scholarly journals The Histone Modifications of Neuronal Plasticity

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Huixia Geng ◽  
Hongyang Chen ◽  
Haiying Wang ◽  
Lai Wang
Keyword(s):  
Gene Expression ◽  
Learning And Memory ◽  
Histone Modifications ◽  
Posttranslational Modifications ◽  
Synapse Formation ◽  
Environmental Changes ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Dynamic Synapse ◽  
Histone Codes

Nucleosomes composed of histone octamer and DNA are the basic structural unit in the eukaryote chromosome. Under the stimulation of various factors, histones will undergo posttranslational modifications such as methylation, phosphorylation, acetylation, and ubiquitination, which change the three-dimensional structure of chromosomes and affect gene expression. Therefore, the combination of different states of histone modifications modulates gene expression is called histone code. The formation of learning and memory is one of the most important mechanisms for animals to adapt to environmental changes. A large number of studies have shown that histone codes are involved in the formation and consolidation of learning and memory. Here, we review the most recent literature of histone modification in regulating neurogenesis, dendritic spine dynamic, synapse formation, and synaptic plasticity.

Mutational synergy during leukemia induction remodels chromatin accessibility, histone modifications and three-dimensional DNA topology to alter gene expression

2021 ◽  
Author(s):  
Haiyang Yun ◽  
Nisha Narayan ◽  
Shabana Vohra ◽  
George Giotopoulos ◽  
Annalisa Mupo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Modifications ◽  
Three Dimensional ◽  
Chromatin Accessibility ◽  
Dna Topology

A murrel cysteine protease, cathepsin L: bioinformatics characterization, gene expression and proteolytic activity

Biologia ◽  
2014 ◽  
Vol 69 (3) ◽  
Author(s):  
Venkatesh Kumaresan ◽  
Prasanth Bhatt ◽  
Rajesh Palanisamy ◽  
Annie Gnanam ◽  
Mukesh Pasupuleti ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacterial Infections ◽  
Cathepsin L ◽  
Three Dimensional ◽  
Structural Similarity ◽  
Data Bank ◽  
Minimum Free Energy ◽  
Dimensional Structure ◽  
Peptide Bonds ◽  
Gene Expression Studies

AbstractCathepsin L, a lysosomal endopeptidase, is a member of the peptidase C1 family (papain-like family) of cysteine proteinases that cleave peptide bonds of lysosomal proteins. In this study, we report a cathepsin L sequence identified from the constructed cDNA library of striped murrel Channa striatus (designated as CsCath L) using genome sequencing FLXTM technology. The full-length CsCath L contains three eukaryotic thiol protease domains at positions 134-145, 278-288 and 299-318. Phylogenetic analysis revealed that the CsCath L was clustered together with other cathepsin L from teleosts. The three-dimensional structure of CsCath L modelled by the I-Tasser program was compared with structures deposited in the Protein Data Bank to find out the structural similarity of CsCath L with experimentally identified structures. The results showed that the CsCath L exhibits maximum structural identity with pro-cathepsin L from human. The RNA fold structure of CsCath L was predicted along with its minimum free energy (−471.93 kcal/mol). The highest CsCath L gene expression was observed in liver, which was also significantly higher (P < 0.05) than that detected in other tissues taken for analysis. In order to investigate the mRNA transcription profile of CsCath L during infection, C. striatus were injected with fungus (Aphanomyces invadans) and bacteria (Aeromonas hydrophila) and its expression was up-regulated in liver at various time points. Similar to gene expression studies, the highest CsCath L enzyme activity was also observed in liver and its activity was up-regulated by fungal and bacterial infections.

Abstracts of the 5th International Conference on Lactoferrin / Résumés du 5e symposium internationeige sur la lactoferrin

2002 ◽  
Vol 80 (1) ◽  
pp. 137-168
Keyword(s):  
Gene Expression ◽  
Cancer Treatment ◽  
Structure Function ◽  
Gene Expression Regulation ◽  
Three Dimensional ◽  
Antimicrobial Properties ◽  
Dimensional Structure ◽  
International Conference ◽  
Immunological Effects ◽  
Potential Use

Sixty-three abstracts are presented from the 5th International Conference on Lactoferrin "Structure, Function and Applications" in Banff, Alberta. The conference focused on lactoferrin’s three-dimensional structure, antimicrobial properties, immunological effects, potential use in cancer treatment, gene expression regulation, and receptors.

