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https://www.readbyqxmd.com/read/29161754/the-sorghum-bicolor-reference-genome-improved-assembly-gene-annotations-a-transcriptome-atlas-and-signatures-of-genome-organization
#1
Ryan F McCormick, Sandra K Truong, Avinash Sreedasyam, Jerry Jenkins, Shengqiang Shu, David Sims, Megan Kennedy, Mojgan Amirebrahimi, Brock D Weers, Brian McKinley, Ashley Mattison, Daryl T Morishige, Jane Grimwood, Jeremy Schmutz, John E Mullet
Sorghum bicolor is a drought tolerant C4 grass used for production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (~800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34,211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp...
November 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29161414/structural-diversity-of-the-nucleosome
#2
Masako Koyama, Hitoshi Kurumizaka
In eukaryotes, genomic DNA is compacted in chromatin, which generally suppresses transcription, replication, repair, and recombination. The fundamental unit of chromatin is the nucleosome, whose structure was first determined at atomic resolution in 1997. However, recent findings have revealed that the nucleosome is not a structurally homogenous entity. Nucleosomes containing histone variants often have subtle but clear differences in their structural and functional characteristics, as compared to the canonical nucleosome...
November 17, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29160422/identification-of-the-difference-in-the-pathogenesis-in-heart-failure-arising-from-different-etiologies-using-a-microarray-dataset
#3
Guodong Yang, Shuping Chen, Aiqun Ma, Jun Lu, Tingzhong Wang
OBJECTIVES: Clinically, patients with chronic heart failure arising from different etiologies receive the same treatment. However, the prognoses of these patients differ. The purpose of this study was to elucidate whether the pathogenesis of heart failure arising from different etiologies differs. METHODS: Heart failure-related dataset GSE1145 was obtained from the Gene Expression Omnibus database. Differentially expressed genes were identified using R. A protein-protein interaction network of the differentially expressed genes was constructed using Search Tool for the Retrieval of Interacting Genes...
October 2017: Clinics
https://www.readbyqxmd.com/read/29155775/mapping-genome-wide-accessible-chromatin-in-primary-human-t-lymphocytes-by-atac-seq
#4
Ivana Grbesa, Miriam Tannenbaum, Avital Sarusi-Portuguez, Michal Schwartz, Ofir Hakim
Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a method used for the identification of open (accessible) regions of chromatin. These regions represent regulatory DNA elements (e.g., promoters, enhancers, locus control regions, insulators) to which transcription factors bind. Mapping the accessible chromatin landscape is a powerful approach for uncovering active regulatory elements across the genome. This information serves as an unbiased approach for discovering the network of relevant transcription factors and mechanisms of chromatin structure that govern gene expression programs...
November 13, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29153328/tdp-43-promotes-neurodegeneration-by-impairing-chromatin-remodeling
#5
Amit Berson, Ashley Sartoris, Raffaella Nativio, Vivianna Van Deerlin, Jon B Toledo, Sílvia Porta, Shichong Liu, Chia-Yu Chung, Benjamin A Garcia, Virginia M-Y Lee, John Q Trojanowski, F Brad Johnson, Shelley L Berger, Nancy M Bonini
Regulation of chromatin structure is critical for brain development and function. However, the involvement of chromatin dynamics in neurodegeneration is less well understood. Here we find, launching from Drosophila models of amyotrophic lateral sclerosis and frontotemporal dementia, that TDP-43 impairs the induction of multiple key stress genes required to protect from disease by reducing the recruitment of the chromatin remodeler Chd1 to chromatin. Chd1 depletion robustly enhances TDP-43-mediated neurodegeneration and promotes the formation of stress granules...
