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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
#1
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 cross-linking 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...
May 16, 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
#2
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...
May 15, 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
#3
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 5, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28424519/mechanism-of-chromatin-remodelling-revealed-by-the-snf2-nucleosome-structure
#4
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 19, 2017: Nature
https://www.readbyqxmd.com/read/28383696/the-lsh-hells-homolog-irc5-contributes-to-cohesin-association-with-chromatin-in-yeast
#5
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...
April 5, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28369616/nap1l1-accelerates-activation-and-decreases-pausing-to-enhance-nucleosome-remodeling-by-csb
#6
Ju Yeon Lee, Robert J Lake, Jaewon Kirk, Vilhelm A Bohr, Hua-Ying Fan, Sungchul Hohng
Cockayne syndrome protein B (CSB) belongs to the SWI2/SNF2 ATP-dependent chromatin remodeler family, and CSB is the only ATP-dependent chromatin remodeler essential for transcription-coupled nucleotide excision DNA repair. CSB alone remodels nucleosomes ∼10-fold slower than the ACF remodeling complex. Strikingly, NAP1-like histone chaperones interact with CSB and greatly enhance CSB-mediated chromatin remodeling. While chromatin remodeling by CSB and NAP1-like proteins is crucial for efficient transcription-coupled DNA repair, the mechanism by which NAP1-like proteins enhance chromatin remodeling by CSB remains unknown...
May 5, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28341648/dna-damage-tolerance-pathway-choice-through-uls1-modulation-of-srs2-sumoylation-in-saccharomyces-cerevisiae
#7
Karol Kramarz, Seweryn Mucha, Ireneusz Litwin, Anna Barg-Wojas, Robert Wysocki, Dorota Dziadkowiec
DNA damage tolerance and homologous recombination pathways function to bypass replication-blocking lesions and ensure completion of DNA replication. However, inappropriate activation of these pathways may lead to increased mutagenesis or formation of deleterious recombination intermediates, often leading to cell death or cancer formation in higher organisms. Post-translational modifications of PCNA regulate the choice of repair pathways at replication forks. Its monoubiquitination favors translesion synthesis, while polyubiquitination stimulates template switching...
May 2017: Genetics
https://www.readbyqxmd.com/read/28337468/comparative-analysis-data-of-sf1-and-sf2-helicases-from-three-domains-of-life
#8
Wafi Chaar, Hiba Ibrahim, Juliana Kozah, Hala Chamieh
SF1 and SF2 helicases are important molecular motors that use the energy of ATP to unwind nucleic acids or nucleic-acid protein complexes. They are ubiquitous enzymes and found in almost all organisms sequenced to date. This article provides a comparative analysis for SF1 and SF2 helicase families from three domains of life archaea, human, bacteria. Seven families are conserved in these three representatives and includes Upf1-like, UvrD-like, Rad3-like, DEAD-box, RecQ-like. Snf2 and Ski2-like. The data highlight conservation of the helicase core motifs for each of these families...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28334870/annealing-helicase-harp-closes-rpa-stabilized-dna-bubbles-non-processively
#9
Daniel R Burnham, Bas Nijholt, Iwijn De Vlaminck, Jinhua Quan, Timur Yusufzai, Cees Dekker
We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a physiologically relevant substrate. We find that HARP closes RPA-stabilized bubbles in a slow reaction, taking on the order of tens of minutes for ∼600 bp of DNA to be re-annealed. The data indicate that DNA re-anneals through the removal of RPA, which is observed as clear steps in the bubble-closing traces...
May 5, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28330902/regulation-of-nucleosome-positioning-by-a-chd-type-iii-chromatin-remodeler-and-its-relationship-to-developmental-gene-expression-in-dictyostelium
#10
James L Platt, Nicholas A Kent, Alan R Kimmel, Adrian J Harwood
Nucleosome placement and repositioning can direct transcription of individual genes; however, the precise interactions of these events are complex and largely unresolved at the whole-genome level. The Chromodomain-Helicase-DNA binding (CHD) Type III proteins are a subfamily of SWI2/SNF2 proteins that control nucleosome positioning and are associated with several complex human disorders, including CHARGE syndrome and autism. Type III CHDs are required for multicellular development of animals and Dictyostelium but are absent in plants and yeast...
