keyword
MENU ▼
Read by QxMD icon Read
search

Nucleosome

keyword
https://www.readbyqxmd.com/read/29792694/biomimetic-artificial-epigenetic-code-for-targeted-acetylation-of-histones
#1
Junichi Taniguchi, Yihong Feng, Ganesh N Pandian, Fumitaka Hashiya, Takuya Hidaka, Kaori Hashiya, Soyoung Park, Toshikazu Bando, Shinji Ito, Hiroshi Sugiyama
While the central role of locus-specific acetylation of histone proteins in eukaryotic gene expression is well established, the availability of designer tools to regulate acetylation at particular nucleosome sites remains limited. Here, we develop a unique strategy to introduce acetylation by constructing a bifunctional molecule designated Bi-PIP. Bi-PIP has a P300/CBP-selective bromodomain inhibitor (Bi) as a P300/CBP recruiter and a pyrrole-imidazole polyamide (PIP) as a sequence-selective DNA binder. Biochemical assays verified that Bi-PIPs recruit P300 to the nucleosomes having their target DNA sequences and extensively accelerate acetylation...
May 24, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29785963/swi-snf-and-rsc-cooperate-to-reposition-and-evict-promoter-nucleosomes-at-highly-expressed-genes-in-yeast
#2
Yashpal Rawal, Răzvan V Chereji, Hongfang Qiu, Sudha Ananthakrishnan, Chhabi K Govind, David J Clark, Alan G Hinnebusch
The nucleosome remodeling complex RSC functions throughout the yeast genome to set the positions of -1 and +1 nucleosomes and thereby determines the widths of nucleosome-depleted regions (NDRs). The related complex SWI/SNF participates in nucleosome remodeling/eviction and promoter activation at certain yeast genes, including those activated by transcription factor Gcn4, but did not appear to function broadly in establishing NDRs. By analyzing the large cohort of Gcn4-induced genes in mutants lacking the catalytic subunits of SWI/SNF or RSC, we uncovered cooperation between these remodelers in evicting nucleosomes from different locations in the promoter and repositioning the +1 nucleosome downstream to produce wider NDRs-highly depleted of nucleosomes-during transcriptional activation...
May 21, 2018: Genes & Development
https://www.readbyqxmd.com/read/29780501/a-bi-terminal-protein-ligation-strategy-to-probe-chromatin-structure-during-dna-damage
#3
Sinan Kilic, Iuliia Boichenko, Carolin C Lechner, Beat Fierz
The cellular response to DNA damage results in a signaling cascade that primes chromatin for repair. Combinatorial post-translational modifications (PTMs) play an important role in this process by altering the physical properties of chromatin and recruiting downstream factors. One key signal integrator is the histone variant H2A.X, which is phosphorylated at a C-terminal serine (S139ph), and ubiquitylated within its N-terminal tail at lysines 13 and 15 (K13/15ub). How these PTMs directly impact chromatin structure and thereby facilitate DNA repair is not well understood...
April 21, 2018: Chemical Science
https://www.readbyqxmd.com/read/29776334/swi-snf-regulates-half-of-its-targets-without-the-need-of-atp-driven-nucleosome-remodeling-by-brahma
#4
Antonio Jordán-Pla, Simei Yu, Johan Waldholm, Thomas Källman, Ann-Kristin Östlund Farrants, Neus Visa
BACKGROUND: Brahma (BRM) is the only catalytic subunit of the SWI/SNF chromatin-remodeling complex of Drosophila melanogaster. The function of SWI/SNF in transcription has long been attributed to its ability to remodel nucleosomes, which requires the ATPase activity of BRM. However, recent studies have provided evidence for a non-catalytic function of BRM in the transcriptional regulation of a few specific genes. RESULTS: Here we have used RNA-seq and ChIP-seq to identify the BRM target genes in S2 cells, and we have used a catalytically inactive BRM mutant (K804R) that is unable to hydrolyze ATP to investigate the magnitude of the non-catalytic function of BRM in transcription regulation...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29776169/effects-of-nucleosome-stability-on-remodeler-catalyzed-repositioning
#5
Aaron M Morgan, Sarah E LeGresley, Koan Briggs, Gada Al-Ani, Christopher J Fischer
Chromatin remodelers are molecular motors that play essential roles in the regulation of nucleosome positioning and chromatin accessibility. These machines couple the energy obtained from the binding and hydrolysis of ATP to the mechanical work of manipulating chromatin structure through processes that are not completely understood. Here we present a quantitative analysis of nucleosome repositioning by the imitation switch (ISWI) chromatin remodeler and demonstrate that nucleosome stability significantly impacts the observed activity...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29775508/lfr-is-functionally-associated-with-as2-to-mediate-leaf-development-in-arabidopsis
#6
Xiaowei Lin, Dandan Gu, Hongtao Zhao, Yue Peng, Guofang Zhang, Mengge Li, Zhijuan Wang, Xiutang Wang, Sujuan Cui
Leaves are essential organs for plants. We previously identified a functional gene possibly encoding a component of the SWI/SNF complex named LFR (Leaf and Flower Related) in Arabidopsis thaliana. Loss-of-function mutants of LFR displayed obvious defects in leaf morphogenesis, indicating its vital role in leaf development. Here an allelic null mutant of ASYMMETRIC LEAVES2 (AS2), as2-6, was isolated as an enhancer of lfr-1 in petiole length, vasculature pattern and leaf margin development. The lfr as2 double mutants showed enhanced ectopic expression of BP than each of the single mutant, which is consistent with their synergistic genetic enhancement in multiple BP-dependent development processes...