November 9, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29152903/reproductive-endocrine-phenotypes-relating-to-chd7-mutations-in-humans
#6
REVIEW
Ravikumar Balasubramanian, William F Crowley
Mutations in the gene CHD7 cause CHARGE syndrome, a rare multi-organ syndromic disorder. Gonadal defects are common in individuals with CHARGE syndrome (seen in ∼60-80% of cases) and represent the letter "G" in the CHARGE syndrome acronym. The gonadal defect in CHARGE syndrome results from congenital deficiency of the hypothalamic hormone Gonadotropin-releasing hormone (GnRH), which manifests clinically as pubertal failure and infertility, and biochemically as hypogonadotropic hypogonadism (low sex steroid hormone levels with inappropriately normal or low gonadotropin levels)...
November 20, 2017: American Journal of Medical Genetics. Part C, Seminars in Medical Genetics
https://www.readbyqxmd.com/read/29151171/clinical-and-serological-associations-of-anti-ribosomal-p0-protein-antibodies-in-systemic-lupus-erythematosus
#7
Yong-Jun Mei, Peng Wang, Chao Jiang, Tao Wang, Lin-Jie Chen, Zhi-Jun Li, Hai-Feng Pan
The purpose of this study is to investigate the clinical and serological associations of anti-ribosomal P0 protein antibodies (anti-Rib-P0) in patients with systemic lupus erythematosus (SLE). The sera of 470 patients with SLE and 124 patients with primary Sjogren's Syndrome (pSS) were collected. Line immunoassay (LIA) was used to detect anti-Rib-P0 and other related antibodies. A complete laboratory evaluation and clinical examination were also performed in each SLE patient. The prevalence of anti-Rib-P0 in SLE patients was significantly higher than that in pSS patients (35...
November 18, 2017: Clinical Rheumatology
https://www.readbyqxmd.com/read/29149297/dna-knots-occur-in-intracellular-chromatin
#8
Antonio Valdés, Joana Segura, Sílvia Dyson, Belén Martínez-García, Joaquim Roca
In vivo DNA molecules are narrowly folded within chromatin fibers and self-interacting chromatin domains. Therefore, intra-molecular DNA entanglements (knots) might occur via DNA strand passage activity of topoisomerase II. Here, we assessed the presence of such DNA knots in a variety of yeast circular minichromosomes. We found that small steady state fractions of DNA knots are common in intracellular chromatin. These knots occur irrespective of DNA replication and cell proliferation, though their abundance is reduced during DNA transcription...
November 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29149060/epigenetic-regulation-of-viral-biological-processes
#9
REVIEW
Lata Balakrishnan, Barry Milavetz
It is increasingly clear that DNA viruses exploit cellular epigenetic processes to control their life cycles during infection. This review will address epigenetic regulation in members of the polyomaviruses, adenoviruses, human papillomaviruses, hepatitis B, and herpes viruses. For each type of virus, what is known about the roles of DNA methylation, histone modifications, nucleosome positioning, and regulatory RNA in epigenetic regulation of the virus infection will be discussed. The mechanisms used by certain viruses to dysregulate the host cell through manipulation of epigenetic processes and the role of cellular cofactors such as BRD4 that are known to be involved in epigenetic regulation of host cell pathways will also be covered...
