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.

scholarly journals Differentiation of Chromatin during DNA Elimination inEuplotes crassus

1999 ◽  
Vol 10 (12) ◽  
pp. 4217-4230 ◽  
Author(s):  
Carolyn L. Jahn
Keyword(s):  
Chromatin Structure ◽  
Histone Variants ◽  
Micrococcal Nuclease ◽  
Base Pairs ◽  
Euplotes Crassus ◽  
Dna Elimination ◽  
Sequence Components ◽  
Nucleosomal Structure

In Euplotes crassus, most of the micronuclear genome is eliminated during formation of a transcriptionally active macronucleus. To understand how this is mediated throughout the genome, we have examined the chromatin structure of the macronucleus-destined sequences and Tec transposons, which are dispersed in 15,000 copies in the micronuclear genome and completely eliminated during formation of the macronuclear genome. Whereas the macronucleus-destined sequences show a typical pattern of nucleosomal repeats in micrococcal nuclease digests, the Tec element chromatin structure digests to a nucleosome-like repeat pattern that is not typical: the minimum digestion products are ∼300–600 base pairs, or “subnucleosomal,” in size. In addition, the excised, circular forms of the Tec elements are exceedingly resistant to nucleases. Nevertheless, an underlying nucleosomal structure of the Tec elements can be demonstrated from the size differences between repeats in partial micrococcal nuclease digests and by trypsin treatment of nuclei, which results in mononucleosome-sized products. Characterization of the most micrococcal nuclease–resistant DNA indicates that micronuclear telomeres are organized into a chromatin structure with digestion properties identical to those of the Tec elements in the developing macronucleus. Thus, these major repetitive sequence components of the micronuclear genome differ in their chromatin structure from the macronuclear-destined sequences during DNA elimination. The potential role of developmental stage–specific histone variants in this chromatin differentiation is discussed.

scholarly journals Chromatin is an ancient innovation conserved between Archaea and Eukarya

eLife ◽  
2012 ◽  
Vol 1 ◽  
Author(s):  
Ron Ammar ◽  
Dax Torti ◽  
Kyle Tsui ◽  
Marinella Gebbia ◽  
Tanja Durbic ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Nucleosome Occupancy ◽  
Regulation Of Gene Expression ◽  
Haloferax Volcanii ◽  
Dna Compaction ◽  
Genome Wide ◽  
Eukaryotic Chromatin ◽  
Transcriptional Start Sites

The eukaryotic nucleosome is the fundamental unit of chromatin, comprising a protein octamer that wraps ∼147 bp of DNA and has essential roles in DNA compaction, replication and gene expression. Nucleosomes and chromatin have historically been considered to be unique to eukaryotes, yet studies of select archaea have identified homologs of histone proteins that assemble into tetrameric nucleosomes. Here we report the first archaeal genome-wide nucleosome occupancy map, as observed in the halophile Haloferax volcanii. Nucleosome occupancy was compared with gene expression by compiling a comprehensive transcriptome of Hfx. volcanii. We found that archaeal transcripts possess hallmarks of eukaryotic chromatin structure: nucleosome-depleted regions at transcriptional start sites and conserved −1 and +1 promoter nucleosomes. Our observations demonstrate that histones and chromatin architecture evolved before the divergence of Archaea and Eukarya, suggesting that the fundamental role of chromatin in the regulation of gene expression is ancient.

scholarly journals Hyperactivation of the Silencing Proteins, Sir2p and Sir3p, Causes Chromosome Loss

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 605-614
Author(s):  
Scott G Holmes ◽  
Alan B Rose ◽  
Kristin Steuerle ◽  
Enrique Saez ◽  
Sandra Sayegh ◽  
...  
Keyword(s):  
Toxic Effect ◽  
Chromatin Structure ◽  
Transcriptional Repression ◽  
Yeast Cells ◽  
Chromosome Stability ◽  
Chromosome Loss ◽  
Gene Products ◽  
Histone H4 ◽  
Sir Proteins

The SIR gene products maintain transcriptional repression at the silent mating type loci and telomeres in Saccharomyces cerevisiae, although no enzymatic or structural activity has been assigned to any of the Sir proteins nor has the role of any of these proteins in transcriptional silencing been clearly defined. We have investigated the functions and interactions of the Sir2, Sir3, and Sir4 proteins by overexpressing them in yeast cells. We find that Sir2p and Sir3p are toxic when overexpressed, while high Sir4p levels have no toxic effect. Epistasis experiments indicate that Sir2p-induced toxicity is diminished in strains lacking the SIR3 gene, while both Sir2p and Sir4p are required for Sir3p to manifest its full toxic effect. In addition, the effects of Sir2 or Sir3 overexpression are exacerbated by specific mutations in the N-terminus of the histone H4 gene. These results are consistent with a model in which Sir2p, Sir3p and Sir4p function as a complex and interact with histones to modify chromatin structure. We find no evidence that toxicity from high levels of the Sir proteins results from widespread repression of transcription. Instead, we find that high levels of Sir2p and/or Sir3p cause a profound decrease in chromosome stability. These results can be appreciated in the context of the effects of Sir2p in histone acetylation and of chromatin structure on chromosome stability.

