Histone variants and histone modifications: A structural perspective

2001 ◽  
Vol 79 (6) ◽  
pp. 693-708 ◽  
Author(s):  
Juan Ausió ◽  
D Wade Abbott ◽  
Xiaoying Wang ◽  
Susan C Moore
Keyword(s):  
Recent Work ◽  
Histone Modifications ◽  
Posttranslational Modifications ◽  
Structural Component ◽  
Functional Role ◽  
Short Range ◽  
Histone Variants ◽  
Current State ◽  
Functional Implications ◽  
Different Levels

In this review, we briefly analyze the current state of knowledge on histone variants and their posttranslational modifications. We place special emphasis on the description of the structural component(s) defining and determining their functional role. The information available indicates that this histone "variability" may operate at different levels: short-range "local" or long-range "global", with different functional implications. Recent work on this topic emphasizes an earlier notion that suggests that, in many instances, the functional response to histone variability is possibly the result of a synergistic structural effect.Key words: histone variants, posttranslational modifications, chromatin.

Four challenges for cognitive neuroscience and the cortico-hippocampal division of memory

2003 ◽  
Vol 26 (6) ◽  
pp. 681-682
Author(s):  
Harry Howard
Keyword(s):  
Independent Component Analysis ◽  
Recent Work ◽  
Cognitive Neuroscience ◽  
Principle Component Analysis ◽  
Pattern Analysis ◽  
Component Analysis ◽  
Independent Component ◽  
Principle Component ◽  
Complementary Methods ◽  
Current State

Jackendoff's criticisms of the current state of theorization in cognitive neuroscience are defused by recent work on the computational complementarity of the hippocampus and neocortex. Such considerations lead to a grounding of Jackendoff's processing model in the complementary methods of pattern analysis effected by independent component analysis (ICA) and principle component analysis (PCA).

A haploid affair: core histone transitions during spermatogenesis

2003 ◽  
Vol 81 (3) ◽  
pp. 131-140 ◽  
Author(s):  
John D Lewis ◽  
D Wade Abbott ◽  
Juan Ausió
Keyword(s):  
Histone Modifications ◽  
Chromatin Structure ◽  
Critical Role ◽  
Diploid Cell ◽  
Histone Variants ◽  
Histone H4 ◽  
Dna Compaction ◽  
Dynamic Composition ◽  
Shed Light

The process of meiosis reduces a diploid cell to four haploid gametes and is accompanied by extensive recombination. Thus, the dynamics of chromatin during meiosis are significantly different than in mitotic cells. As spermatogenesis progresses, there is a widespread reorganization of the haploid genome followed by extensive DNA compaction. It has become increasingly clear that the dynamic composition of chromatin plays a critical role in the activities of enzymes and processes that act upon it. Therefore, an analysis of the role of histone variants and modifications in these processes may shed light upon the mechanisms involved and the control of chromatin structure in general. Histone variants such as histone H3.3, H2AX, and macroH2A appear to play key roles in the various stages of spermiogenesis, in addition to the specifically modulated acetylation of histone H4 (acH4), ubiquitination of histones H2A and H2B (uH2A, uH2B), and phosphorylation of histone H3 (H3p). This review will examine recent discoveries concerning the role of histone modifications and variants during meiosis and spermatogenesis.Key words: histone variants, histone modifications, chromatin structure, meiosis.

Aging, cellular senescence and cancer: epigenetic alterations and nuclear remodeling

2019 ◽  
pp. 238-253
Author(s):  
John C. Lucchesi
Keyword(s):  
Histone Modifications ◽  
Cellular Senescence ◽  
Aging Process ◽  
Nuclear Architecture ◽  
Gene Mutations ◽  
Histone Variants ◽  
Premature Aging ◽  
Model Organisms ◽  
Premature Aging Syndromes ◽  
Nuclear Remodeling

