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https://www.readbyqxmd.com/read/28804761/unfolding-of-core-nucleosomes-by-parp-1-revealed-by-spfret-microscopy
#1
Daniel C Sultanov, Nadezhda S Gerasimova, Kseniya S Kudryashova, Natalya V Maluchenko, Elena Y Kotova, Marie-France Langelier, John M Pascal, Mikhail P Kirpichnikov, Alexey V Feofanov, Vasily M Studitsky
DNA accessibility to various protein complexes is essential for various processes in the cell and is affected by nucleosome structure and dynamics. Protein factor PARP-1 (poly(ADP-ribose)polymerase 1) increases the accessibility of DNA in chromatin to repair proteins and transcriptional machinery, but the mechanism and extent of this chromatin reorganization are unknown. Here we report on the effects of PARP-1 on single nucleosomes revealed by spFRET (single-particle Förster Resonance Energy Transfer) microscopy...
2017: AIMS Genetics
https://www.readbyqxmd.com/read/28801910/application-of-synthetic-tumor-specific-promoters-responsive-to-the-tumor-microenvironment
#2
Eduardo G Cafferata, Maria Veronica Lopez, Felipe J Nuñez, Maria A R Maenza, Osvaldo L Podhajcer
Activity of endogenous promoters can be altered by including additional responsive elements (REs). These elements can be responsive to features of the tumor environment or alternatively to signaling pathways specifically activated in cancer cells. These REs incorporated into tumor-specific promoters can improve cancer targeting, the replicative capacity, and lytic activity of conditionally replicative adenovirus. Here we outline an approach to incorporate hypoxia and inflammation REs into a specific fragment of the SPARC promoter and the steps to clone a nucleosome positioning sequence (NPS ) identified in the osteocalcin promoter that contains a Wnt RE upstream of a heterologous synthetic promoter...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28801535/expansion-of-the-iswi-chromatin-remodeler-family-with-new-active-complexes
#3
Mariano Oppikofer, Tianyi Bai, Yutian Gan, Benjamin Haley, Peter Liu, Wendy Sandoval, Claudio Ciferri, Andrea G Cochran
ISWI chromatin remodelers mobilize nucleosomes to control DNA accessibility. Complexes isolated to date pair one of six regulatory subunits with one of two highly similar ATPases. However, we find that each endogenously expressed ATPase co-purifies with every regulatory subunit, substantially increasing the diversity of ISWI complexes, and we additionally identify BAZ2B as a novel, seventh regulatory subunit. Through reconstitution of catalytically active human ISWI complexes, we demonstrate that the new interactions described here are stable and direct...
August 11, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28800611/using-local-chromatin-structure-to-improve-crispr-cas9-efficiency-in-zebrafish
#4
Yunru Chen, Shiyang Zeng, Ruikun Hu, Xiangxiu Wang, Weilai Huang, Jiangfang Liu, Luying Wang, Guifen Liu, Ying Cao, Yong Zhang
Although the CRISPR/Cas9 has been successfully applied in zebrafish, considerable variations in efficiency have been observed for different gRNAs. The workload and cost of zebrafish mutant screening is largely dependent on the mutation rate of injected embryos; therefore, selecting more effective gRNAs is especially important for zebrafish mutant construction. Besides the sequence features, local chromatin structures may have effects on CRISPR/Cas9 efficiency, which remain largely unexplored. In the only related study in zebrafish, nucleosome organization was not found to have an effect on CRISPR/Cas9 efficiency, which is inconsistent with recent studies in vitro and in mammalian cell lines...
2017: PloS One
https://www.readbyqxmd.com/read/28799233/stochastics-of-cellular-differentiation-explained-by-epigenetics-the-case-of-t-cell-differentiation-and-functional-plasticity
#5
REVIEW
Jaydeep Bhat, Johannes Helmuth, Guranda Chitadze, Léonce Kouakanou, Christian Peters, Martin Vingron, Ole Ammerpohl, Dieter Kabelitz
Epigenetic marks including histone modifications and DNA methylation are associated to the regulation of gene expression and activity. In addition, an increasing number of non-coding RNAs with regulatory activity on gene expression have been identified. Alongside, technological advancements allow for the analysis of these mechanisms with high resolution - up to the single-cell level. For instance, the assay for transposase-accessible chromatin using sequencing (ATAC-seq) simultaneously probes for chromatin accessibility and nucleosome positioning...
