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https://www.readbyqxmd.com/read/29019976/nucleosome-chd1-structure-and-implications-for-chromatin-remodelling
#1
Lucas Farnung, Seychelle M Vos, Christoph Wigge, Patrick Cramer
Chromatin-remodelling factors change nucleosome positioning and facilitate DNA transcription, replication, and repair. The conserved remodelling factor chromodomain-helicase-DNA binding protein 1(Chd1) can shift nucleosomes and induce regular nucleosome spacing. Chd1 is required for the passage of RNA polymerase IIthrough nucleosomes and for cellular pluripotency. Chd1 contains the DNA-binding domains SANT and SLIDE, a bilobal motor domain that hydrolyses ATP, and a regulatory double chromodomain. Here we report the cryo-electron microscopy structure of Chd1 from the yeast Saccharomyces cerevisiae bound to a nucleosome at a resolution of 4...
October 11, 2017: Nature
https://www.readbyqxmd.com/read/28954549/functions-of-smarcal1-zranb3-and-hltf-in-maintaining-genome-stability
#2
Lisa A Poole, David Cortez
A large number of SNF2 family, DNA and ATP-dependent motor proteins are needed during transcription, DNA replication, and DNA repair to manipulate protein-DNA interactions and change DNA structure. SMARCAL1, ZRANB3, and HLTF are three related members of this family with specialized functions that maintain genome stability during DNA replication. These proteins are recruited to replication forks through protein-protein interactions and bind DNA using both their motor and substrate recognition domains (SRDs)...
September 28, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28852706/ultra-rare-mutations-in-srcap-segregate-in-caribbean-hispanic-families-with-alzheimer-disease
#3
Badri N Vardarajan, Giuseppe Tosto, Roger Lefort, Lei Yu, David A Bennett, Philip L De Jager, Sandra Barral, Dolly Reyes-Dumeyer, Peter L Nagy, Joseph H Lee, Rong Cheng, Martin Medrano, Rafael Lantigua, Ekaterina Rogaeva, Peter St George-Hyslop, Richard Mayeux
OBJECTIVE: To identify rare coding variants segregating with late-onset Alzheimer disease (LOAD) in Caribbean Hispanic families. METHODS: Whole-exome sequencing (WES) was completed in 110 individuals from 31 Caribbean Hispanic families without APOE ε4 homozygous carriers. Rare coding mutations segregating in families were subsequently genotyped in additional families and in an independent cohort of Caribbean Hispanic patients and controls. SRCAP messenger RNA (mRNA) expression was assessed in whole blood from mutation carriers with LOAD, noncarriers with LOAD, and healthy elderly controls, and also from autopsied brains in 2 clinical neuropathologic cohort studies of aging and dementia...
October 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28807921/candida-albicans-swi-snf-and-mediator-complexes-differentially-regulate-mrr1-induced-mdr1-expression-and-fluconazole-resistance
#4
Zhongle Liu, Lawrence C Myers
Long-term azole treatment of patients with chronic Candida albicans infections can lead to drug resistance. Gain-of-function (GOF) mutations in the transcription factor Mrr1 and the consequent transcriptional activation of MDR1, a drug efflux coding gene, is a common pathway by which this human fungal pathogen acquires fluconazole resistance. This work elucidates the previously unknown downstream transcription mechanisms utilized by hyperactive Mrr1. We've identified the Swi/Snf chromatin remodeling complex as a key co-activator for Mrr1, which is required to maintain basal and induced 'open' chromatin, and Mrr1 occupancy, at the MDR1 promoter...
August 14, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28790150/phosphorylation-of-histone-h2a-at-serine-95-a-plant-specific-mark-involved-in-flowering-time-regulation-and-h2a-z-deposition
#5
Yanhua Su, Shiliang Wang, Fei Zhang, Han Zheng, Yanan Liu, Tongtong Huang, Yong Ding
Phosphorylation of histone H3 affects transcription, chromatin condensation, and chromosome segregation. However, the role of phosphorylation of histone H2A remains unclear. Here, we found that Arabidopsis thaliana MUT9P-LIKE-KINASE (MLK4) phosphorylates histone H2A on serine 95, a plant-specific modification in the histone core domain. Mutations in MLK4 caused late flowering under long-day conditions but no notable phenotype under short days. MLK4 interacts with CIRCADIAN CLOCK ASSOCIATED1 (CCA1), which allows MLK4 to bind to the GIGANTEA (GI) promoter...
