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https://www.readbyqxmd.com/read/29643509/structural-basis-for-atp-dependent-chromatin-remodelling-by-the-ino80-complex
#1
Sebastian Eustermann, Kevin Schall, Dirk Kostrewa, Kristina Lakomek, Mike Strauss, Manuela Moldt, Karl-Peter Hopfner
In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone composition of nucleosomes is governed by ATP-dependent chromatin remodellers1-3 such as the 15-subunit INO80 complex 4 . INO80 regulates gene expression, DNA repair and replication by sliding nucleosomes, the exchange of histone H2A.Z with H2A, and the positioning of + 1 and -1 nucleosomes at promoter DNA5-8 . The structures and mechanisms of these remodelling reactions are currently unknown...
April 11, 2018: Nature
https://www.readbyqxmd.com/read/29643506/structure-and-regulation-of-the-human-ino80-nucleosome-complex
#2
Rafael Ayala, Oliver Willhoft, Ricardo J Aramayo, Martin Wilkinson, Elizabeth A McCormack, Lorraine Ocloo, Dale B Wigley, Xiaodong Zhang
Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines 1 . Biochemical studies2-4 have placed the motor domains of several chromatin remodellers in the superhelical location 2 region of the nucleosome. Structural studies of yeast Chd1 and Snf2-a subunit in the complex with the capacity to remodel the structure of chromatin (RSC)-in complex with nucleosomes5-7 have provided insights into the basic mechanism of nucleosome sliding performed by these complexes...
April 11, 2018: Nature
https://www.readbyqxmd.com/read/29616272/a-lead-free-two-dimensional-perovskite-for-a-high-performance-flexible-photoconductor-and-a-light-stimulated-synaptic-device
#3
Liu Qian, Yilin Sun, Mingmao Wu, Chun Li, Dan Xie, Liming Ding, Gaoquan Shi
Organo-lead halide perovskites have emerged as promising materials for high-performance photodetectors. However, the toxicity of lead cations in these materials limits their further applications. Here, a flexible photoconductor is developed based on lead-free two-dimensional (2D) perovskite (PEA)2SnI4 via a one-step solution processing method. The flexible transparent electrodes are patterned from rGO/(PEDOT:PSS) hybrid films. The stability and reproducibility of the devices are significantly improved on adding 30 mol% SnF2 to the perovskite...
April 4, 2018: Nanoscale
https://www.readbyqxmd.com/read/29616070/the-rice-rolled-fine-striped-rfs-chd3-mi-2-chromatin-remodeling-factor-epigenetically-regulates-genes-involved-in-oxidative-stress-responses-during-leaf-development
#4
Sung-Hwan Cho, Chung-Hee Lee, Eunji Gi, Yehyun Yim, Hee-Jong Koh, Kiyoon Kang, Nam-Chon Paek
In rice ( Oryza sativa ), moderate leaf rolling increases photosynthetic competence and raises grain yield; therefore, this important agronomic trait has attracted much attention from plant biologists and breeders. However, the relevant molecular mechanism remains unclear. Here, we isolated and characterized Rolled Fine Striped ( RFS ), a key gene affecting rice leaf rolling, chloroplast development, and reactive oxygen species (ROS) scavenging. The rfs-1 gamma-ray allele and the rfs-2 T-DNA insertion allele of RFS failed to complement each other and their mutants had similar phenotypes, producing extremely incurved leaves due to defective development of vascular cells on the adaxial side...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29538349/the-effect-of-laminin-surface-modification-of-electrospun-silica-nanofiber-substrate-on-neuronal-tissue-engineering
#5
Wen Shuo Chen, Ling Yu Guo, Chia Chun Tang, Cheng Kang Tsai, Hui Hua Huang, Ting Yu Chin, Mong-Lin Yang, Yui Whei Chen-Yang
In this study, we first synthesized a slow-degrading silica nanofiber (SNF2) through an electrospun solution with an optimized tetraethyl orthosilicate (TEOS) to polyvinyl pyrrolidone (PVP) ratio. Then, laminin-modified SNF2, namely SNF2-AP-S-L, was obtained through a series of chemical reactions to attach the extracellular matrix protein, laminin, to its surface. The SNF2-AP-S-L substrate was characterized by a combination of scanning electron microscopy (SEM), Fourier transform-infrared (FTIR) spectroscopy, nitrogen adsorption/desorption isotherms, and contact angle measurements...
