The nucleosome: a little variation goes a long wayThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

2006 ◽  
Vol 84 (4) ◽  
pp. 505-507 ◽  
Author(s):  
Emily Bernstein ◽  
Sandra B. Hake
Keyword(s):  
Peer Review Process ◽  
Gene Activation ◽  
Epigenetic Inheritance ◽  
Histone Variants ◽  
Post Translational Modifications ◽  
Chromatin Compaction ◽  
Cellular Processes ◽  
Chromatin Template ◽  
Mitosis And Meiosis ◽  
Selection Of

Changes in the overall structure of chromatin are essential for the proper regulation of cellular processes, including gene activation and silencing, DNA repair, chromosome segregation during mitosis and meiosis, X chromosome inactivation in female mammals, and chromatin compaction during apoptosis. Such alterations of the chromatin template occur through at least 3 interrelated mechanisms: post-translational modifications of histones, ATP-dependent chromatin remodeling, and the incorporation (or replacement) of specialized histone variants into chromatin. Of these mechanisms, the exchange of variants into and out of chromatin is the least well understood. However, the exchange of conventional histones for variant histones has distinct and profound consequences within the cell. This review focuses on the growing number of mammalian histone variants, their particular biological functions and unique features, and how they may affect the structure of the nucleosome. We propose that a given nucleosome might not consist of heterotypic variants, but rather, that only specific histone variants come together to form a homotypic nucleosome, a hypothesis that we refer to as the nucleosome code. Such nucleosomes might in turn participate in marking specific chromatin domains that may contribute to epigenetic inheritance.

Structural and functional implications of phosphorylation and acetylation in the regulation of the AAA+ protein p97This paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (1) ◽  
pp. 41-48 ◽  
Author(s):  
Caroline A. Ewens ◽  
Patrik Kloppsteck ◽  
Andreas Förster ◽  
Xiaodong Zhang ◽  
Paul S. Freemont
Keyword(s):  
Review Process ◽  
Peer Review Process ◽  
Adaptor Proteins ◽  
Post Translational Modifications ◽  
Aaa Atpase ◽  
Cellular Processes ◽  
Transcription Factor Activation ◽  
Functional Implications ◽  
Aaa Protein ◽  
Selection Of

p97, also known as VCP (valosin-containing protein), is a hexameric AAA+ ATPase that participates in a variety of cellular processes. It is believed that p97 mediates these processes through the binding of various adaptor proteins. Many factors govern adaptor binding and the regulatory mechanisms are not yet well understood. Sites of phosphorylation and acetylation on p97 have been identified and such post-translational modifications may be involved in regulating p97 function. Phosphorylation and, to a lesser extent, acetylation of p97 have been shown to modify its properties — for example, by modulating adaptor binding and directing subcellular localization. These modifications have been implicated in a number of p97-mediated processes, including misfolded protein degradation, membrane fusion, and transcription factor activation. This review describes the known phosphorylation and acetylation sites on p97 and discusses their possible structural and functional implications.

Reuniting the contrasting functions of H2A.ZThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

2006 ◽  
Vol 84 (4) ◽  
pp. 528-535 ◽  
Author(s):  
Benoît Guillemette ◽  
Luc Gaudreau
Keyword(s):  
Chromatin Structure ◽  
Peer Review Process ◽  
Histone Variants ◽  
Molecular Techniques ◽  
Binding Assays ◽  
Post Translational Modifications ◽  
Genome Wide ◽  
On Chip ◽  
Inactive Chromatin ◽  
Selection Of

It is now well established that cells modify chromatin to set transcriptionally active or inactive regions. Such control of chromatin structure is essential for proper development of organisms. In addition to the growing number of histone post-translational modifications, cells can exchange canonical histones with different variants that can directly or indirectly change chromatin structure. Moreover, enzymatic complexes that can exchange specific histone variants within the nucleosome have now been identified. One such variant, H2A.Z, has recently been the focus of many studies. H2A.Z is highly conserved in evolution and has many different functions, while defining both active and inactive chromatin in different contexts. Advanced molecular techniques, such as genome-wide binding assays (chromatin immunoprecipitation on chip) have recently given researchers many clues as to how H2A.Z is targeted to chromatin and how it affects nuclear functions. We wish to review the recent literature and summarize our understanding of the mechanisms and functions of H2A.Z.

Transcriptional and epigenetic functions of histone variant H2A.ZThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 19-25 ◽  
Author(s):  
Ryan Draker ◽  
Peter Cheung
Keyword(s):  
Gene Expression ◽  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Histone Variants ◽  
Histone Variant ◽  
Post Translational Modifications ◽  
Chromatin Dynamics ◽  
Transcription Process ◽  
A Genome ◽  
Selection Of

The chromatin organization of a genome ultimately dictates the gene expression profile of the cell. It is now well recognized that key mechanisms that regulate chromatin structure include post-translational modifications of histones and the incorporation of histone variants at strategic sites within the genome. H2A.Z is a variant of H2A that is localized to the 5′ end of many genes and is required for proper regulation of gene expression. However, its precise function in the transcription process is not yet well defined. In this review, we discuss some of the recent findings related to this histone variant, how it associates with other histone epigenetic marks, and how post-translational modifications of H2A.Z further define its function.