September 2017: Plant Cell
https://www.readbyqxmd.com/read/28746399/coordination-of-matrix-attachment-and-atp-dependent-chromatin-remodeling-regulate-auxin-biosynthesis-and-arabidopsis-hypocotyl-elongation
#6
Kyounghee Lee, Pil Joon Seo
Hypocotyl elongation is extensively controlled by hormone signaling networks. In particular, auxin metabolism and signaling play key roles in light-dependent hypocotyl growth. The nuclear matrix facilitates organization of DNA within the nucleus, and dynamic interactions between nuclear matrix and DNA are related to gene regulation. Conserved scaffold/matrix attachment regions (S/MARs) are anchored to the nuclear matrix by the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) proteins in Arabidopsis. Here, we found that ESCAROLA (ESC)/AHL27 and SUPPRESSOR OF PHYTOCHROME B-4 #3 (SOB3)/AHL29 redundantly regulate auxin biosynthesis in the control of hypocotyl elongation...
2017: PloS One
https://www.readbyqxmd.com/read/28739803/chromatin-remodeling-swi-snf-complex-regulates-coenzyme-q6-synthesis-and-a-metabolic-shift-to-respiration-in-yeast
#7
Agape M Awad, Srivats Venkataramanan, Anish Nag, Anoop Raj Galivanche, Michelle C Bradley, Lauren T Neves, Stephen Douglass, Catherine F Clarke, Tracy L Johnson
Despite its relatively streamlined genome, there are many important examples of regulated RNA splicing in Saccharomyces cerevisiae Here, we report a role for the chromatin remodeler SWI/SNF in respiration, partially via the regulation of splicing. We find that a nutrient-dependent decrease in Snf2 leads to an increase in splicing of the PTC7 transcript. The spliced PTC7 transcript encodes a mitochondrial phosphatase regulator of biosynthesis of coenzyme Q6 (ubiquinone or CoQ6) and a mitochondrial redox-active lipid essential for electron and proton transport in respiration...
September 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28657808/chronologic-trends-in-studies-on-fluoride-mechanisms-of-action
#8
H J Oh, H W Oh, D W Lee, C H Kim, J Y Ahn, Y Kim, H B Shin, C Y Kim, S H Park, J G Jeon
Fluoride has been widely used for the prevention of dental caries since the mid-20th century. The aim of this study was to investigate the chronologic trends in studies on fluoride mechanisms of action against dental caries during the years 1950 to 2015. To this aim, queries such as "fluoride," "fluoride and demineralization," "fluoride and remineralization," "fluoride and (plaque or biofilms)," and "fluoride and (bacteria or microbials)" were submitted to PubMed to collect research article information, including titles, abstracts, publication dates, author affiliations, and publication journals...
June 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28657701/clinical-effects-of-stabilized-stannous-fluoride-dentifrice-in-reducing-plaque-microbial-virulence-i-microbiological-and-receptor-cell-findings
#9
Malgorzata Klukowska, John Christian Haught, Sancai Xie, Ben Circello, Cheryl S Tansky, Deepa Khambe, Tom Huggins, Donald J White
OBJECTIVES: Lipopolysaccharides (LPSs) and lipoteichoic acids (LTAs), or bacterial endotoxins, bind with Toll-like receptors (TLRs) that are expressed on host cells of the periodontium, thereby contributing to the periodontal pathogenicity of oral bacteria. Stannous fluoride (SnF2), an antibacterial fluoride that treats and controls gingivitis, has been shown to react with lipophilic domains/anionic charges in LPS and LTA. The effects of bacterial species and dental plaque on toll receptors can be studied using genetically engineered cell lines containing linked toll receptors on their surfaces...
June 2017: Journal of Clinical Dentistry
https://www.readbyqxmd.com/read/28652142/a-randomised-exploratory-clinical-evaluation-of-dentifrices-used-as-controls-in-dentinal-hypersensitivity-studies
#10
John Gallob, Farzana Sufi, Pejmon Amini, Muhammad Siddiqi, Stephen Mason
OBJECTIVES: To explore relative efficacy of six negative-control dentifrices utilised as controls in clinical studies compared with two dentine hypersensitivity (DH)-relief dentifrices used 2×/day for 8 weeks. METHODS: Six control dentifrices differing in terms of fluoride source (sodium fluoride/sodium monofluorophosphate), abrasive base (silica/dicalcium phosphate), relative dentine abrasivity (RDA) (∼17 to ∼180) and colour (white/blue/multicoloured stripes) were compared with a depolarising dentifrice (5% KNO3; RDA ∼70-97; 'Test 1') and an occlusion-technology dentifrice (0...
