scholarly journals The Interactions of Yeast SWI/SNF and RSC with the Nucleosome before and after Chromatin Remodeling

2001 ◽  
Vol 276 (16) ◽  
pp. 12636-12644 ◽  
Author(s):  
Sarojini M. Sengupta ◽  
Michael VanKanegan ◽  
Jim Persinger ◽  
Colin Logie ◽  
Bradley R. Cairns ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Before And After

scholarly journals Dual Chromatin Remodeling Roles for RSC during DNA Double Strand Break Induction and Repair at the Yeast MAT Locus

2007 ◽  
Vol 282 (38) ◽  
pp. 27693-27701 ◽  
Author(s):  
Nicholas A. Kent ◽  
Anna L. Chambers ◽  
Jessica A. Downs
Keyword(s):  
Chromatin Remodeling ◽  
Dna Cleavage ◽  
Strand Break ◽  
Histone H2a ◽  
Dna Double Strand Breaks ◽  
Dna Double Strand Break ◽  
Before And After ◽  
Mating Type Switching ◽  
Set Up ◽  
Mat Locus

DNA double strand breaks (DSBs) are potentially serious chromosomal lesions. However, cells sometimes deliberately cleave their own DNA to facilitate certain chromosomal processes, and there is much interest in how such self-inflicted breaks are effectively managed. Eukaryotic DSBs occur in the context of chromatin and the RSC chromatin-remodeling ATPase complex has been shown to promote DSB repair at the budding yeast MAT locus DSB, created by the HO endonuclease during mating type switching. We show that the role of RSC at MAT is highly specialized. The Rsc1p subunit of RSC directs nucleosome sliding immediately after DSB creation at both MAT and generally and is required for efficient DNA damage-induced histone H2A phosphorylation and strand resection during repair by homologous recombination. However, the Rsc2p and Rsc7p subunits are additionally required to set up a basal MAT locus structure. This RSC-dependent chromatin structure at MAT ensures accessibility to the HO endonuclease. The RSC complex therefore has chromatin remodeling roles both before and after DSB induction at MAT, promoting both DNA cleavage and subsequent repair.

scholarly journals ΔNp63 is a pioneer factor that binds inaccessible chromatin and elicit chromatin remodeling

2020 ◽  
Author(s):  
Xinyang Yu ◽  
Prashant K. Singh ◽  
Shamira Tabrejee ◽  
Satrajit Sinha ◽  
Michael Buck
Keyword(s):  
Chromatin Remodeling ◽  
Histone Modifications ◽  
Binding Sites ◽  
Transcriptional Regulator ◽  
Binding Assays ◽  
Cellular Processes ◽  
Binding Inhibition ◽  
Before And After ◽  
Pioneer Factor ◽  
Nucleosome Binding

Abstract Background: ΔNp63 is a master transcriptional regulator playing critical roles in epidermal development and other cellular processes. Recent studies suggest that ΔNp63 functions as a pioneer factor that can target its binding sites within inaccessible chromatin and induce chromatin remodeling. Methods: In order to examine if ΔNp63 can bind to inaccessible chromatin and to determine if specific histone modifications are required for binding we induced ΔNp63 expression in two p63 naive cell line. ΔNp63 binding was then examined by ChIP-seq and the chromatin at ΔNp63 targets sites was examined before and after binding. Further analysis with competitive nucleosome binding assays was used to determine how ΔNp63 directly interacts with nucleosomes. Results: Our results show that before ΔNp63 binding, targeted sites lack histone modifications, indicating ΔNp63’s capability to bind at unmodified chromatin. Moreover, the majority of the sites that are bound by ectopic ΔNp63 expression exist in an inaccessible state. Once bound ΔNp63 induces acetylation of the histone and the repositioning of nucleosomes at its binding sites. Further analysis with competitive nucleosome binding assays reveal that ΔNp63 can bind directly to nucleosome edges with significant binding inhibition occurring within 50 bp of the nucleosome dyad. Conclusion: Overall, our results demonstrate that ΔNp63 is a pioneer factor that binds nucleosome edges at inaccessible un-modified chromatin sites and induces histone acetylation and nucleosome repositioning.

