone tails, causes developmental disorders or has a role in tumorigenesis. More recently, modifications affecting the globular histone core have been uncovered as being crucial for DNA repair, pluripotency and oncogenesis...
September 18, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28919981/regulation-of-cancer-epigenomes-with-a-histone-binding-synthetic-transcription-factor
#10
David B Nyer, Rene M Daer, Daniel Vargas, Caroline Hom, Karmella A Haynes
Chromatin proteins have expanded the mammalian synthetic biology toolbox by enabling control of active and silenced states at endogenous genes. Others have reported synthetic proteins that bind DNA and regulate genes by altering chromatin marks, such as histone modifications. Previously, we reported the first synthetic transcriptional activator, the "Polycomb-based transcription factor" (PcTF) that reads histone modifications through a protein-protein interaction between the polycomb chromodomain motif and trimethylated lysine 27 of histone H3 (H3K27me3)...
2017: NPJ Genomic Medicine
https://www.readbyqxmd.com/read/28916762/time-resolved-analysis-of-dna-protein-interactions-in-living-cells-by-uv-laser-pulses
#11
Angela Nebbioso, Rosaria Benedetti, Mariarosaria Conte, Vincenzo Carafa, Floriana De Bellis, Jani Shaik, Filomena Matarese, Bartolomeo Della Ventura, Felice Gesuele, Raffaele Velotta, Joost H A Martens, Hendrik G Stunnenberg, Carlo Altucci, Lucia Altucci
Interactions between DNA and proteins are mainly studied through chemical procedures involving bi-functional reagents, mostly formaldehyde. Chromatin immunoprecipitation is used to identify the binding between transcription factors (TFs) and chromatin, and to evaluate the occurrence and impact of histone/DNA modifications. The current bottleneck in probing DNA-protein interactions using these approaches is caused by the fact that chemical crosslinkers do not discriminate direct and indirect bindings or short-lived chromatin occupancy...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916515/reversing-thyroid-hormone-mediated-repression-of-a-hsv-1-promoter-via-computationally-guided-mutagenesis
#12
Robert W Figliozzi, Feng Chen, Shaochung V Hsia
Thyroid hormones (TH or T3) and their DNA binding nuclear receptors (TRs), direct transcriptional regulation in diverse ways depending on the host cell environment and specific promoter characteristics of TH sensitive genes. This study sought to elucidate the impact on transcriptional repression of nucleotide sequence/orientation within TR binding sites, TR elements, (TREs) of TH sensitive promoters, to better understand ligand dependent transcriptional repression of wild-type promoters. Computational analysis of the HSV-1 thymidine kinase (TK) gene TRE bound by TR and RXR revealed a single TRE point mutation sufficient to reverse the TRE orientation...
September 15, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28912372/genome-wide-maps-of-alkylation-damage-repair-and-mutagenesis-in-yeast-reveal-mechanisms-of-mutational-heterogeneity
#13
Peng Mao, Alexander J Brown, Ewa P Malc, Piotr A Mieczkowski, Michael J Smerdon, Steven A Roberts, John J Wyrick
DNA base damage is an important contributor to genome instability, but how the formation and repair of these lesions is affected by the genomic landscape and contributes to mutagenesis is unknown. Here, we describe genome-wide maps of DNA base damage, repair, and mutagenesis at single nucleotide resolution in yeast treated with the alkylating agent methyl methanesulfonate (MMS). Analysis of these maps revealed that base excision repair (BER) of alkylation damage is significantly modulated by chromatin, with faster repair in nucleosome-depleted regions, and slower repair and higher mutation density within strongly positioned nucleosomes...
September 14, 2017: Genome Research
https://www.readbyqxmd.com/read/28912063/differential-expression-by-chromatin-modifications-of-alcohol-dehydrogenase-1-of-chorispora-bungeana-in-cold-stress
#14
Lijun Liu, Yuan Song, Jun Xu, Dongming Li, Gaopeng Li, Lizhe An
Epigenetic modifications regulate plant genes to cope with a variety of environmental stresses. Chorispora bungeana is an alpine subnival plant with strong tolerance to multiple abiotic stresses, especially cold stress. In this study, we characterized the alcohol dehydrogenase 1 gene from Chorispora bungeana, CbADH1, that is up-regulated in cold conditions. Overexpression of CbADH1 in Arabidopsis thaliana improved cold tolerance, as indicated by a decreased lethal temperature (LT50). Chromatin immunoprecipitation assays showed that histone H3 is removed from the promoter region and the middle-coding region of the gene...