May 18, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29774579/integrative-epigenetic-analysis-reveals-therapeutic-targets-to-the-dna-methyltransferase-inhibitor-sgi-110-in-hepatocellular-carcinoma
#7
Minmin Liu, Lian Zhang, Hongtao Li, Toshinori Hinoue, Wanding Zhou, Hitoshi Ohtani, Anthony El-Khoueiry, John Daniels, Casey O'Connell, Tanya B Dorff, Qianjin Lu, Daniel J Weisenberger, Gangning Liang
There is an urgent need for developing more effective therapies for hepatocellular carcinoma (HCC) because of its aggressiveness. Guadecitabine (SGI-110) is a second-generation DNA methyltransferase inhibitor (DNMTi) currently in clinical trials for HCC and shows greater stability and performance over first generation DNMTis. In order to identify potential therapeutic targets of SGI-110 for clinical trials, HCC cell lines (SNU398, HepG2 and SNU475) were used to evaluate effects of transient SGI-110 treatment by an integrative analysis of DNA methylation, nucleosome accessibility, gene expression profiles and its clinical relevance by comparisons to TCGA HCC clinical data...
May 18, 2018: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/29773913/auxin-decreases-chromatin-accessibility-through-the-tir1-afbs-auxin-signaling-pathway-in-proliferative-cells
#8
Junko Hasegawa, Takuya Sakamoto, Satoru Fujimoto, Tomoe Yamashita, Takamasa Suzuki, Sachihiro Matsunaga
Chromatin accessibility is closely associated with chromatin functions such as gene expression, DNA replication, and maintenance of DNA integrity. However, the relationship between chromatin accessibility and plant hormone signaling has remained elusive. Here, based on the correlation between chromatin accessibility and DNA damage, we used the sensitivity to DNA double strand breaks (DSBs) as an indicator of chromatin accessibility and demonstrated that auxin regulates chromatin accessibility through the TIR1/AFBs signaling pathway in proliferative cells...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29771637/quantitative-imaging-of-chromatin-decompaction-in-living-cells
#9
Elisa Dultz, Roberta Mancini, Guido Polles, Pascal Vallotton, Frank Alber, Karsten Weis
Chromatin organization is highly dynamic and regulates transcription. Upon transcriptional activation, chromatin is remodeled and referred to as "open", but quantitative and dynamic data of this decompaction process are lacking. Here, we have developed a quantitative high-resolution microscopy assay in living yeast cells to visualize and quantify chromatin dynamics using the GAL7-10-1 locus as a model system. Upon transcriptional activation of these three clustered genes, we detect an increase of the mean distance across this locus by >100 nm...
May 17, 2018: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/29769315/characterization-of-additional-components-of-the-environmental-ph-sensing-complex-in-the-pathogenic-fungus-cryptococcus-neoformans
#10
Kaila M Pianalto, Kyla S Ost, Hannah E Brown, J Andrew Alspaugh
Pathogenic microorganisms must adapt to changes in their immediate surroundings, including alterations in pH, to survive the shift from the external environment to that of the infected host. In the basidiomycete fungal pathogen Cryptococcus neoformans , these pH changes are primarily sensed by the fungal-specific, alkaline pH-sensing Rim/Pal pathway. The C. neoformans Rim pathway has diverged significantly from that described in ascomycete fungi. We recently identified the C. neoformans putative pH sensor Rra1, which activates the Rim pathway in response to elevated pH...