Epigenetic modifications correlated with aging and oncogenesis are changes in the pattern of DNA methylation and of histone modifications, and changes in the level of histone variants (H3.3, macroH2A, H2A.Z) and gene mutations. The sirtuins are a set of highly conserved protein deacetylases of particular significance to the aging process. Many cancer types are found to carry mutations in chromatin-modifying genes such as those encoding methyl or acetyl transferases, affecting the histone modifications of promoters and enhancers. The aging process and oncogenesis present a number of changes in the nuclear architecture. Mutations in the lamina-coding genes lead to premature aging syndromes. Mutations in remodeling complexes are found in different cancers. Modifications that affect the architectural protein binding sites at topologically associating domain (TAD) borders can cause the merging of neighboring TADs. The levels of short non-coding RNAs (sncRNAs) are altered in model organisms and are associated with cancer. Changes in the position of chromosome territories often occur in tumor cells. Nevertheless, cellular senescence, due mostly to the absence of telomerase, represents a mechanism of tumor suppression.

Histone Variants and Histone Modifications in Neurogenesis

2020 ◽  
Vol 30 (11) ◽  
pp. 869-880
Author(s):  
Mengtian Zhang ◽  
Jinyue Zhao ◽  
Yuqing Lv ◽  
Wenwen Wang ◽  
Chao Feng ◽  
...  
Keyword(s):  
Histone Modifications ◽  
Histone Variants

scholarly journals PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping

GigaScience ◽  
2019 ◽  
Vol 8 (8) ◽  
Author(s):  
Luis Francisco Hernández Sánchez ◽  
Bram Burger ◽  
Carlos Horro ◽  
Antonio Fabregat ◽  
Stefan Johansson ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Posttranslational Modifications ◽  
Knowledge Bases ◽  
Protein Isoforms ◽  
Biomedical Data ◽  
Protein Protein Interactions ◽  
Gene Sets ◽  
Functional Knowledge ◽  
Pathway Analyses ◽  
Different Levels

Abstract Background Mapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers (e.g., gene sets) in pathway knowledge bases. However, the isoform and posttranslational modification states of proteins are lost when converting input and pathways into gene-centric lists. Findings Based on the Reactome knowledge base, we built a network of protein-protein interactions accounting for the documented isoform and modification statuses of proteins. We then implemented a command line application called PathwayMatcher (github.com/PathwayAnalysisPlatform/PathwayMatcher) to query this network. PathwayMatcher supports multiple types of omics data as input and outputs the possibly affected biochemical reactions, subnetworks, and pathways. Conclusions PathwayMatcher enables refining the network representation of pathways by including proteoforms defined as protein isoforms with posttranslational modifications. The specificity of pathway analyses is hence adapted to different levels of granularity, and it becomes possible to distinguish interactions between different forms of the same protein.

Dynamics in the expression of epigenetic modifiers and histone modifications in perinatal rat germ cells during de novo DNA methylation†

2020 ◽  
Author(s):  
Arlette Rwigemera ◽  
Rhizlane El omri-Charai ◽  
Laetitia L Lecante ◽  
Geraldine Delbes
Keyword(s):  
Dna Methylation ◽  
Germ Cell ◽  
Histone Modifications ◽  
Germ Cells ◽  
Posttranslational Modifications ◽  
Fluorescent Protein ◽  
De Novo ◽  
Expression Patterns ◽  
Dna Methyltransferases ◽  
Epigenetic Modifiers