New developments in post-translational modifications and functions of histone H2A variantsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 7-17 ◽  
Author(s):  
Anita A. Thambirajah ◽  
Andra Li ◽  
Toyotaka Ishibashi ◽  
Juan Ausió
Keyword(s):  
Review Process ◽  
Peer Review Process ◽  
Histone Variants ◽  
Histone H2a ◽  
Post Translational Modifications ◽  
New Developments ◽  
Chromatin Dynamics ◽  
Recent Developments ◽  
The Individual ◽  
Selection Of

Structural variability within histone families, such as H2A, can be achieved through 2 primary mechanisms: the expression of histone variants and the incorporation of chemical modifications. The histone H2A family contains several variants in addition to the canonical H2A forms. In this review, recent developments in the study of the heteromorphous variants H2A.X, H2A.Z, and macroH2A will be discussed. Particular focus will be given to the post-translational modifications (PTMs) of these variants, including phosphorylation, ubiquitination, acetylation, and methylation. The combination of the newly identified N- and C-terminal tail PTMs expands the multiplicity of roles that the individual H2A variants can perform. It is of additional interest that analogous sites within these different histone variants can be similarly modified. Whether this is a redundant function or a finely tuned one, designed to meet specific needs, remains to be elucidated.

Structural and temporal regulation of centromeric chromatinThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 255-264 ◽  
Author(s):  
Barbara G. Mellone
Keyword(s):  
Peer Review Process ◽  
Genetic Material ◽  
Mitotic Checkpoint ◽  
Unique Type ◽  
Temporal Regulation ◽  
Structural Nature ◽  
Chromosomal Site ◽  
Chromosome Attachment ◽  
Mitosis And Meiosis ◽  
Selection Of

Normal inheritance of genetic material requires that chromosomes segregate faithfully during mitosis and meiosis. The kinetochore is a unique structure that attaches chromosomes to the microtubule spindle, monitors proper chromosome attachment to the spindle through the mitotic checkpoint, and couples spindle and motor protein forces to move chromosomes during prometaphase and anaphase. The centromere is a specialized chromosomal site that is the structural and functional foundation for kinetochore formation, and is characterized by a unique type of chromatin that needs to be reconstituted after each replication cycle. In this review, recent progress in understanding the structural nature of this chromatin and how it is specifically maintained through cell division are discussed.

HIPK2: a multitalented partner for transcription factors in DNA damage response and developmentThis paper is one of a selection of papers published in this Special Issue, entitled 28th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

2007 ◽  
Vol 85 (4) ◽  
pp. 411-418 ◽  
Author(s):  
Cinzia Rinaldo ◽  
Andrea Prodosmo ◽  
Francesca Siepi ◽  
Silvia Soddu
Keyword(s):  
Transcription Factors ◽  
Gene Transcription ◽  
Review Process ◽  
Peer Review Process ◽  
Post Translational Modification ◽  
Interacting Protein ◽  
Cellular Processes ◽  
New Family ◽  
Damage Response ◽  
Selection Of

Protein phosphorylation is a widely diffuse and versatile post-translational modification that controls many cellular processes, from signal transduction to gene transcription. The homeodomain-interacting protein kinases (HIPKs) belong to a new family of serine–threonine kinases first identified as corepressors for homeodomain transcription factors. Different screenings for the identification of new partners of transcription factors have indicated that HIPK2, the best characterized member of the HIPK family, is a multitalented coregulator of an increasing number of transcription factors and cofactors. The aim of this review is to describe the different mechanisms through which HIPK2 regulates gene transcription.

scholarly journals Functional redundancy of variant and canonical histone H3 lysine 9 modification in Drosophila

2017 ◽  
Author(s):  
Taylor J.R. Penke ◽  
Daniel J. McKay ◽  
Brian D. Strahl ◽  
A. Gregory Matera ◽  
Robert J. Duronio
Keyword(s):  
Gene Activation ◽  
Histone H3 ◽  
Histone Variants ◽  
Protein Coding ◽  
Post Translational Modifications ◽  
Histone Ptms ◽  
Repressive Chromatin ◽  
Expression Of Genes ◽  
Canonical Histone