August 10, 2017: Scandinavian Journal of Immunology
https://www.readbyqxmd.com/read/28798133/structure-of-histone-based-chromatin-in-archaea
#6
Francesca Mattiroli, Sudipta Bhattacharyya, Pamela N Dyer, Alison E White, Kathleen Sandman, Brett W Burkhart, Kyle R Byrne, Thomas Lee, Natalie G Ahn, Thomas J Santangelo, John N Reeve, Karolin Luger
Small basic proteins present in most Archaea share a common ancestor with the eukaryotic core histones. We report the crystal structure of an archaeal histone-DNA complex. DNA wraps around an extended polymer, formed by archaeal histone homodimers, in a quasi-continuous superhelix with the same geometry as DNA in the eukaryotic nucleosome. Substitutions of a conserved glycine at the interface of adjacent protein layers destabilize archaeal chromatin, reduce growth rate, and impair transcription regulation, confirming the biological importance of the polymeric structure...
August 11, 2017: Science
https://www.readbyqxmd.com/read/28792846/nanodosimetric-simulation-of-direct-ion-induced-dna-damage-using-different-chromatin-geometry-models
#7
N T Henthorn, J W Warmenhoven, M Sotiropoulos, R I Mackay, K J Kirkby, M J Merchant
Monte Carlo based simulation has proven useful in investigating the effect of proton-induced DNA damage and the processes through which this damage occurs. Clustering of ionizations within a small volume can be related to DNA damage through the principles of nanodosimetry. For simulation, it is standard to construct a small volume of water and determine spatial clusters. More recently, realistic DNA geometries have been used, tracking energy depositions within DNA backbone volumes. Traditionally a chromatin fiber is built within the simulation and identically replicated throughout a cell nucleus, representing the cell in interphase...
August 9, 2017: Radiation Research
https://www.readbyqxmd.com/read/28791511/centromere-inheritance-through-the-germline
#8
REVIEW
Arunika Das, Evan M Smoak, Ricardo Linares-Saldana, Michael A Lampson, Ben E Black
The centromere directs chromosome segregation and genetic inheritance but is not itself heritable in a canonical, DNA-based manner. In most species, centromeres are epigenetically defined by the presence of a histone H3 variant centromere protein A (CENP-A), independent of underlying DNA sequence. Therefore, centromere inheritance depends on maintaining the CENP-A nucleosome mark across generations. Experiments in cycling somatic cells have led to a model in which centromere identity is maintained by a cell cycle-coupled CENP-A chromatin assembly pathway...
August 8, 2017: Chromosoma
https://www.readbyqxmd.com/read/28789639/cipher-a-flexible-and-extensive-workflow-platform-for-integrative-next-generation-sequencing-data-analysis-and-genomic-regulatory-element-prediction
#9
Carlos Guzman, Iván D'Orso
BACKGROUND: Next-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs. Although these technologies are frequently used in biological studies, NGS data analysis remains a challenging, time-consuming, and often irreproducible process. Therefore, there is a need for a comprehensive and flexible workflow platform that can accelerate data processing and analysis so more time can be spent on functional studies. RESULTS: We have developed an integrative, stand-alone workflow platform, named CIPHER, for the systematic analysis of several commonly used NGS datasets including ChIP-seq, RNA-seq, MNase-seq, DNase-seq, GRO-seq, and ATAC-seq data...
August 8, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28783137/acetylation-and-methylation-related-epigenetic-proteins-in-the-context-of-their-targets
#10
REVIEW
Nasir Javaid, Sangdun Choi
The nucleosome surface is covered with multiple modifications that are perpetuated by eight different classes of enzymes. These enzymes modify specific target sites both on DNA and histone proteins, and these modifications have been well identified and termed "epigenetics". These modifications play critical roles, either by affecting non-histone protein recruitment to chromatin or by disturbing chromatin contacts. Their presence dictates the condensed packaging of DNA and can coordinate the orderly recruitment of various enzyme complexes for DNA manipulation...