March 14, 2018: Nanomaterials
https://www.readbyqxmd.com/read/29535137/-lnckdm2b-controls-self-renewal-of-embryonic-stem-cells-via-activating-expression-of-transcription-factor-zbtb3
#6
Buqing Ye, Benyu Liu, Liuliu Yang, Xiaoxiao Zhu, Dongdong Zhang, Wei Wu, Pingping Zhu, Yanying Wang, Shuo Wang, Pengyan Xia, Ying Du, Shu Meng, Guanling Huang, Jiayi Wu, Runsheng Chen, Yong Tian, Zusen Fan
Divergent long noncoding RNAs (lncRNAs) represent a major lncRNA biotype in mouse and human genomes. The biological and molecular functions of the divergent lncRNAs remain largely unknown. Here, we show that lncKdm2b , a divergent lncRNA for Kdm2b gene, is conserved among five mammalian species and highly expressed in embryonic stem cells (ESCs) and early embryos. LncKdm2b knockout impairs ESC self-renewal and causes early embryonic lethality. LncKdm2b can activate Zbtb3 by promoting the assembly and ATPase activity of Snf2-related CREBBP activator protein (SRCAP) complex in trans Zbtb3 potentiates the ESC self-renewal in a Nanog-dependent manner...
March 13, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29523178/the-bromodomain-containing-protein-ibd1-links-multiple-chromatin-related-protein-complexes-to-highly-expressed-genes-in-tetrahymena-thermophila
#7
Alejandro Saettone, Jyoti Garg, Jean-Philippe Lambert, Syed Nabeel-Shah, Marcelo Ponce, Alyson Burtch, Cristina Thuppu Mudalige, Anne-Claude Gingras, Ronald E Pearlman, Jeffrey Fillingham
BACKGROUND: The chromatin remodelers of the SWI/SNF family are critical transcriptional regulators. Recognition of lysine acetylation through a bromodomain (BRD) component is key to SWI/SNF function; in most eukaryotes, this function is attributed to SNF2/Brg1. RESULTS: Using affinity purification coupled to mass spectrometry (AP-MS) we identified members of a SWI/SNF complex (SWI/SNFTt ) in Tetrahymena thermophila. SWI/SNFTt is composed of 11 proteins, Snf5Tt , Swi1Tt , Swi3Tt , Snf12Tt , Brg1Tt , two proteins with potential chromatin-interacting domains and four proteins without orthologs to SWI/SNF proteins in yeast or mammals...
March 9, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29408941/chromatin-remodeler-alc1-prevents-replication-fork-collapse-by-slowing-fork-progression
#8
Masato Ooka, Takuya Abe, Kosai Cho, Kaoru Koike, Shunichi Takeda, Kouji Hirota
ALC1 (amplified in liver cancer 1), an SNF2 superfamily chromatin-remodeling factor also known as CHD1L (chromodomain helicase/ATPase DNA binding protein 1-like), is implicated in base-excision repair, where PARP (Poly(ADP-ribose) polymerase) mediated Poly(ADP-ribose) signaling facilitates the recruitment of this protein to damage sites. We here demonstrate the critical role played by ALC1 in the regulation of replication-fork progression in cleaved template strands. To analyze the role played by ALC1 as well as its functional relationship with PARP1, we generated ALC1-/-, PARP1-/-, and ALC1-/-/PARP1-/- cells from chicken DT40 cells...
2018: PloS One
https://www.readbyqxmd.com/read/29383823/perthes-disease-a-new-finding-in-floating-harbor-syndrome
#9
Donatella Milani, Giulietta Scuvera, Marta Gatti, Gianluca Tolva, Francesca Bonarrigo, Susanna Esposito, Cristina Gervasini
Floating-Harbor Syndrome (FHS; OMIM #136140) is an ultra-rare autosomal dominant genetic condition characterized by expressive language delay, short stature with delayed bone mineralization, a triangular face with a prominent nose, and deep-set eyes, and hand anomalies. First reported in 1973, FHS is associated with mutations in the SRCAP gene, which encodes SNF2-related CREBBP activator protein. Mutations in the CREBBP gene cause Rubinstein-Taybi Syndrome (RSTS; OMIM #180849, #613684), another rare disease characterized by broad thumbs and halluces, facial dysmorphisms, short stature, and intellectual disability, which has a phenotypic overlap with FHS...
January 31, 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29372964/-the-role-of-remodeling-complexes-chd1-and-iswi-in-spontaneous-and-uv-induced-mutagenesis-control-in-yeast-saccharomyces-cerevisiae
#10
T A Evstiukhina, E A Alekseeva, D V Fedorov, V T Peshekhonov, V G Korolev
Chromatin remodulators are special multiprotein machines capable of transforming the structure, constitution, and positioning of nucleosomes on DNA. Biochemical activities of remodeling complexes CHD1 and ISWI from the SWI2/SNF2 family are well established. They ensure correct positioning of nucleosomes along the genome, which is probably critical for genome stability, in particular, after action of polymerases, repair enzymes, and transcription. In this paper, we show that single mutations in genes ISW1, ISW2, and CHD1 weakly affect repair and mutagenic processes in yeast cells...
