Faculty Opinions recommendation of The SIN domain of the histone octamer is essential for intramolecular folding of nucleosomal arrays.

2002 ◽  
Author(s):  
Jerry Workman
Keyword(s):  
Histone Octamer

In Silico Insight into Nucleosome Repositioning Via Oxygen Delivery and Extracellular Movement

2021 ◽  
Author(s):  
Jacob Duane Madison
Keyword(s):  
In Silico ◽  
Binding Motif ◽  
Oxygen Intake ◽  
Ph Domain ◽  
Nutrient Delivery ◽  
Histone Octamer ◽  
Partial Pressures ◽  
Energy Dependent ◽  
Insight Into ◽  
Biomechanical Strain

Abstract OBJECTIVEHistones and resulting nucleosomes occur within DNA regulating gene expression by slowing, pausing, or halting transcriptional machinery. Positions within the genome have been found with higher affinity for the histone octamer than others. Histone/nucleosome repositioning is adjusted via energy dependent remodeling complexes, and a harmonizing array of constellation proteins and molecules. The energy required to create transcriptional environments is created through oxygen intake, nutrient presence, and extracellular movement. In this paper we aim to help facilitate an in silico framework for further experimentation into how partial pressures of oxygen and other gases impact genetic transcription along with extracellular movement and nutrient delivery.RESULTSCell and tissue culture experimentation with biomechanical strain and variable partial pressures of oxygen and other gases can be made into the expression levels of genes such as PH domain leucine-rich repeat-containing protein phosphatase 1 (PHLPP1), and Neuroligin 1 (NLGN1). These genes show in silico to have a higher affinity for a histone octamer binding motif, needing adequate cellular energy to be expressed. Extracellular movement and adequate cellular oxygenation are required to properly reposition nucleosome sequences for transcription.

Characterizing Circulating Nucleosomes in the Plasma of Dogs with Lymphoma

2021 ◽  
Author(s):  
Christopher Dolan ◽  
Tasha Miller ◽  
Jarvis Jill ◽  
Jason Terrell ◽  
Theresa Kelly ◽  
...  
Keyword(s):  
Fold Increase ◽  
Monitoring Tool ◽  
Treatment Results ◽  
Canine Lymphoma ◽  
Histone Octamer ◽  
Objective Monitoring ◽  
Remission Status ◽  
T Cell Lymphomas ◽  
Healthy Dogs ◽  
Multicentric Lymphoma

Abstract Background: Nucleosomes consist of DNA wrapped around a histone octamer core like beads on a string so that DNA can be condensed as chromatin into chromosomes. Diseases such as cancer or inflammation lead to cell death where chromatin is fragmentated and released as mononucleosomes into the blood. The Nu.QTM H3.1 assay measures total nucleosome concentration in plasma of humans and has been used to detect and identify cancer even at early stages. The objectives of this study were to determine if nucleosome levels could be used to distinguish between healthy dogs and dogs with various stages of lymphoma (LSA) using the Nu.Q™ H3.1 assay. A total of 126 dogs diagnosed with LSA and 134 healthy controls were recruited for this study. Plasma was collected from each dog and stored in K2-EDTA tubes. The LSA patient samples were recruited from TAMU or purchased from various biobanks. All control cases were recruited from TAMU. Samples were also collected longitudinally from 3 dogs undergoing treatment for multicentric lymphoma at TAMU as a pilot study to investigate the pattern of nucleosome concentrations in plasma during treatment. Results: Dogs with LSA had an approximately 7-fold increase in their plasma nucleosome concentrations compared to controls (AUC 87.8%). Nucleosome concentrations increased with cancer stage and dogs with B cell lymphomas had significantly higher nucleosome concentrations than dogs with T cell lymphomas. Nucleosome concentrations from serially monitored patients were elevated at diagnosis and progression with subsequent decreases in nucleosome concentration that corresponded to clinically detectable responses to therapy. Conclusions: The Nu.QTM H3.1 assay was able to reliably detect elevated nucleosome concentrations in the plasma of dogs with LSA. Furthermore, it appears that nucleosomes are useful for differentiating cancer from healthy individuals in canines. Results from serially monitored patients indicate that nucleosomes could be an objective monitoring tool for remission status in canine lymphoma patients.

scholarly journals Nucleosome Positioning with Set of Key Positions and Nucleosome Affinity