Three-dimensional imaging of nucleosomes from transcriptionally active genes using electron spectroscopic imaging

1996 ◽  
Vol 54 ◽  
pp. 54-55
Author(s):  
G. J. Czarnota ◽  
D. P. Bazett-Jones ◽  
F. P. Ottensmeyer
Keyword(s):  
Gene Expression ◽  
Three Dimensional ◽  
Spectroscopic Imaging ◽  
Dimensional Structure ◽  
Crystallographic Structure ◽  
Electron Spectroscopic Imaging ◽  
Nucleosome Structure ◽  
Active Genes

The three-dimensional structure of the nucleosome was determined using particles purified from transcriptionally active genes in conjunction with electron spectroscopic imaging, and quaternion-assisted angular reconstitution procedures. The results reveal a configuration which is very different from the canonical compact crystallographic structure for this fundamental chromosome subunit, implying a structural disruption of the nucleosome with the activation of gene expression in accord with numerous physico-chemical observations.Previous analyses of nucleosomes purified from transcriptionally quiescent genes have indicated numerous structural states dependent on factors in vitro which modify charge based interactions in nucleoprotein complexes. Nucleosomes from transcriptionally active genes undergo chemical alterations in vivo which similarly modify charge based interactions. In order to investigate the effects of the gene expression associated chemical alterations on nucleosome structure, particles were purified from transcriptionally active genes using mercury affinity chromatography. These nucleosome particles are hyperacetylated with respect to particles from transcriptionally quiescent genes. Here additionally, sulphydryls normally buried within the protein core of the transcriptionally inactive particle are exposed to chemical modifying agents thus facilitating purification as described.

scholarly journals Epigenetic inheritance uncoupled from sequence-specific recruitment

Science ◽  
2014 ◽  
Vol 348 (6230) ◽  
pp. 1258699 ◽  
Author(s):  
Kaushik Ragunathan ◽  
Gloria Jih ◽  
Danesh Moazed
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Histone Modifications ◽  
Posttranslational Modifications ◽  
Histone H3 ◽  
Epigenetic Inheritance ◽  
Meiotic Cell ◽  
Epigenetic Information ◽  
Cell Divisions ◽  
Jmjc Domain

Changes in histone posttranslational modifications are associated with epigenetic states that define distinct patterns of gene expression. It remains unclear whether epigenetic information can be transmitted through histone modifications independently of specific DNA sequence, DNA methylation, or RNA interference. Here we show that, in the fission yeast Schizosaccharomyces pombe, ectopically induced domains of histone H3 lysine 9 methylation (H3K9me), a conserved marker of heterochromatin, are inherited through several mitotic and meiotic cell divisions after removal of the sequence-specific initiator. The putative JmjC domain H3K9 demethylase, Epe1, and the chromodomain of the H3K9 methyltransferase, Clr4/Suv39h, play opposing roles in maintaining silent H3K9me domains. These results demonstrate how a direct “read-write” mechanism involving Clr4 propagates histone modifications and allows histones to act as carriers of epigenetic information.

scholarly journals Approaches to Understanding Mechanisms of Dentilisin Protease Complex Expression in Treponema denticola

2021 ◽  
Vol 11 ◽  
Author(s):  
M. Paula Goetting-Minesky ◽  
Valentina Godovikova ◽  
J. Christopher Fenno
Keyword(s):  
Gene Expression ◽  
Periodontal Disease ◽  
Host Cell ◽  
Protease Activity ◽  
Alveolar Bone ◽  
Three Dimensional ◽  
Periodontal Pathogen ◽  
Dimensional Structure ◽  
Treponema Denticola ◽  
Protease Gene

The oral spirochete Treponema denticola is a keystone periodontal pathogen that, in association with members of a complex polymicrobial oral biofilm, contributes to tissue damage and alveolar bone loss in periodontal disease. Virulence-associated behaviors attributed to T. denticola include disruption of the host cell extracellular matrix, tissue penetration and disruption of host cell membranes accompanied by dysregulation of host immunoregulatory factors. T. denticola dentilisin is associated with several of these behaviors. Dentilisin is an outer membrane-associated complex of acylated subtilisin-family PrtP protease and two other lipoproteins, PrcB and PrcA, that are unique to oral spirochetes. Dentilisin is encoded in a single operon consisting of prcB-prcA-prtP. We employ multiple approaches to study mechanisms of dentilisin assembly and PrtP protease activity. To determine the role of each protein in the protease complex, we have made targeted mutations throughout the protease locus, including polar and nonpolar mutations in each gene (prcB, prcA, prtP) and deletions of specific PrtP domains, including single base mutagenesis of key PrtP residues. These will facilitate distinguishing between host cell responses to dentilisin protease activity and its acyl groups. The boundaries of the divergent promoter region and the relationship between dentilisin and the adjacent iron transport operon are being resolved by incremental deletions in the sequence immediately 5’ to the protease locus. Comparison of the predicted three-dimensional structure of PrtP to that of other subtilisin-like proteases shows a unique PrtP C-terminal domain of approximately 250 residues. A survey of global gene expression in the presence or absence of protease gene expression reveals potential links between dentilisin and iron uptake and homeostasis in T. denticola. Understanding the mechanisms of dentilisin transport, assembly and activity of this unique protease complex may lead to more effective prophylactic or therapeutic treatments for periodontal disease.