ABSTRACTHistone post-translational modifications (PTMs) and differential incorporation of variant and canonical histones into chromatin are central modes of epigenetic regulation. Despite similar protein sequences, histone variants are enriched for different suites of PTMs compared to their canonical counterparts. For example, variant histone H3.3 occurs primarily in transcribed regions and is enriched for “active” histone PTMs like Lys9 acetylation (H3.3K9ac), whereas the canonical histone H3 is enriched for Lys9 methylation (H3K9me), which is found in transcriptionally silent heterochromatin. To determine the functions of K9 modification on variant versus canonical H3, we compared the phenotypes caused by engineering H3.3K9R and H3K9R mutant genotypes in Drosophila melanogaster. Whereas most H3.3K9R and a small number of H3K9R mutant animals are capable of completing development and do not have substantially altered protein coding transcriptomes, all H3.3K9RH3K9R combined mutants die soon after embryogenesis and display decreased expression of genes enriched for K9ac. These data suggest that the role of K9ac in gene activation during development can be provided by either H3 or H3.3. Conversely, we found that H3.3K9 is methylated at telomeric transposons, and this mark contributes to repressive chromatin architecture, supporting a role for H3.3 in heterochromatin that is distinct from that of H3. Thus, our genetic and molecular analyses demonstrate that K9 modification of variant and canonical H3 have overlapping roles in development and transcriptional regulation, though to differing extents in euchromatin and heterochromatin.

Recent developments in mass spectrometry-based quantitative phosphoproteomicsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process.

2008 ◽  
Vol 86 (2) ◽  
pp. 137-148 ◽  
Author(s):  
Jeffrey C. Smith ◽  
Daniel Figeys
Keyword(s):  
Mass Spectrometry ◽  
Protein Phosphorylation ◽  
Review Process ◽  
Peer Review Process ◽  
Cellular Systems ◽  
Post Translational Modification ◽  
Dynamic Nature ◽  
Cellular Processes ◽  
Recent Developments ◽  
Selection Of

Protein phosphorylation is a reversible post-translational modification that is involved in virtually all eukaryotic cellular processes and has been studied in great detail in recent years. Many developments in mass spectrometry (MS)-based proteomics have been successfully applied to study protein phosphorylation in highly complicated samples. Furthermore, the emergence of a variety of enrichment strategies has allowed some of the challenges associated with low phosphorylation stoichiometry and phosphopeptide copy number to be overcome. The dynamic nature of protein phosphorylation complicates its analysis; however, a number of methods have been developed to successfully quantitate phosphorylation changes in a variety of cellular systems. The following review details some of the most recent breakthroughs in the study of protein phosphorylation, or phosphoproteomics, using MS-based approaches. The majority of the focus is placed on detailing strategies that are currently used to conduct MS-based quantitative phosphoproteomics.

scholarly journals DNA methylation in bull spermatozoa: evolutionary impacts, interindividual variability, and contribution to the embryo

2020 ◽  
Vol 100 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Hélène Kiefer ◽  
Jean-Philippe Perrier
Keyword(s):  
Dna Methylation ◽  
Interindividual Variability ◽  
Epigenetic Inheritance ◽  
Genome Plasticity ◽  
Model Species ◽  
Chromatin Compaction ◽  
Bull Semen ◽  
Bull Sperm ◽  
Selection Of

The DNA methylome of spermatozoa results from a unique epigenetic reprogramming crucial for chromatin compaction and the protection of the paternal genetic heritage. Although bull semen is widely used for artificial insemination (AI), little is known about the sperm epigenome in cattle. The purpose of this review is to synthetize recent work on the bull sperm methylome in light of the knowledge accumulated in humans and model species. We will address sperm-specific DNA methylation features and their potential evolutionary impacts, with particular emphasis on hypomethylated regions and repetitive elements. We will review recent examples of interindividual variability and intra-individual plasticity of the bull sperm methylome as related to fertility and age, respectively. Finally, we will address paternal methylome reprogramming after fertilization, as well as the mechanisms potentially involved in epigenetic inheritance, and provide some examples of disturbances that alter the dynamics of reprogramming in cattle. Because the selection of AI bulls is closely based on their genotypes, we will also discuss the complex interplay between sequence polymorphism and DNA methylation, which represents both a difficulty in addressing the role of DNA methylation in shaping phenotypes and an opportunity to better understand genome plasticity.

A moment’s pause: putative nucleosome-based influences on MeCP2 regulationThis paper is one of a selection of papers published in this Special Issue, entitled 30th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (5) ◽  
pp. 791-798 ◽  
Author(s):  
Anita A. Thambirajah ◽  
Juan Ausió
Keyword(s):  
Peer Review ◽  
Critical Points ◽  
Review Process ◽  
Peer Review Process ◽  
Special Issue ◽  
The Past ◽  
Chromatin Template ◽  
The Brain ◽  
Complex Activities ◽  
Selection Of

There has been a hotbed of activity surrounding MeCP2 research in the past number of years. Despite better characterizing the functions and nature of this protein, it has become abundantly clear that MeCP2 is involved in far more complex activities than perhaps initially anticipated. Recent publications have shown that MeCP2 is dynamically post-translationally modified, and it is possible that these marks permit MeCP2 to inhabit very diverse chromatin environments. It is also of interest to consider how nucleosome composition differs in these varying chromatin regions, and how the chromatin template itself contributes to diversifying the regulatory roles of MeCP2. These will be critical points to examine when seeking to understand how MeCP2 behaviour differentiates in tissues other than the brain. By understanding the chromatin and (or) tissue context in which MeCP2 interacts, it may be possible to discern the specific etiology of diseases linked to MeCP2 dysfunction.

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