August 7, 2017: Genes
https://www.readbyqxmd.com/read/28780612/invisible-cities-segregated-domains-in-the-yeast-genome-with-distinct-structural-and-functional-attributes
#11
Christoforos Nikolaou
Recent advances in our understanding of the three-dimensional organization of the eukaryotic nucleus have rendered the spatial distribution of genes increasingly relevant. In a recent work (Tsochatzidou et al., Nucleic Acids Res 45:5818-5828, 2017), we proposed the existence of a functional compartmentalization of the yeast genome according to which, genes occupying the chromosomal regions at the nuclear periphery have distinct structural, functional and evolutionary characteristics compared to their centromeric-proximal counterparts...
August 5, 2017: Current Genetics
https://www.readbyqxmd.com/read/28777518/a-single-air-dive-induces-apoptotic-gene-regulation-but-no-increase-in-nucleosomes
#12
Lars Eichhorn, Christian Nietzel, Stefan Schröder, Ullrich Siekmann, Andreas Koch, Stefan Weber
BACKGROUND: Oxidative stress caused by elevated partial pressure of oxygen during diving is a major contributor of inflammation and apoptosis. The underlying molecular mechanisms are poorly understood. The aim of the study was to describe apoptotic gene regulation induced by a single air dive. METHODS: 19 healthy volunteers were exposed to a 30-minute dive at 2.8 atmospheres (ATA) absolute in a pressure chamber in ambient air. Blood samples were obtained before, directly after and 24 hours after exposure...
November 2016: Undersea & Hyperbaric Medicine: Journal of the Undersea and Hyperbaric Medical Society, Inc
https://www.readbyqxmd.com/read/28776025/three-dimensional-positioning-and-structure-of-chromosomes-in-a-human-prophase-nucleus
#13
Bo Chen, Mohammed Yusuf, Teruo Hashimoto, Ana Katrina Estandarte, George Thompson, Ian Robinson
The human genetic material is packaged into 46 chromosomes. The structure of chromosomes is known at the lowest level, where the DNA chain is wrapped around a core of eight histone proteins to form nucleosomes. Around a million of these nucleosomes, each about 11 nm in diameter and 6 nm in thickness, are wrapped up into the complex organelle of the chromosome, whose structure is mostly known at the level of visible light microscopy to form a characteristic cross shape in metaphase. However, the higher-order structure of human chromosomes, between a few tens and hundreds of nanometers, has not been well understood...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28775067/running-training-experience-attenuates-disuse-atrophy-in-fast-twitch-skeletal-muscles-of-rats
#14
Keisuke Nakamura, Ikumi Ohsawa, Ryo Masuzawa, Ryotaro Konno, Atsuya Watanabe, Fuminori Kawano
Responsiveness to physiological stimuli, such as exercise and muscular inactivation, differs in individuals. However, the mechanisms responsible for these individual differences remain poorly understood. We tested whether a prior experience of exercise training affects the responses of skeletal muscles to unloading. Young rats were assigned to perform daily running training using a treadmill for 8 weeks. After an additional 8 weeks of normal habitation, the rats were hindlimb unloaded by tail suspension for 1 week...
August 3, 2017: Journal of Applied Physiology
https://www.readbyqxmd.com/read/28771342/yeast-terminator-function-can-be-modulated-and-designed-based-on-predictions-of-nucleosome-occupancy
#15
Nicholas Morse, Madan Gopal, James Wagner, Hal S Alper
The design of improved synthetic parts is a major goal of synthetic biology. Mechanistically, nucleosome occupancy in the 3' terminator region of a gene has been found to correlate with transcriptional expression. Here, we seek to establish a predictive relationship between terminator function and nucleosome positioning to design synthetic terminators in the yeast Saccharomyces cerevisiae. In doing so, terminators improved net protein output from these expression cassettes nearly 4-fold over their original sequence with observed increases in termination efficiency to 96%...