April 2017: Genome Research
https://www.readbyqxmd.com/read/28318821/snf2-family-protein-fft3-suppresses-nucleosome-turnover-to-promote-epigenetic-inheritance-and-proper-replication
#11
Nitika Taneja, Martin Zofall, Vanivilasini Balachandran, Gobi Thillainadesan, Tomoyasu Sugiyama, David Wheeler, Ming Zhou, Shiv I S Grewal
Heterochromatin can be epigenetically inherited in cis, leading to stable gene silencing. However, the mechanisms underlying heterochromatin inheritance remain unclear. Here, we identify Fft3, a fission yeast homolog of the mammalian SMARCAD1 SNF2 chromatin remodeler, as a factor uniquely required for heterochromatin inheritance, rather than for de novo assembly. Importantly, we find that Fft3 suppresses turnover of histones at heterochromatic loci to facilitate epigenetic transmission of heterochromatin in cycling cells...
April 6, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28249160/loss-of-snf5-induces-formation-of-an-aberrant-swi-snf-complex
#12
Payel Sen, Jie Luo, Arjan Hada, Solomon G Hailu, Mekonnen Lemma Dechassa, Jim Persinger, Sandipan Brahma, Somnath Paul, Jeff Ranish, Blaine Bartholomew
The SWI/SNF chromatin remodeling complex is highly conserved from yeast to human, and aberrant SWI/SNF complexes contribute to human disease. The Snf5/SMARCB1/INI1 subunit of SWI/SNF is a tumor suppressor frequently lost in pediatric rhabdoid cancers. We examined the effects of Snf5 loss on the composition, nucleosome binding, recruitment, and remodeling activities of yeast SWI/SNF. The Snf5 subunit is shown by crosslinking-mass spectrometry (CX-MS) and subunit deletion analysis to interact with the ATPase domain of Snf2 and to form a submodule consisting of Snf5, Swp82, and Taf14...
February 28, 2017: Cell Reports
https://www.readbyqxmd.com/read/28249159/composition-and-function-of-mutant-swi-snf-complexes
#13
Arnob Dutta, Mihaela Sardiu, Madelaine Gogol, Joshua Gilmore, Daoyong Zhang, Laurence Florens, Susan M Abmayr, Michael P Washburn, Jerry L Workman
The 12-subunit Swi/Snf chromatin remodeling complex is conserved from yeast to humans. It functions to alter nucleosome positions by either sliding nucleosomes on DNA or evicting histones. Interestingly, 20% of all human cancers carry mutations in subunits of the Swi/Snf complex. Many of these mutations cause protein instability and loss, resulting in partial Swi/Snf complexes. Although several studies have shown that histone acetylation and activator-dependent recruitment of Swi/Snf regulate its function, it is less well understood how subunits regulate stability and function of the complex...
February 28, 2017: Cell Reports
https://www.readbyqxmd.com/read/28057214/chromatin-remodeling-and-plant-immunity
#14
W Chen, Q Zhu, Y Liu, Q Zhang
Chromatin remodeling, an important facet of the regulation of gene expression in eukaryotes, is performed by two major types of multisubunit complexes, covalent histone- or DNA-modifying complexes, and ATP-dependent chromosome remodeling complexes. Snf2 family DNA-dependent ATPases constitute the catalytic subunits of ATP-dependent chromosome remodeling complexes, which accounts for energy supply during chromatin remodeling. Increasing evidence indicates a critical role of chromatin remodeling in the establishment of long-lasting, even transgenerational immune memory in plants, which is supported by the findings that DNA methylation, histone deacetylation, and histone methylation can prime the promoters of immune-related genes required for disease defense...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28056110/selection-of-reference-genes-for-qrt-pcr-analysis-of-gene-expression-in-stipa-grandis-during-environmental-stresses
#15
Dongli Wan, Yongqing Wan, Qi Yang, Bo Zou, Weibo Ren, Yong Ding, Zhen Wang, Ruigang Wang, Kai Wang, Xiangyang Hou
Stipa grandis P. Smirn. is a dominant plant species in the typical steppe of the Xilingole Plateau of Inner Mongolia. Selection of suitable reference genes for the quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) is important for gene expression analysis and research into the molecular mechanisms underlying the stress responses of S. grandis. In the present study, 15 candidate reference genes (EF1 beta, ACT, GAPDH, SamDC, CUL4, CAP, SNF2, SKIP1, SKIP5, SKIP11, UBC2, UBC15, UBC17, UCH, and HERC2) were evaluated for their stability as potential reference genes for qRT-PCR under different stresses...