scholarly journals ΔNp63 is a pioneer factor that binds inaccessible chromatin and elicits chromatin remodeling

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Xinyang Yu ◽  
Prashant K. Singh ◽  
Shamira Tabrejee ◽  
Satrajit Sinha ◽  
Michael J. Buck
Keyword(s):  
Chromatin Remodeling ◽  
Histone Modifications ◽  
Binding Sites ◽  
Transcriptional Regulator ◽  
Binding Assays ◽  
Cellular Processes ◽  
Binding Inhibition ◽  
Before And After ◽  
Pioneer Factor ◽  
Nucleosome Binding

Abstract Background ΔNp63 is a master transcriptional regulator playing critical roles in epidermal development and other cellular processes. Recent studies suggest that ΔNp63 functions as a pioneer factor that can target its binding sites within inaccessible chromatin and induce chromatin remodeling. Methods In order to examine if ΔNp63 can bind to inaccessible chromatin and to determine if specific histone modifications are required for binding, we induced ΔNp63 expression in two p63-naïve cell lines. ΔNp63 binding was then examined by ChIP-seq and the chromatin at ΔNp63 targets sites was examined before and after binding. Further analysis with competitive nucleosome binding assays was used to determine how ΔNp63 directly interacts with nucleosomes. Results Our results show that before ΔNp63 binding, targeted sites lack histone modifications, indicating ΔNp63’s capability to bind at unmodified chromatin. Moreover, the majority of the sites that are bound by ectopic ΔNp63 expression exist in an inaccessible state. Once bound, ΔNp63 induces acetylation of the histone and the repositioning of nucleosomes at its binding sites. Further analysis with competitive nucleosome binding assays reveal that ΔNp63 can bind directly to nucleosome edges with significant binding inhibition occurring within 50 bp of the nucleosome dyad. Conclusion Overall, our results demonstrate that ΔNp63 is a pioneer factor that binds nucleosome edges at inaccessible and unmodified chromatin sites and induces histone acetylation and nucleosome repositioning.

Deformation Replication

1970 ◽  
Vol 28 ◽  
pp. 280-281
Author(s):  
J. Temple Black
Keyword(s):  
Cutting Speed ◽  
Machining Process ◽  
Depth Of Cut ◽  
Rake Face ◽  
Orthogonal Machining ◽  
Aluminum Chips ◽  
Before And After ◽  
Materials Used ◽  
Glass Knife ◽  
Very High

Tool materials used in ultramicrotomy are glass, developed by Latta and Hartmann (1) and diamond, introduced by Fernandez-Moran (2). While diamonds produce more good sections per knife edge than glass, they are expensive; require careful mounting and handling; and are time consuming to clean before and after usage, purchase from vendors (3-6 months waiting time), and regrind. Glass offers an easily accessible, inexpensive material ($0.04 per knife) with very high compressive strength (3) that can be employed in microtomy of metals (4) as well as biological materials. When the orthogonal machining process is being studied, glass offers additional advantages. Sections of metal or plastic can be dried down on the rake face, coated with Au-Pd, and examined directly in the SEM with no additional handling (5). Figure 1 shows aluminum chips microtomed with a 75° glass knife at a cutting speed of 1 mm/sec with a depth of cut of 1000 Å lying on the rake face of the knife.