May 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29768498/genomic-variants-in-an-inbred-mouse-model-predict-mania-like-behaviors
#11
Michael C Saul, Sharon A Stevenson, Changjiu Zhao, Terri M Driessen, Brian E Eisinger, Stephen C Gammie
Contemporary rodent models for bipolar disorders split the bipolar spectrum into complimentary behavioral endophenotypes representing mania and depression. Widely accepted mania models typically utilize single gene transgenics or pharmacological manipulations, but inbred rodent strains show great potential as mania models. Their acceptance is often limited by the lack of genotypic data needed to establish construct validity. In this study, we used a unique strategy to inexpensively explore and confirm population allele differences in naturally occurring candidate variants in a manic rodent strain, the Madison (MSN) mouse strain...
2018: PloS One
https://www.readbyqxmd.com/read/29764937/cyclin-dependent-kinase-1-cdk1-and-cdk2-have-opposing-roles-in-regulating-interactions-of-splicing-factor-3b1-with-chromatin
#12
Tushar Murthy, Theresa Bluemn, Abhishek Gupta, Michael Reimer, Sridhar Rao, Manoj M Pillai, Alex C Minella
Splicing factor 3B1 (SF3B1) is a core splicing protein that stabilizes the interaction between the U2 snRNA and the branch point in the mRNA target during splicing. SF3B1 is heavily phosphorylated at its N terminus and a substrate of cyclin-dependent kinases (CDKs). Although SF3B1 phosphorylation coincides with splicing catalysis, the functional significance of SF3B1 phosphorylation is largely undefined. Here, we show that SF3B1 phosphorylation follows a dynamic pattern during cell cycle progression that depends on CDK activity...
May 15, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29761578/identification-of-the-coiled-coil-domain-as-an-essential-mbd3-element-for-preserving-lineage-commitment-potential-of-embryonic-stem-cells
#13
Masataka Hirasaki, Atsushi Ueda, Masamitsu N Asaka, Kousuke Uranishi, Ayumu Suzuki, Masakazu Kohda, Yosuke Mizuno, Yasushi Okazaki, Masazumi Nishimoto, Jafar Sharif, Haruhiko Koseki, Akihiko Okuda
Embryonic stem cells (ESCs) exhibit two salient features beneficial for regenerative medicine: unlimited self-renewal and pluripotency. Methyl-CpG-binding domain protein 3 (Mbd3), a scaffolding component of the nucleosome remodeling deacetylase complex, is a specific regulator of pluripotency, as ESCs lacking Mbd3 are defective for lineage commitment potential but retain normal self-renewal properties. However, functional similarities and dissimilarities among the three Mbd3 isoforms (a, b, and c) have not been intensively explored...
May 15, 2018: Stem Cells
https://www.readbyqxmd.com/read/29760053/size-tagged-preferred-ends-in-maternal-plasma-dna-shed-light-on-the-production-mechanism-and-show-utility-in-noninvasive-prenatal-testing
#14
Kun Sun, Peiyong Jiang, Ada I C Wong, Yvonne K Y Cheng, Suk Hang Cheng, Haiqiang Zhang, K C Allen Chan, Tak Y Leung, Rossa W K Chiu, Y M Dennis Lo
Cell-free DNA in human plasma is nonrandomly fragmented and reflects genomewide nucleosomal organization. Previous studies had demonstrated tissue-specific preferred end sites in plasma DNA of pregnant women. In this study, we performed integrative analysis of preferred end sites with the size characteristics of plasma DNA fragments. We mined the preferred end sites in short and long plasma DNA molecules separately and found that these "size-tagged" ends showed improved accuracy in fetal DNA fraction estimation and enhanced noninvasive fetal trisomy 21 testing...
May 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29759984/ndf-a-nucleosome-destabilizing-factor-that-facilitates-transcription-through-nucleosomes
#15
Jia Fei, Haruhiko Ishii, Marten A Hoeksema, Franz Meitinger, George A Kassavetis, Christopher K Glass, Bing Ren, James T Kadonaga
Our understanding of transcription by RNA polymerase II (Pol II) is limited by our knowledge of the factors that mediate this critically important process. Here we describe the identification of NDF, a nucleosome-destabilizing factor that facilitates Pol II transcription in chromatin. NDF has a PWWP motif, interacts with nucleosomes near the dyad, destabilizes nucleosomes in an ATP-independent manner, and facilitates transcription by Pol II through nucleosomes in a purified and defined transcription system as well as in cell nuclei...