2017: PloS One
https://www.readbyqxmd.com/read/28045388/crystal-structure-of-the-atpase-c-domain-of-the-chromatin-remodeller-fun30-from-saccharomyces-cerevisiae
#16
Lan Liu, Tao Jiang
Fun30 (Function unknown now 30) is a chromatin remodeller belonging to the Snf2 family. It has previously been reported to be a regulator of several cellular activities, including DNA repair, gene silencing and maintenance of chromatin structure. Here, the crystal structure of the Fun30 ATPase-C domain (the C-lobe of the ATPase domain) is reported at 1.95 Å resolution. Although the structure displays overall similarities to those of other Snf2 family members, a new structural module was found to be specific to the Fun30 subfamily...
January 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28043139/structural-stability-vibrational-properties-and-photoluminescence-in-cssni3-perovskite-upon-the-addition-of-snf2
#17
Athanassios G Kontos, Andreas Kaltzoglou, Eirini Siranidi, Dimitrios Palles, Giasemi K Angeli, Michalis K Arfanis, Vassilis Psycharis, Yannis S Raptis, Efstratios I Kamitsos, Pantelis N Trikalitis, Constantinos C Stoumpos, Mercouri G Kanatzidis, Polycarpos Falaras
The CsSnI3 perovskite and the corresponding SnF2-containing material with nominal composition CsSnI2.95F0.05 were synthesized by solid-state reactions and structurally characterized by powder X-ray diffraction. Both materials undergo rapid phase transformation upon exposure to air from the black orthorhombic phase (B-γ-CsSnI3) to the yellow orthorhombic phase (Y-CsSnI3), followed by irreversible oxidation into Cs2SnI6 within several hours. The phase transition occurs at a significantly lower rate in the SnF2-containing material rather than in the pure perovskite...
January 3, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/27957274/effect-of-toothpastes-containing-different-naf-concentrations-or-a-snf2-naf-combination-on-root-dentine-erosive-lesions-in-vitro
#18
Iliana Diamanti, Haroula Koletsi-Kounari, Eleni Mamai-Homata
BACKGROUND: Fluoride toothpastes presumably offer some protection against acid erosion. However, uncertainty exists towards fluoride's efficacy relatively to the concentration and the type of chemical compound used. This in vitro study evaluated the relative efficacy of toothpastes containing sodium fluoride in different concentrations or a stabilized stannous fluoride/sodium fluoride system on root dentine erosion. MATERIAL AND METHODS: Bovine dentin specimens were allocated into four groups (n=10): control (no F), 1450ppm F (as NaF), 5000ppm F (as NaF) and 1450ppm F (1100ppm as stabilized SnF2 and 350ppm as NaF)/sodium hexamethaphosphate...
December 2016: Journal of Clinical and Experimental Dentistry
https://www.readbyqxmd.com/read/27934915/the-defining-dna-methylation-signature-of-floating-harbor-syndrome
#19
Rebecca L Hood, Laila C Schenkel, Sarah M Nikkel, Peter J Ainsworth, Guillaume Pare, Kym M Boycott, Dennis E Bulman, Bekim Sadikovic
Floating-Harbor syndrome (FHS) is an autosomal dominant genetic condition characterized by short stature, delayed osseous maturation, expressive language impairment, and unique facial dysmorphology. We previously identified mutations in the chromatin remodeling protein SRCAP (SNF2-related CBP Activator Protein) as the cause of FHS. SRCAP has multiple roles in chromatin and transcriptional regulation; however, specific epigenetic consequences of SRCAP mutations remain to be described. Using high resolution genome-wide DNA methylation analysis, we identified a unique and highly specific DNA methylation "epi-signature" in the peripheral blood of individuals with FHS...
December 9, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27919072/structure-and-regulation-of-the-chromatin-remodeller-iswi
#20
Lijuan Yan, Li Wang, Yuanyuan Tian, Xian Xia, Zhucheng Chen
ISWI is a member of the SWI2/SNF2 family of chromatin remodellers, which also includes Snf2, Chd1, and Ino80. ISWI is the catalytic subunit of several chromatin remodelling complexes, which mobilize nucleosomes along genomic DNA, promoting replication progression, transcription repression, heterochromatin formation, and many other nuclear processes. The ATPase motor of ISWI is an autonomous remodelling machine, whereas its carboxy (C)-terminal HAND-SAND-SLIDE (HSS) domain functions in binding extranucleosomal linker DNA...
December 15, 2016: Nature
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