September 11, 2017: Gene
https://www.readbyqxmd.com/read/28910574/o-glcnacylation-of-boundary-element-associated-factor-beaf-32-in-drosophila-melanogaster-correlates-with-active-histone-marks-at-the-promoters-of-its-target-genes
#15
Debaditya De, Satish Kallappagoudar, Jae-Min Lim, Rashmi U Pathak, Rakesh K Mishra
Boundary Element-Associated Factor 32 (BEAF 32) is a sequence specific DNA binding protein involved in functioning of chromatin domain boundaries in Drosophila. Several studies also show it to be involved in transcriptional regulation of a large number of genes, many of which are annotated to have cell cycle, development and differentiation related function. Since post-translational modifications (PTMs) of proteins add to their functional capacity, we investigated the PTMs on BEAF 32. The protein is known to be phosphorylated and O-GlcNAcylated...
September 14, 2017: Nucleus
https://www.readbyqxmd.com/read/28910569/hierarchical-recruitment-of-polycomb-complexes-revisited
#16
Eshagh Dorafshan, Tatyana G Kahn, Yuri B Schwartz
Polycomb Group (PcG) proteins epigenetically repress key developmental genes and thereby control alternative cell fates. PcG proteins act as complexes that can modify histones and these histone modifications play a role in transmitting the "memory" of the repressed state as cells divide. Here we consider mainstream models that link histone modifications to hierarchical recruitment of PcG complexes and compare them to results of a direct test of interdependence between PcG complexes for recruitment to Drosophila genes...
September 14, 2017: Nucleus
https://www.readbyqxmd.com/read/28910411/molecular-population-genetics-of-the-polycomb-genes-in-drosophila-subobscura
#17
Juan M Calvo-Martín, Montserrat Papaceit, Carmen Segarra
Polycomb group (PcG) proteins are important regulatory factors that modulate the chromatin state. They form protein complexes that repress gene expression by the introduction of posttranslational histone modifications. The study of PcG proteins divergence in Drosophila revealed signals of coevolution among them and an acceleration of the nonsynonymous evolutionary rate in the lineage ancestral to the obscura group species, mainly in subunits of the Pcl-PRC2 complex. Herein, we have studied the nucleotide polymorphism of PcG genes in a natural population of D...
2017: PloS One
https://www.readbyqxmd.com/read/28904641/histone-code-and-long-non-coding-rnas-lncrnas-aberrations-in-lung-cancer-implications-in-the-therapy-response
#18
REVIEW
Abril Marcela Herrera-Solorio, Leonel Armas-López, Oscar Arrieta, Joaquín Zúñiga, Patricia Piña-Sánchez, Federico Ávila-Moreno
Respiratory diseases hold several genome, epigenome, and transcriptional aberrations as a cause of the accumulated damage promoted by, among others, environmental risk factors. Such aberrations can also come about as an adaptive response when faced with therapeutic oncological drugs. In epigenetic terms, aberrations in DNA methylation patterns, histone code marks balance, and/or chromatin-remodeling complexes recruitment, among Polycomb Repressive Complex-2 (PRC2) versus Trithorax (TRX) Activator Complex, have been proposed to be affected by several previously characterized functional long non-coding RNAs (lncRNAs)...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28903997/mitotic-post-translational-modifications-of-histones-promote-chromatin-compaction-in-vitro
#19
Alisa Zhiteneva, Juan Jose Bonfiglio, Alexandr Makarov, Thomas Colby, Paola Vagnarelli, Eric C Schirmer, Ivan Matic, William C Earnshaw
How eukaryotic chromosomes are compacted during mitosis has been a leading question in cell biology since the nineteenth century. Non-histone proteins such as condensin complexes contribute to chromosome shaping, but appear not to be necessary for mitotic chromatin compaction. Histone modifications are known to affect chromatin structure. As histones undergo major changes in their post-translational modifications during mitotic entry, we speculated that the spectrum of cell-cycle-specific histone modifications might contribute to chromosome compaction during mitosis...
September 2017: Open Biology
https://www.readbyqxmd.com/read/28903048/set2-methyltransferase-facilitates-dna-replication-and-promotes-genotoxic-stress-responses-through-mbf-dependent-transcription
#20
Chen-Chun Pai, Anastasiya Kishkevich, Rachel S Deegan, Andrea Keszthelyi, Lisa Folkes, Stephen E Kearsey, Nagore De León, Ignacio Soriano, Robertus Antonius Maria de Bruin, Antony M Carr, Timothy C Humphrey
Chromatin modification through histone H3 lysine 36 methylation by the SETD2 tumor suppressor plays a key role in maintaining genome stability. Here, we describe a role for Set2-dependent H3K36 methylation in facilitating DNA replication and the transcriptional responses to both replication stress and DNA damage through promoting MluI cell-cycle box (MCB) binding factor (MBF)-complex-dependent transcription in fission yeast. Set2 loss leads to reduced MBF-dependent ribonucleotide reductase (RNR) expression, reduced deoxyribonucleoside triphosphate (dNTP) synthesis, altered replication origin firing, and a checkpoint-dependent S-phase delay...
September 12, 2017: Cell Reports
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