2014 ◽  
Vol 8 (1) ◽  
pp. 166-170 ◽  
Author(s):  
Jia Wang ◽  
Shuai Liu ◽  
Weina Fu
Keyword(s):  
Neural Network ◽  
Experimental Data ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Nucleosome Positioning ◽  
Experimental Results ◽  
Negative Effects ◽  
Sequence Structure ◽  
Precise Positioning ◽  
Histone Octamer

The formation and precise positioning of nucleosome in chromatin occupies a very important role in studying life process. Today, there are many researchers who discovered that the positioning where the location of a DNA sequence fragment wraps around a histone octamer in genome is not random but regular. However, the positioning is closely relevant to the concrete sequence of core DNA. So in this paper, we analyzed the relation between the affinity and sequence structure of core DNA, and extracted the set of key positions. In these positions, the nucleotide sequences probably occupy mainly action in the binding. First, we simplified and formatted the experimental data with the affinity. Then, to find the key positions in the wrapping, we used neural network to analyze the positive and negative effects of nucleosome generation for each position in core DNA sequences. However, we reached a class of weights with every position to describe this effect. Finally, based on the positions with high weights, we analyzed the reason why the chosen positions are key positions, and used these positions to construct a model for nucleosome positioning prediction. Experimental results show the effectiveness of our method.

scholarly journals Histone octamer functionin vivo: mutations in the dimer-tetramer interfaces disrupt both gene activation and repression

1997 ◽  
Vol 16 (9) ◽  
pp. 2493-2506 ◽  
Author(s):  
Maria Soledad Santisteban ◽  
Gina Arents ◽  
Evangelos N. Moudrianakis ◽  
M.Mitchell Smith
Keyword(s):  
Gene Activation ◽  
Histone Octamer

scholarly journals ATP-Dependent Histone Octamer Sliding Mediated by the Chromatin Remodeling Complex NURF

Cell ◽  
1999 ◽  
Vol 97 (7) ◽  
pp. 833-842 ◽  
Author(s):  
Ali Hamiche ◽  
Raphael Sandaltzopoulos ◽  
David A Gdula ◽  
Carl Wu
Keyword(s):  
Chromatin Remodeling ◽  
Histone Octamer ◽  
Chromatin Remodeling Complex

scholarly journals Structural rearrangements of the histone octamer translocate DNA

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Silvija Bilokapic ◽  
Mike Strauss ◽  
Mario Halic
Keyword(s):  
Structural Rearrangements ◽  
Histone Octamer

Nucleosomal location of the STE6 TATA box and Mat alpha 2p-mediated repression

1994 ◽  
Vol 14 (6) ◽  
pp. 4002-4010
Author(s):  
H G Patterton ◽  
R T Simpson
Keyword(s):  
Reporter Gene ◽  
Tata Box ◽  
Chromatin Domain ◽  
Specific Gene ◽  
Multicopy Plasmid ◽  
Alpha Cells ◽  
Lacz Reporter ◽  
Lacz Reporter Gene ◽  
Histone Octamer ◽  
Repression Domain

It has been proposed that yeast MATa cell-specific genes are repressed in MAT alpha cells by the Mat alpha 2p repressor-directed placement of a nucleosome in a position that incorporates the TATA box of the MATa-specific gene close to the nucleosomal pseudodyad. In this study, we address this proposal directly with a series of plasmids designed to place the MATa-specific STE6 TATA box at different locations in a nucleosome and in the internucleosomal linker. These plasmids contain different lengths of synthetic random DNA between the Mat alpha 2p operator and the TATA box of the STE6 promoter, which is located upstream of a lacZ reporter gene in a multicopy plasmid. We show that in MAT alpha cells, a nucleosome is retained in an identical translational frame relative to the Mat alpha 2p operator in all the constructs investigated, irrespective of the sequence of the DNA wrapped onto the histone octamer. This result shows that the nucleosomal organization of the STE6 promoter in MAT alpha cells is not conferred by the sequence of the promoter itself. No expression of the lacZ reporter gene was detectable in MAT alpha cells in any of the constructs, even with the TATA box located in a short internucleosomal linker. These data indicate that repression of MATa-specific genes in MAT alpha cells does not require the precise translational placement of the TATA box close to the nucleosomal pseudodyad; the gene remains repressed when the TATA box is located within the investigated 250-bp region in the organized chromatin domain abutting the Mat alpha 2p operator in MAT alpha cells and may remain repressed with the TATA box located anywhere within this organized repression domain.

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