The “Gene Cube”: A Novel Approach to Three-dimensional Clustering of Gene Expression Data

2019 ◽  
Vol 14 (8) ◽  
pp. 721-727 ◽  
Author(s):  
George I. Lambrou ◽  
Maria Sdraka ◽  
Dimitrios Koutsouris
Keyword(s):  
Gene Expression ◽  
Clustering Algorithms ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Tissue Samples ◽  
Novel Approach ◽  
Local Background ◽  
3D Matrix ◽  
Public Datasets

Background: A very popular technique for isolating significant genes from cancerous tissues is the application of various clustering algorithms on data obtained by DNA microarray experiments. Aim: The objective of the present work is to take into consideration the chromosomal identity of every gene before the clustering, by creating a three-dimensional structure of the form Chromosomes×Genes×Samples. Further on, the k-Means algorithm and a triclustering technique called δ- TRIMAX, are applied independently on the structure. Materials and Methods: The present algorithm was developed using the Python programming language (v. 3.5.1). For this work, we used two distinct public datasets containing healthy control samples and tissue samples from bladder cancer patients. Background correction was performed by subtracting the median global background from the median local Background from the signal intensity. The quantile normalization method has been applied for sample normalization. Three known algorithms have been applied for testing the “gene cube”, a classical k-means, a transformed 3D k-means and the δ-TRIMAX. Results: Our proposed data structure consists of a 3D matrix of the form Chromosomes×Genes×Samples. Clustering analysis of that structure manifested very good results as we were able to identify gene expression patterns among samples, genes and chromosomes. Discussion: to the best of our knowledge, this is the first time that such a structure is reported and it consists of a useful tool towards gene classification from high-throughput gene expression experiments. Conclusion: Such approaches could prove useful towards the understanding of disease mechanics and tumors in particular.

scholarly journals Histone Modifications and Other Facets of Epigenetic Regulation in Trypanosomatids: Leaving Their Mark

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Swati Saha
Keyword(s):  
Histone Modifications ◽  
Epigenetic Regulation ◽  
Posttranslational Modifications ◽  
High Resolution Mass Spectrometry ◽  
Three Dimensional ◽  
Early Years ◽  
Host Immune System ◽  
3D Genome ◽  
Cellular Processes ◽  
The Impact

ABSTRACT Histone posttranslational modifications (PTMs) modulate several eukaryotic cellular processes, including transcription, replication, and repair. Vast arrays of modifications have been identified in conventional eukaryotes over the last 20 to 25 years. While initial studies uncovered these primarily on histone tails, multiple modifications were subsequently found on the central globular domains as well. Histones are evolutionarily conserved across eukaryotes, and a large number of their PTMs and the functional relevance of these PTMs are largely conserved. Trypanosomatids, however, are early diverging eukaryotes. Although possessing all four canonical histones as well as several variants, their sequences diverge from those of other eukaryotes, particularly in the tails. Consequently, the modifications they carry also vary. Initial analyses almost 15 years ago suggested that trypanosomatids possessed a smaller collection of histone modifications. However, exhaustive high resolution mass spectrometry analyses in the last few years have overturned this belief, and it is now evident that the “histone code” proposed by Allis and coworkers in the early years of this century is as complex in these organisms as in other eukaryotes. Trypanosomatids cause several diseases, and the members of this group of organisms have varied lifestyles, evolving diverse mechanisms to evade the host immune system, some of which have been found to be principally controlled by epigenetic mechanisms. This minireview aims to acquaint the reader with the impact of histone PTMs on trypanosomatid cellular processes, as well as other facets of trypanosomatid epigenetic regulation, including the influence of three-dimensional (3D) genome architecture, and discusses avenues for future investigations.

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