June 23, 2017: Journal of Dentistry
https://www.readbyqxmd.com/read/28637241/the-chromatin-remodeling-complex-swi-snf-regulates-splicing-of-meiotic-transcripts-in-saccharomyces-cerevisiae
#11
Srivats Venkataramanan, Stephen Douglass, Anoop R Galivanche, Tracy L Johnson
Despite its relatively streamlined genome, there are important examples of regulated RNA splicing in Saccharomyces cerevisiae, such as splicing of meiotic transcripts. Like other eukaryotes, S. cerevisiae undergoes a dramatic reprogramming of gene expression during meiosis, including regulated splicing of a number of crucial meiosis-specific RNAs. Splicing of a subset of these is dependent upon the splicing activator Mer1. Here we show a crucial role for the chromatin remodeler Swi/Snf in regulation of splicing of meiotic genes and find that the complex affects meiotic splicing in two ways...
July 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28600722/genetic-dissection-of-plant-growth-habit-in-chickpea
#12
Hari D Upadhyaya, Deepak Bajaj, Rishi Srivastava, Anurag Daware, Udita Basu, Shailesh Tripathi, Chellapilla Bharadwaj, Akhilesh K Tyagi, Swarup K Parida
A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs...
June 9, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28569786/brg1-mediated-nrf2-ho-1-pathway-activation-alleviates-hepatic-ischemia-reperfusion-injury
#13
Mian Ge, Weifeng Yao, Dongdong Yuan, Shaoli Zhou, Xi Chen, Yihan Zhang, Haobo Li, Zhengyuan Xia, Ziqing Hei
Cytoprotective gene heme oxygenase 1 (HO-1) could be induced by nuclear factor E2-related factor 2 (Nrf2) nuclear translocation. The purpose of this study was to determine the role of Brahma-related gene 1 (Brg1), a catalytic subunit of SWI2/SNF2-like chromatin remodeling complexes, in Nrf2/HO-1 pathway activation during hepatic ischemia-reperfusion (HIR). Our results showed that hepatic Brg1 was inhibited during early HIR while Brg1 overexpression reduced oxidative injury in CMV-Brg1 mice subjected to HIR...
June 1, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28552615/sumo-targeted-dna-translocase-rrp2-protects-the-genome-from-top2-induced-dna-damage
#14
Yi Wei, Li-Xue Diao, Shan Lu, Hai-Tao Wang, Fang Suo, Meng-Qiu Dong, Li-Lin Du
The action of DNA topoisomerase II (Top2) creates transient DNA breaks that are normally concealed inside Top2-DNA covalent complexes. Top2 poisons, including ubiquitously present natural compounds and clinically used anti-cancer drugs, trap Top2-DNA complexes. Here, we show that cells actively prevent Top2 degradation to avoid the exposure of concealed DNA breaks. A genome-wide screen revealed that fission yeast cells lacking Rrp2, an Snf2-family DNA translocase, are strongly sensitive to Top2 poisons. Loss of Rrp2 enhances SUMOylation-dependent ubiquitination and degradation of Top2, which in turn increases DNA damage at sites where Top2-DNA complexes are trapped...
June 1, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28535603/realizing-full-coverage-of-stable-perovskite-film-by-modified-anti-solvent-process
#15
Long Ji, Ting Zhang, Yafei Wang, Peng Zhang, Detao Liu, Zhi Chen, Shibin Li
Lead-free solution-processed solid-state photovoltaic devices based on formamidinium tin triiodide (FASnI3) and cesium tin triiodide (CsSnI3) perovskite semiconductor as the light harvester are reported. In this letter, we used solvent engineering and anti-solvent dripping method to fabricate perovskite films. SnCl2 was used as an inhibitor of Sn(4+) in FASnI3 precursor solution. We obtained the best films under the function of toluene or chlorobenzene in anti-solvent dripping method and monitored the oxidation of FASnI3 films in air...