February 2017: Genetika
https://www.readbyqxmd.com/read/29355427/stannous-fluoride-effects-on-gene-expression-of-streptococcus-mutans-and-actinomyces-viscosus
#11
Y Shi, R Li, D J White, A R Biesbrock
A genome-wide transcriptional analysis was performed to elucidate the bacterial cellular response of Streptococcus mutans and Actinomyces viscosus to NaF and SnF2 . The minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) of SnF2 were predetermined before microarray study. Gene expression profiling microarray experiments were carried out in the absence (control) and presence (experimental) of 10 ppm and 100 ppm Sn2+ (in the form of SnF2 ) and fluoride controls for 10-min exposures (4 biological replicates/treatment)...
February 2018: Advances in Dental Research
https://www.readbyqxmd.com/read/29343848/a-novel-protein-encoded-by-the-circular-form-of-the-shprh-gene-suppresses-glioma-tumorigenesis
#12
Maolei Zhang, Nunu Huang, Xuesong Yang, Jingyan Luo, Sheng Yan, Feizhe Xiao, Wenping Chen, Xinya Gao, Kun Zhao, Huangkai Zhou, Ziqiang Li, Liu Ming, Bo Xie, Nu Zhang
Circular RNAs (circRNAs) are recognized as functional non-coding transcripts in eukaryotic cells. Recent evidence has indicated that even though circRNAs are generally expressed at low levels, they may be involved in many physiological or pathological processes, such as gene regulation, tissue development and carcinogenesis. Although the 'microRNA sponge' function is well characterized, most circRNAs do not contain perfect trapping sites for microRNAs, which suggests the possibility that circRNAs have functions that have not yet been defined...
January 18, 2018: Oncogene
https://www.readbyqxmd.com/read/29339483/hells-and-cdca7-comprise-a-bipartite-nucleosome-remodeling-complex-defective-in-icf-syndrome
#13
Christopher Jenness, Simona Giunta, Manuel M Müller, Hiroshi Kimura, Tom W Muir, Hironori Funabiki
Mutations in CDCA7, the SNF2 family protein HELLS (LSH), or the DNA methyltransferase DNMT3b cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome. While it has been speculated that DNA methylation defects cause this disease, little is known about the molecular function of CDCA7 and its functional relationship to HELLS and DNMT3b. Systematic analysis of how the cell cycle, H3K9 methylation, and the mitotic kinase Aurora B affect proteomic profiles of chromatin in Xenopus egg extracts revealed that HELLS and CDCA7 form a stoichiometric complex on chromatin, in a manner sensitive to Aurora B...
January 30, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29334437/a-randomized-clinical-trial-to-measure-the-erosion-protection-benefits-of-a-novel-stabilized-stannous-fluoride-dentifrice-versus-a-control-dentifrice
#14
Xinyi Zhao, Tao He, Yanyan He, Cathy Cheng, Haijing Chen
OBJECTIVES: The aim of this investigation was to assess the erosion protection ability of a novel stabilized stannous fluoride (SnF2) dentifrice and a control sodium fluoride dentifrice (NaF) using a well-credentialed human in situ model. METHODS: A novel smooth texture 0.454% stabilized SnF2 dentifrice (Crest® Pro-Health™ smooth formula) and a 0.23% NaF marketed control dentifrice with 5% potassium nitrate (Sensodyne® Pronamel®) were compared in a 10-day, single center, randomized, controlled, double-blind, two-treatment, three-period crossover in situ clinical trial...
December 2017: Journal of Clinical Dentistry
https://www.readbyqxmd.com/read/29284678/the-cue1-domain-of-the-snf2-like-chromatin-remodeler-smarcad1-mediates-its-association-with-krab-associated-protein-1-kap1-and-kap1-target-genes
#15
Dong Ding, Philipp Bergmaier, Parysatis Sachs, Marius Klangwart, Tamina Rückert, Nora Bartels, Jeroen Demmers, Mike Dekker, Raymond A Poot, Jacqueline E Mermoud
Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. Depletion of the remodeler SMARCAD1, an ATPase of the SNF2 family, has been shown to affect stem cell state, but the mechanistic explanation for this effect is unknown. Here, we set out to gain further insights into the function of SMARCAD1 in mouse ESCs. We identified KRAB-associated protein 1 (KAP1) as the stoichiometric binding partner of SMARCAD1 in ESCs...