August 3, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28771339/specific-acetylation-patterns-of-h2a-z-form-transient-interactions-with-the-bptf-bromodomain
#16
Gabriella T Perell, Neeraj K Mishra, Babu Sudhamalla, Peter D Ycas, Kabirul Islam, William C K Pomerantz
Post-translational lysine acetylation of histone tails affect both chromatin accessibility and recruitment of multi-functional bromodomain-containing proteins for modulating transcription. Bromodomain and PHD finger-containing protein (BPTF) regulates transcription, but has also been implicated with high gene expression levels in a variety of cancers. In this report, the histone variant H2A.Z, which replaces H2A in chromatin, is evaluated for affinity towards BPTF with a specific recognition pattern of acetylated lysine residues of the N-terminal tail region...
August 3, 2017: Biochemistry
https://www.readbyqxmd.com/read/28768201/human-tfiih-kinase-cdk7-regulates-transcription-associated-chromatin-modifications
#17
Christopher C Ebmeier, Benjamin Erickson, Benjamin L Allen, Mary A Allen, Hyunmin Kim, Nova Fong, Jeremy R Jacobsen, Kaiwei Liang, Ali Shilatifard, Robin D Dowell, William M Old, David L Bentley, Dylan J Taatjes
CDK7 phosphorylates the RNA polymerase II (pol II) C-terminal domain CTD and activates the P-TEFb-associated kinase CDK9, but its regulatory roles remain obscure. Here, using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3' ends upon CDK7 inhibition. We also noted that CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5' ends and H3K36me3 was displaced toward gene 3' ends in CDK7as cells...
August 1, 2017: Cell Reports
https://www.readbyqxmd.com/read/28767641/iswi-chromatin-remodellers-sense-nucleosome-modifications-to-determine-substrate-preference
#18
Geoffrey P Dann, Glen Liszczak, John D Bagert, Manuel M Müller, Uyen T T Nguyen, Felix Wojcik, Zachary Z Brown, Jeffrey Bos, Tatyana Panchenko, Rasmus Pihl, Samuel B Pollock, Katharine L Diehl, C David Allis, Tom W Muir
ATP-dependent chromatin remodelers regulate access to genetic information by controlling nucleosome positions in vivo(1). However, the mechanism by which remodelers discriminate between different nucleosome substrates is poorly understood. Considering that many chromatin remodeling proteins possess conserved protein domains that interact with nucleosomal features(2), we employed a quantitative high-throughput approach, based on the use of a DNA-barcoded mononucleosome library, to profile the biochemical activity of human ISWI remodelers in response to a diverse set of nucleosome modifications...
August 2, 2017: Nature
https://www.readbyqxmd.com/read/28764714/testis-specific-histone-2b-is-associated-with-sperm-chromatin-dynamics-and-bull-fertility-a-pilot-study
#19
Naseer A Kutchy, Ana Velho, Erika S B Menezes, Marie Jacobsen, Giselle Thibaudeau, Robert W Wills, Arlindo Moura, Abdullah Kaya, Andy Perkins, Erdogan Memili
BACKGROUND: Bull fertility is the degree of sperm's ability to fertilize and activate the egg and support embryo development, and this is critical for herd reproductive performance. We used the bull as a unique model organism for the study of male fertility because cattle genetics and physiology is similar to those of other mammals including humans. Moreover, reliable fertility data along with well-established in vitro systems are available for bovine. The objective of this original study was to ascertain evolutionary diversification and expression dynamics of Testis Specific Histone 2B (TH2B) in sperm from Holstein bulls with different fertility scores...
August 1, 2017: Reproductive Biology and Endocrinology: RB&E
https://www.readbyqxmd.com/read/28760814/sall1-nurd-interaction-regulates-multipotent-nephron-progenitors-and-is-required-for-loop-of-henle-formation
#20
Jeannine M Basta, Lynn Robbins, Darcy R Denner, Grant R Kolar, Michael Rauchman
The formation of the proper number of nephrons requires a tightly regulated balance between renal progenitor cell self-renewal and differentiation. The molecular pathways that regulate the transition from renal progenitor to renal vesicle are not well understood. Here we show that Sall1interacts with the Nucleosome Remodeling and Deacetylase Complex (NuRD) to inhibit premature differentiation of nephron progenitor cells. Disruption of Sall1-NuRD in vivo in knock-in mice (ΔSRM) resulted in accelerated differentiation of nephron progenitors and bilateral renal hypoplasia...
July 31, 2017: Development
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