November 17, 2017: Viruses
https://www.readbyqxmd.com/read/29146919/nucleosome-acidic-patch-targeting-binuclear-ruthenium-compounds-induce-aberrant-chromatin-condensation
#10
Gabriela E Davey, Zenita Adhireksan, Zhujun Ma, Tina Riedel, Deepti Sharma, Sivaraman Padavattan, Daniela Rhodes, Alexander Ludwig, Sara Sandin, Benjamin S Murray, Paul J Dyson, Curt A Davey
The 'acidic patch' is a highly electronegative cleft on the histone H2A-H2B dimer in the nucleosome. It is a fundamental motif for protein binding and chromatin dynamics, but the cellular impact of targeting this potentially therapeutic site with exogenous molecules remains unclear. Here, we characterize a family of binuclear ruthenium compounds that selectively target the nucleosome acidic patch, generating intra-nucleosomal H2A-H2B cross-links as well as inter-nucleosomal cross-links. In contrast to cisplatin or the progenitor RAPTA-C anticancer drugs, the binuclear agents neither arrest specific cell cycle phases nor elicit DNA damage response, but rather induce an irreversible, anomalous state of condensed chromatin that ultimately results in apoptosis...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29145649/single-molecule-compaction-of-megabase-long-chromatin-molecules-by-multivalent-cations
#11
Anatoly Zinchenko, Nikolay V Berezhnoy, Sai Wang, William M Rosencrans, Nikolay Korolev, Johan R C van der Maarel, Lars Nordenskiöld
To gain insight into the conformational properties and compaction of megabase-long chromatin molecules, we reconstituted chromatin from T4 phage DNA (165 kb) and recombinant human histone octamers (HO). The unimolecular compaction, induced by divalent Mg2+ or tetravalent spermine4+ cations, studied by single-molecule fluorescence microscopy (FM) and dynamic light scattering (DLS) techniques, resulted in the formation of 250-400 nm chromatin condensates. The compaction on this scale of DNA size is comparable to that of chromatin topologically associated domains (TAD) in vivo...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29141908/two-distinct-regulatory-mechanisms-of-transcriptional-initiation-in-response-to-nutrient-signaling
#12
Jannatul Ferdoush, Rwik Sen, Amala Kaja, Priyanka Barman, Sukesh R Bhaumik
SAGA (Spt-Ada-Gcn5-Acetyltransferase) and TFIID (transcription factor IID) have been previously shown to facilitate the PIC (pre-initiation complex) formation at the promoters of two distinct sets of genes. Here, we demonstrate that TFIID and SAGA differentially participate in stimulation of the PIC formation (and hence transcriptional initiation) at the promoter of PHO84, a gene for high affinity inorganic phosphate (Pi) transporter for crucial cellular functions, in response to nutrient signaling. We show that transcriptional initiation of PHO84 occurs predominantly in the TFIID-dependent manner in the absence of Pi in the growth medium...
November 15, 2017: Genetics
https://www.readbyqxmd.com/read/29140247/ddm1-and-lsh-remodelers-allow-methylation-of-dna-wrapped-in-nucleosomes
#13
David B Lyons, Daniel Zilberman
Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo...
November 15, 2017: ELife
https://www.readbyqxmd.com/read/29138400/accessibility-of-the-histone-h3-tail-in-the-nucleosome-for-binding-of-paired-readers
#14
Jovylyn Gatchalian, Xiaodong Wang, Jinzen Ikebe, Khan L Cox, Adam H Tencer, Yi Zhang, Nathaniel L Burge, Luo Di, Matthew D Gibson, Catherine A Musselman, Michael G Poirier, Hidetoshi Kono, Jeffrey J Hayes, Tatiana G Kutateladze
Combinatorial polyvalent contacts of histone-binding domains or readers commonly mediate localization and activities of chromatin-associated proteins. A pair of readers, the PHD fingers of the protein CHD4, has been shown to bivalently recognize histone H3 tails. Here we describe a mechanism by which these linked but independent readers bind to the intact nucleosome core particle (NCP). Comprehensive NMR, chemical reactivity, molecular dynamics, and fluorescence analyses point to the critical roles of intra-nucleosomal histone-DNA interactions that reduce the accessibility of H3 tails in NCP, the nucleosomal DNA, and the linker between readers in modulating nucleosome- and/or histone-binding activities of the readers...