May 14, 2018: Genes & Development
https://www.readbyqxmd.com/read/29759374/dependence-of-chromatosome-structure-on-linker-histone-sequence-and-posttranslational-modification
#16
Mehmet Ali Öztürk, Vlad Cojocaru, Rebecca C Wade
Linker histone (LH) proteins play a key role in higher-order structuring of chromatin for the packing of DNA in eukaryotic cells and in the regulation of genomic function. The common fruit fly (Drosophila melanogaster) has a single somatic isoform of the LH (H1). It is thus a useful model organism for investigating the effects of the LH on nucleosome compaction and the structure of the chromatosome, the complex formed by binding of an LH to a nucleosome. The structural and mechanistic details of how LH proteins bind to nucleosomes are debated...
May 11, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29755673/role-of-epigenetic-factors-in-the-selection-of-the-alternative-splicing-isoforms-of-human-kras-in-colorectal-cancer-cell-lines
#17
Ángela L Riffo-Campos, Francisco Gimeno-Valiente, Fernanda M Rodríguez, Andrés Cervantes, Gerardo López-Rodas, Luis Franco, Josefa Castillo
Mutation-driven activation of KRAS is crucial to cancer development. The human gene yields four mRNA splicing isoforms, 4A and 4B being translated to protein. Their different properties and oncogenic potential have been studied, but the mechanisms deciding the ratio 4A/4B are not known. To address this issue, the expression of the four KRAS isoforms was determined in 9 human colorectal cancer cell lines. HCT116 and SW48 were further selected because they present the highest difference in the ratio 4A/4B (twice as much in HCT116 than in SW48)...
April 17, 2018: Oncotarget
https://www.readbyqxmd.com/read/29751847/asf1-is-required-to-load-histones-on-the-hira-complex-in-preparation-of-paternal-chromatin-assembly-at-fertilization
#18
Béatrice Horard, Laure Sapey-Triomphe, Emilie Bonnefoy, Benjamin Loppin
BACKGROUND: Anti-Silencing Factor 1 (ASF1) is a conserved H3-H4 histone chaperone involved in both Replication-Coupled and Replication-Independent (RI) nucleosome assembly pathways. At DNA replication forks, ASF1 plays an important role in regulating the supply of H3.1/2 and H4 to the CAF-1 chromatin assembly complex. ASF1 also provides H3.3-H4 dimers to HIRA and DAXX chaperones for RI nucleosome assembly. The early Drosophila embryo is an attractive system to study chromatin assembly in a developmental context...
May 11, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29748240/rec-a-like-domain-2-of-active-dna-dependent-atpase-domain-a-swi2-snf2-protein-mediates-conformational-integrity-and-atp-hydrolysis
#19
Ritu Bansal, Vijendra Arya, Ramesh Sethy, Radhakrishnan Rakesh, Rohini Muthuswami
ATP-dependent chromatin remodeling proteins use the energy released from ATP hydrolysis to reposition nucleosomes in DNA-dependent processes.  These proteins are classified as SF2 helicases. SMARCAL1, a member of this protein family, is known to modulate both DNA repair and transcription by specifically recognizing DNA molecules possessing double-strand to single-strand transition regions.  Mutations in this gene cause a rare autosomal recessive disorder known as Schimke Immuno-Osseous Dysplasia (SIOD). Structural studies have shown that the ATP-dependent chromatin remodeling proteins possess two Rec A-like domains termed as Rec A-like domain 1 and Rec A-like domain 2...
May 10, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29743638/screen-and-verification-for-transgene-integration-sites-in-pigs
#20
Linyuan Ma, Yuzhe Wang, Haitao Wang, Yiqing Hu, Jingyao Chen, Tan Tan, Man Hu, Xiaojuan Liu, Ran Zhang, Yiming Xing, Yiqiang Zhao, Xiaoxiang Hu, Ning Li
Efficient transgene expression in recipient cells constitutes the primary step in gene therapy. However, random integration in host genome comprises too many uncertainties. Our study presents a strategy combining bioinformatics and functional verification to find transgene integration sites in pig genome. Using an in silico approach, we screen out two candidate sites, namely, Pifs302 and Pifs501, located in actively transcribed intergenic regions with low nucleosome formation potential and without potential non-coding RNAs...
May 9, 2018: Scientific Reports
keyword
keyword
12928
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"