Abstract Epigenetic reprogramming during perinatal germ cell development is essential for genomic imprinting and cell differentiation; however, the actors of this key event and their dynamics are poorly understood in rats. Our study aimed to characterize the expression patterns of epigenetic modifiers and the changes in histone modifications in rat gonocytes at the time of de novo DNA methylation. Using transgenic rats expressing Green Fluorescent Protein (GFP) specifically in germ cells, we purified male gonocytes by fluorescent activated cell sorting at various stages of perinatal development and established the transcriptomic profile of 165 epigenetic regulators. Using immunofluorescence on gonad sections, we tracked six histone modifications in rat male and female perinatal germ cells over time, including methylation of histone H3 on lysines 27, 9, and 4; ubiquitination of histone H2A on lysine119; and acetylation of histone H2B on lysine 20. The results revealed the dynamics in the expression of ten-eleven translocation enzymes and DNA methyltransferases in male gonocytes at the time of de novo DNA methylation. Moreover, our transcriptomic data indicate a decrease in histone ubiquitination and methylation coinciding with the beginning of de novo DNA methylation. Decreases in H2AK119Ub and H3K27me3 were further confirmed by immunofluorescence in the male germ cells but were not consistent for all H3 methylation sites examined. Together, our data highlighted transient chromatin remodeling involving histone modifications during de novo DNA methylation. Further studies addressing how these dynamic changes in histone posttranslational modifications could guide de novo DNA methylation will help explain the complex establishment of the male germ cell epigenome.

Primitive forms of Response to the Matrices Test

1953 ◽  
Vol 99 (416) ◽  
pp. 374-393 ◽  
Author(s):  
D. B. Bromley
Keyword(s):  
Recent Work ◽  
Present Situation ◽  
Convincing Evidence ◽  
Intelligence Tests ◽  
Old People ◽  
Exact Determination ◽  
Primitive Forms ◽  
Mental Defectives ◽  
Different Levels

I. Problem and Method.Recent work on the psychology of intelligence and thinking suggests that perceptual types of intelligence tests are inadequate for dealing with psychiatric cases, young children, old people, mental defectives, and primitive peoples. The argument is that, in these groups, intellectual processes have either deteriorated from or failed to develop to that level with which most perceptual intelligence tests are concerned. The methods of scoring also assume that the correct answers are always reached in the same way, but this is by no means always the case, as Goldstein and Scheerer (1941, p. 14) have pointed out. The studies of Werner (1948), Piaget (1951), Goldstein (1940), Hanfmann and Kasanin (1942), Rapaport (1951), Moursy (1952) et al. show convincing evidence that cognition can take place at different “levels.” The exact determination of the number, nature, and scope of the different levels remains a task for the future, since the present situation is confused, to say the least.

scholarly journals ISOGlyP: de novo prediction of isoform-specific mucin-type O-glycosylation

Glycobiology ◽  
2020 ◽  
Author(s):  
Jonathon E Mohl ◽  
Thomas A Gerken ◽  
Ming-Ying Leung
Keyword(s):  
Amino Acid ◽  
Posttranslational Modifications ◽  
Prediction Accuracy ◽  
Short Range ◽  
De Novo ◽  
Specific Amino Acid ◽  
Glycosylation Sites ◽  
Specific Enhancement ◽  
A Site

Abstract Mucin-type O-glycosylation is one of the most common posttranslational modifications of proteins. The abnormal expression of various polypeptide GalNAc-transferases (GalNAc-Ts) which initiate and define sites of O-glycosylation are linked to many cancers and other diseases. Current O-glycosyation prediction programs utilize O-glycoproteomics data obtained without regard to the transferase isoform (s) responsible for the glycosylation. With 20 different GalNAc-Ts in humans, having an ability to predict and interpret O-glycosylation sites in terms of specific GalNAc-T isoforms is invaluable. To fill this gap, ISOGlyP (Isoform-Specific O-Glycosylation Prediction) has been developed. Using position-specific enhancement values generated based on GalNAc-T isoform-specific amino acid preferences, ISOGlyP predicts the propensity that a site would be glycosylated by a specific transferase. ISOGlyP gave an overall prediction accuracy of 70% against in vivo data, which is comparable to that of the NetOGlyc4.0 predictor. Additionally, ISOGlyP can identify the known effects of long- and short-range prior glycosylation and can generate potential peptide sequences selectively glycosylated by specific isoforms. ISOGlyP is freely available for use at ISOGlyP.utep.edu. The code is also available on GitHub (https://github.com/jonmohl/ISOGlyP).

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