February 23, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29250846/realizing-efficient-lead-free-formamidinium-tin-triiodide-perovskite-solar-cells-via-a-sequential-deposition-route
#16
Zonglong Zhu, Chu-Chen Chueh, Nan Li, Chengyi Mao, Alex K-Y Jen
Recently, the evolved intermediate phase based on iodoplumbate anions that mediates perovskite crystallization has been embodied as the Lewis acid-base adduct formed by metal halides (serve as Lewis acid) and polar aprotic solvents (serve as Lewis base). Based on this principle, it is proposed to constitute efficient Lewis acid-base adduct in the SnI2 deposition step to modulate its volume expansion and fast reaction with methylammonium iodide (MAI)/formamidinium iodide (FAI) (FAI is studied hereafter). Herein, trimethylamine (TMA) is employed as the additional Lewis base in the tin halide solution to form SnY2 -TMA complexes (Y = I- , F- ) in the first-step deposition, followed by intercalating with FAI to convert into FASnI...
February 2018: Advanced Materials
https://www.readbyqxmd.com/read/29244498/labile-low-valent-tin-azides-syntheses-structural-characterization-and-thermal-properties
#17
Rory Campbell, Sumit Konar, Steven Hunter, Colin Pulham, Peter Portius
The first two examples of the class of tetracoordinate low-valent, mixed-ligand tin azido complexes, Sn(N3 )2 (L)2 , are shown to form upon reaction of SnCl2 with NaN3 and SnF2 with Me3 SiN3 in either pyridine or 4-picoline (2, L = py; 3, L = pic). These adducts of Sn(N3 )2 are shock- and friction-insensitive and stable at r.t. under an atmosphere of pyridine or picoline, respectively. A new, fast, and efficient method for the preparation of Sn(N3 )2 (1) directly from SnF2 , and by the stepwise de-coordination of py from 2 at r...
January 2, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/29203878/atm-and-cdk2-control-chromatin-remodeler-csb-to-inhibit-rif1-in-dsb-repair-pathway-choice
#18
Nicole L Batenburg, John R Walker, Sylvie M Noordermeer, Nathalie Moatti, Daniel Durocher, Xu-Dong Zhu
CSB, a member of the SWI2/SNF2 superfamily, is implicated in DNA double-strand break (DSB) repair. However, how it regulates this repair process is poorly understood. Here we uncover that CSB interacts via its newly identified winged helix domain with RIF1, an effector of 53BP1, and that this interaction mediates CSB recruitment to DSBs in S phase. At DSBs, CSB remodels chromatin by evicting histones, which limits RIF1 and its effector MAD2L2 but promotes BRCA1 accumulation. The chromatin remodeling activity of CSB requires not only damage-induced phosphorylation on S10 by ATM but also cell cycle-dependent phosphorylation on S158 by cyclin A-CDK2...
December 4, 2017: Nature Communications
https://www.readbyqxmd.com/read/29178559/arid1a-a-component-of-swi-snf-chromatin-remodeling-complexes-is-required-for-porcine-embryo-development
#19
Yu-Chun Tseng, Birgit Cabot, Ryan A Cabot
Mammalian embryos undergo dramatic epigenetic remodeling that can have a profound impact on both gene transcription and overall embryo developmental competence. Members of the SWI/SNF (Switch/Sucrose non-fermentable) family of chromatin-remodeling complexes reposition nucleosomes and alter transcription factor accessibility. These large, multi-protein complexes possess an SNF2-type ATPase (either SMARCA4 or SMARCA2) as their core catalytic subunit, and are directed to specific loci by associated subunits. Little is known about the identity of specific SWI/SNF complexes that serve regulatory roles during cleavage development...
December 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/29168508/structural-basis-for-the-initiation-of-eukaryotic-transcription-coupled-dna-repair
#20
Jun Xu, Indrajit Lahiri, Wei Wang, Adam Wier, Michael A Cianfrocco, Jenny Chong, Alissa A Hare, Peter B Dervan, Frank DiMaio, Andres E Leschziner, Dong Wang
Eukaryotic transcription-coupled repair (TCR) is an important and well-conserved sub-pathway of nucleotide excision repair that preferentially removes DNA lesions from the template strand that block translocation of RNA polymerase II (Pol II). Cockayne syndrome group B (CSB, also known as ERCC6) protein in humans (or its yeast orthologues, Rad26 in Saccharomyces cerevisiae and Rhp26 in Schizosaccharomyces pombe) is among the first proteins to be recruited to the lesion-arrested Pol II during the initiation of eukaryotic TCR...
November 30, 2017: Nature
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