November 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/29126175/conventional-and-pioneer-modes-of-glucocorticoid-receptor-interaction-with-enhancer-chromatin-in-vivo
#15
Thomas A Johnson, Razvan V Chereji, Diana A Stavreva, Stephanie A Morris, Gordon L Hager, David J Clark
Glucocorticoid hormone plays a major role in metabolism and disease. The hormone-bound glucocorticoid receptor (GR) binds to a specific set of enhancers in different cell types, resulting in unique patterns of gene expression. We have addressed the role of chromatin structure in GR binding by mapping nucleosome positions in mouse adenocarcinoma cells. Before hormone treatment, GR-enhancers exist in one of three chromatin states: (i) Nucleosome-depleted enhancers that are DNase I-hypersensitive, associated with the Brg1 chromatin remodeler and flanked by nucleosomes incorporating histone H2A...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29118204/mitotic-chromosome-assembly-in-vitro-functional-cross-talk-between-nucleosomes-and-condensins
#16
Keishi Shintomi, Tatsuya Hirano
The mitotic chromosome is a macromolecular assembly that ensures error-free transmission of the genome during cell division. It has long been a big mystery how long stretches of DNA might be folded into rod-shaped chromosomes or how such an elaborate process might be accomplished at a mechanistic level. Cell-free extracts made from frog eggs offer a unique opportunity to address these questions by enabling mitotic chromosomes to be assembled in a test tube. Moreover, the core part of the chromosome assembly reaction can now be reconstituted with a limited number of purified factors...
November 8, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29117687/performing-selex-experiments-in-silico
#17
J A J Wondergem, H Schiessel, M Tompitak
Due to the sequence-dependent nature of the elasticity of DNA, many protein-DNA complexes and other systems in which DNA molecules must be deformed have preferences for the type of DNA sequence they interact with. SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments and similar sequence selection experiments have been used extensively to examine the (indirect readout) sequence preferences of, e.g., nucleosomes (protein spools around which DNA is wound for compactification) and DNA rings...
November 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29116202/acetylated-histone-variant-h2a-z-is-involved-in-the-activation-of-neo-enhancers-in-prostate-cancer
#18
Fátima Valdés-Mora, Cathryn M Gould, Yolanda Colino-Sanguino, Wenjia Qu, Jenny Z Song, Kylie M Taylor, Fabian A Buske, Aaron L Statham, Shalima S Nair, Nicola J Armstrong, James G Kench, Kenneth M L Lee, Lisa G Horvath, Minru Qiu, Alexei Ilinykh, Nicole S Yeo-Teh, David Gallego-Ortega, Clare Stirzaker, Susan J Clark
Acetylation of the histone variant H2A.Z (H2A.Zac) occurs at active promoters and is associated with oncogene activation in prostate cancer, but its role in enhancer function is still poorly understood. Here we show that H2A.Zac containing nucleosomes are commonly redistributed to neo-enhancers in cancer resulting in a concomitant gain of chromatin accessibility and ectopic gene expression. Notably incorporation of acetylated H2A.Z nucleosomes is a pre-requisite for activation of Androgen receptor (AR) associated enhancers...
November 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/29115978/depletion-of-somatic-mutations-in-splicing-associated-sequences-in-cancer-genomes
#19
Laurence D Hurst, Nizar N Batada
BACKGROUND: An important goal of cancer genomics is to identify systematically cancer-causing mutations. A common approach is to identify sites with high ratios of non-synonymous to synonymous mutations; however, if synonymous mutations are under purifying selection, this methodology leads to identification of false-positive mutations. Here, using synonymous somatic mutations (SSMs) identified in over 4000 tumours across 15 different cancer types, we sought to test this assumption by focusing on coding regions required for splicing...
November 7, 2017: Genome Biology
https://www.readbyqxmd.com/read/29113904/site-specific-disulfide-crosslinked-nucleosomes-with-enhanced-stability
#20
Timothy D Frouws, Philip D Barth, Timothy J Richmond
We engineered nucleosome core particles (NCPs) with two site-specific cysteine crosslinks that increase the stability of the particle. The first disulfide was introduced between the two copies of H2A via a H2A-N38C point mutation, effectively crosslinking the two H2A/H2B heterodimers together to stabilize the histone octamer against H2A/H2B dimer dissociation. The second crosslink was engineered between a R40C point mutation on the N-terminal tail of H3 and the NCP DNA ends by the introduction of a convertible nucleotide...
November 4, 2017: Journal of Molecular Biology
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