The Clinical, Roentgenological and Morphological Effects of an Acute Exposure of Phosgene on the Lungs of Dogs

1971 ◽  
Vol 29 ◽  
pp. 236-237
Author(s):  
R. F. Bils ◽  
W. F. Diller ◽  
F. Huth
Keyword(s):  
Latent Period ◽  
Chemical Industry ◽  
Toxic Substance ◽  
Lung Edema ◽  
X Rays ◽  
Beagle Dogs ◽  
Male And Female ◽  
Morphological Alterations ◽  
Before And After ◽  
Electron Microscopes

Phosgene still plays an important role as a toxic substance in the chemical industry. Thiess (1968) recently reported observations on numerous cases of phosgene poisoning. A serious difficulty in the clinical handling of phosgene poisoning cases is a relatively long latent period, up to 12 hours, with no obvious signs of severity. At about 12 hours heavy lung edema appears suddenly, however changes can be seen in routine X-rays taken after only a few hours' exposure (Diller et al., 1969). This study was undertaken to correlate these early changes seen by the roengenologist with morphological alterations in the lungs seen in the'light and electron microscopes.Forty-two adult male and female Beagle dogs were selected for these exposure experiments. Treated animals were exposed to 94.5-107-5 ppm phosgene for 10 min. in a 15 m3 chamber. Roentgenograms were made of the thorax of each animal before and after exposure, up to 24 hrs.

Ultrastructure of Melanin Formation in Curvularia sp., Alternaria sp., and Drechslera Sorokiniana

1977 ◽  
Vol 35 ◽  
pp. 398-399
Author(s):  
M. H. Wheeler ◽  
W. J. Tolmsoff ◽  
A. A. Bell
Keyword(s):  
Potassium Phosphate ◽  
Thielaviopsis Basicola ◽  
Wild Type ◽  
Potassium Phosphate Buffer ◽  
Transmission Microscopy ◽  
Electron Transmission ◽  
Melanin Formation ◽  
Before And After ◽  
Alternaria Sp ◽  
Electron Transmission Microscopy

(+)-Scytalone [3,4-dihydro-3,6,8-trihydroxy-l-(2Hj-naphthalenone] and 1,8-di- hydroxynaphthalene (DHN) have been proposed as intermediates of melanin synthesis in the fungi Verticillium dahliae (1, 2, 3, 4) and Thielaviopsis basicola (4, 5). Scytalone is enzymatically dehydrated by V. dahliae to 1,3,8-trihydroxynaphthalene which is then reduced to (-)-vermelone [(-)-3,4- dihydro-3,8-dihydroxy-1(2H)-naphthalenone]. Vermelone is subsequently dehydrated to DHN which is enzymatically polymerized to melanin.Melanin formation in Curvularia sp., Alternaria sp., and Drechslera soro- kiniana was examined by light and electron-transmission microscopy. Wild-type isolates of each fungus were compared with albino mutants before and after treatment with 1 mM scytalone or 0.1 mM DHN in 50 mM potassium phosphate buffer, pH 7.0. Both chemicals were converted to dark pigments in the walls of hyphae and conidia of the albino mutants. The darkened cells were similar in appearance to corresponding cells of the wild types under the light microscope.

Evaluation of Freezing Methods by Low Temperature X-Ray Diffraction

1977 ◽  
Vol 35 ◽  
pp. 330-333
Author(s):  
T. Gulik-Krzywicki ◽  
M.J. Costello
Keyword(s):  
Biological Materials ◽  
Molecular Organization ◽  
X Ray Diffraction ◽  
Glass Capillary ◽  
X Ray ◽  
Rate Dependent ◽  
Before And After ◽  
Freeze Etching ◽  
Diffraction Patterns ◽  
Set Up

Freeze-etching electron microscopy is currently one of the best methods for studying molecular organization of biological materials. Its application, however, is still limited by our imprecise knowledge about the perturbations of the original organization which may occur during quenching and fracturing of the samples and during the replication of fractured surfaces. Although it is well known that the preservation of the molecular organization of biological materials is critically dependent on the rate of freezing of the samples, little information is presently available concerning the nature and the extent of freezing-rate dependent perturbations of the original organizations. In order to obtain this information, we have developed a method based on the comparison of x-ray diffraction patterns of samples before and after freezing, prior to fracturing and replication.Our experimental set-up is shown in Fig. 1. The sample to be quenched is placed on its holder which is then mounted on a small metal holder (O) fixed on a glass capillary (p), whose position is controlled by a micromanipulator.