December 2017: Nanoscale Research Letters
https://www.readbyqxmd.com/read/28509359/the-dna-translocase-rad5a-acts-independently-of-the-other-main-dna-repair-pathways-and-requires-both-its-atpase-and-ring-domain-for-activity-in-arabidopsis-thaliana
#16
Tobias Klemm, Anja Mannuß, Daniela Kobbe, Alexander Knoll, Oliver Trapp, Annika Dorn, Holger Puchta
Multiple pathways exist to repair DNA damage induced by methylating and crosslinking agents in Arabidopsis thaliana. The SWI2/SNF2 translocase RAD5A, the functional homolog of budding yeast Rad5 that is required for the error-free branch of post-replicative repair, plays a surprisingly prominent role in the repair of both kinds of lesions in Arabidopsis. Here we show that both the ATPase domain and the ubiquitination function of the RING domain of the Arabidopsis protein are essential for the cellular response to different forms of DNA damage...
August 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28507246/the-pneumococcal-type-1-pilus-genes-are-thermoregulated-and-are-repressed-by-a-member-of-the-snf2-protein-family
#17
Alan Basset, Muriel Herd, Raecliffe Daly, Simon L Dove, Richard Malley
In Streptococcus pneumoniae, the type 1 pilus is involved in many steps of pathogenesis, including adherence to epithelial cells, mediation of inflammation, escape from macrophages, and the formation of biofilms. The type 1 pilus genes are expressed in a bistable fashion with cells switching between "on" and "off" expression states. Bistable expression of these genes is due to their control by RlrA, a positive regulator subject to control by a positive-feedback loop. The type 1 pilus genes are also thought to be negatively regulated by a large number of repressors...
August 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28475613/sumo-targeted-ubiquitin-ligase-activity-can-either-suppress-or-promote-genome-instability-depending-on-the-nature-of-the-dna-lesion
#18
Minghua Nie, Bettina A Moser, Toru M Nakamura, Michael N Boddy
The posttranslational modifiers SUMO and ubiquitin critically regulate the DNA damage response (DDR). Important crosstalk between these modifiers at DNA lesions is mediated by the SUMO-targeted ubiquitin ligase (STUbL), which ubiquitinates SUMO chains to generate SUMO-ubiquitin hybrids. These SUMO-ubiquitin hybrids attract DDR proteins able to bind both modifiers, and/or are degraded at the proteasome. Despite these insights, specific roles for SUMO chains and STUbL in the DDR remain poorly defined. Notably, fission yeast defective in SUMO chain formation exhibit near wild-type resistance to genotoxins and moreover, have a greatly reduced dependency on STUbL activity for DNA repair...
May 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28424519/mechanism-of-chromatin-remodelling-revealed-by-the-snf2-nucleosome-structure
#19
Xiaoyu Liu, Meijing Li, Xian Xia, Xueming Li, Zhucheng Chen
Chromatin remodellers are helicase-like, ATP-dependent enzymes that alter chromatin structure and nucleosome positions to allow regulatory proteins access to DNA. Here we report the cryo-electron microscopy structure of chromatin remodeller Switch/sucrose non-fermentable (SWI2/SNF2) from Saccharomyces cerevisiae bound to the nucleosome. The structure shows that the two core domains of Snf2 are realigned upon nucleosome binding, suggesting activation of the enzyme. The core domains contact each other through two induced Brace helices, which are crucial for coupling ATP hydrolysis to chromatin remodelling...
April 27, 2017: Nature
https://www.readbyqxmd.com/read/28383696/the-lsh-hells-homolog-irc5-contributes-to-cohesin-association-with-chromatin-in-yeast
#20
Ireneusz Litwin, Tomasz Bakowski, Ewa Maciaszczyk-Dziubinska, Robert Wysocki
Accurate chromosome segregation is essential for every living cell as unequal distribution of chromosomes during cell division may result in genome instability that manifests in carcinogenesis and developmental disorders. Irc5 from Saccharomyces cerevisiae is a member of the conserved Snf2 family of ATP-dependent DNA translocases and its function is poorly understood. Here, we identify Irc5 as a novel interactor of the cohesin complex. Irc5 associates with Scc1 cohesin subunit and contributes to cohesin binding to chromatin...
June 20, 2017: Nucleic Acids Research
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