The Precipitation of Si in AlCuSi Thin Films

1973 ◽  
Vol 31 ◽  
pp. 34-35 ◽  
Author(s):  
R. M. Anderson
Keyword(s):  
Electron Microscopy ◽  
Thin Films ◽  
Heat Treatment ◽  
Solid Solution ◽  
Integrated Circuit ◽  
Copper Film ◽  
Solution Concentration ◽  
X Ray ◽  
Silicon Thin Films ◽  
Before And After

Aluminum-copper-silicon thin films have been considered as an interconnection metallurgy for integrated circuit applications. Various schemes have been proposed to incorporate small percent-ages of silicon into films that typically contain two to five percent copper. We undertook a study of the total effect of silicon on the aluminum copper film as revealed by transmission electron microscopy, scanning electron microscopy, x-ray diffraction and ion microprobe techniques as a function of the various deposition methods.X-ray investigations noted a change in solid solution concentration as a function of Si content before and after heat-treatment. The amount of solid solution in the Al increased with heat-treatment for films with ≥2% silicon and decreased for films <2% silicon.

An Electron Microscope Study of Interdiffusion and Compound Formation in Ta-Au Thin Films

1973 ◽  
Vol 31 ◽  
pp. 32-33 ◽  
Author(s):  
T. C. Tisone ◽  
S. Lau
Keyword(s):  
Electron Microscope ◽  
Electron Microscope Study ◽  
Thermally Grown Oxide ◽  
Ion Milling ◽  
Compound Formation ◽  
Technology Application ◽  
Transmission Electron ◽  
Before And After ◽  
Au Thin Films

In a study of the properties of a Ta-Au metallization system for thin film technology application, the interdiffusion between Ta(bcc)-Au, βTa-Au and Ta2M-Au films was studied. Considered here is a discussion of the use of the transmission electron microscope(TEM) in the identification of phases formed and characterization of the film microstructures before and after annealing.The films were deposited by sputtering onto silicon wafers with 5000 Å of thermally grown oxide. The film thicknesses were 2000 Å of Ta and 2000 Å of Au. Samples for TEM observation were prepared by ultrasonically cutting 3mm disks from the wafers. The disks were first chemically etched from the silicon side using a HNO3 :HF(19:5) solution followed by ion milling to perforation of the Au side.

Absolute inner-shell cross section determination for EELS analysis

1988 ◽  
Vol 46 ◽  
pp. 534-535
Author(s):  
P.A. Crozier
Keyword(s):  
Cross Section ◽  
Cross Sections ◽  
Absolute Cross Section ◽  
Specimen Thickness ◽  
Mass Thickness ◽  
Scattering Cross ◽  
Before And After ◽  
Estimated Error ◽  
Scattering Cross Sections ◽  
Electron Microscopist

Absolute inelastic scattering cross sections or mean free paths are often used in EELS analysis for determining elemental concentrations and specimen thickness. In most instances, theoretical values must be used because there have been few attempts to determine experimental scattering cross sections from solids under the conditions of interest to electron microscopist. In addition to providing data for spectral quantitation, absolute cross section measurements yields useful information on many of the approximations which are frequently involved in EELS analysis procedures. In this paper, experimental cross sections are presented for some inner-shell edges of Al, Cu, Ag and Au.Uniform thin films of the previously mentioned materials were prepared by vacuum evaporation onto microscope cover slips. The cover slips were weighed before and after evaporation to determine the mass thickness of the films. The estimated error in this method of determining mass thickness was ±7 x 107g/cm2. The films were floated off in water and mounted on Cu grids.

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