scholarly journals Transcriptionally Active Chromatin—Lessons Learned from the Chicken Erythrocyte Chromatin Fractionation

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1354
Author(s):  
Tasnim H. Beacon ◽  
James R. Davie
Keyword(s):  
Histone Modifications ◽  
Histone Variants ◽  
Structural Features ◽  
Lessons Learned ◽  
Open Chromatin ◽  
Chicken Erythrocyte ◽  
Histone H4 ◽  
Active Chromatin ◽  
Chromatin Structural ◽  
Chromatin Fractionation

The chicken erythrocyte model system has been valuable to the study of chromatin structure and function, specifically for genes involved in oxygen transport and the innate immune response. Several seminal features of transcriptionally active chromatin were discovered in this system. Davie and colleagues capitalized on the unique features of the chicken erythrocyte to separate and isolate transcriptionally active chromatin and silenced chromatin, using a powerful native fractionation procedure. Histone modifications, histone variants, atypical nucleosomes (U-shaped nucleosomes) and other chromatin structural features (open chromatin) were identified in these studies. More recently, the transcriptionally active chromosomal domains in the chicken erythrocyte genome were mapped by combining this chromatin fractionation method with next-generation DNA and RNA sequencing. The landscape of histone modifications relative to chromatin structural features in the chicken erythrocyte genome was reported in detail, including the first ever mapping of histone H4 asymmetrically dimethylated at Arg 3 (H4R3me2a) and histone H3 symmetrically dimethylated at Arg 2 (H3R2me2s), which are products of protein arginine methyltransferases (PRMTs) 1 and 5, respectively. PRMT1 is important in the establishment and maintenance of chicken erythrocyte transcriptionally active chromatin.

scholarly journals Effect of histone H4 tail on nucleosome stability and internucleosomal interactions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tommy Stormberg ◽  
Sridhar Vemulapalli ◽  
Shaun Filliaux ◽  
Yuri L. Lyubchenko
Keyword(s):  
Chromatin Structure ◽  
Histone H4 ◽  
Nucleosome Assembly ◽  
Dna Templates ◽  
Histone Tails ◽  
Force Microscopy ◽  
Atomic Force ◽  
Dna Unwrapping ◽  
Nucleosome Stability

AbstractChromatin structure is dictated by nucleosome assembly and internucleosomal interactions. The tight wrapping of nucleosomes inhibits gene expression, but modifications to histone tails modulate chromatin structure, allowing for proper genetic function. The histone H4 tail is thought to play a large role in regulating chromatin structure. Here we investigated the structure of nucleosomes assembled with a tail-truncated H4 histone using Atomic Force Microscopy. We assembled tail-truncated H4 nucleosomes on DNA templates allowing for the assembly of mononucleosomes or dinucleosomes. Mononucleosomes assembled on nonspecific DNA led to decreased DNA wrapping efficiency. This effect is less pronounced for nucleosomes assembled on positioning motifs. Dinucleosome studies resulted in the discovery of two effects- truncation of the H4 tail does not diminish the preferential positioning observed in full-length nucleosomes, and internucleosomal interaction eliminates the DNA unwrapping effect. These findings provide insight on the role of histone H4 in chromatin structure and stability.

scholarly journals Monomethylation of Lysine 20 on Histone H4 Facilitates Chromatin Maturation

2008 ◽  
Vol 29 (1) ◽  
pp. 57-67 ◽  
Author(s):  
Annette N. D. Scharf ◽  
Karin Meier ◽  
Volker Seitz ◽  
Elisabeth Kremmer ◽  
Alexander Brehm ◽  
...  
Keyword(s):  
Histone Modifications ◽  
Chromatin Structure ◽  
Chromatin Assembly ◽  
Assembly System ◽  
Histone H4 ◽  
Dynamic Changes ◽  
Histone Deposition

ABSTRACT Histone modifications play an important role in shaping chromatin structure. Here, we describe the use of an in vitro chromatin assembly system from Drosophila embryo extracts to investigate the dynamic changes of histone modifications subsequent to histone deposition. In accordance with what has been observed in vivo, we find a deacetylation of the initially diacetylated isoform of histone H4, which is dependent on chromatin assembly. Immediately after deposition of the histones onto DNA, H4 is monomethylated at K20, which is required for an efficient deacetylation of the H4 molecule. H4K20 methylation-dependent dl(3)MBT association with chromatin and the identification of a dl(3)MBT-dRPD3 complex suggest that a deacetylase is specifically recruited to the monomethylated substrate through interaction with dl(3)MBT. Our data demonstrate that histone modifications are added and removed during chromatin assembly in a highly regulated manner.

scholarly journals A review of epigenetic changes in asthma: methylation and acetylation

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Mojgan Sheikhpour ◽  
Mobina Maleki ◽  
Maryam Ebrahimi Vargoorani ◽  
Vahid Amiri
Keyword(s):  
Dna Methylation ◽  
Histone Modifications ◽  
Histone Methylation ◽  
Epigenetic Changes ◽  
External Effects ◽  
The Past ◽  
Immune Pathways ◽  
Shed Light ◽  
Histone Methylation And Acetylation

AbstractSeveral studies show that childhood and adulthood asthma and its symptoms can be modulated through epigenetic modifications. Epigenetic changes are inheritable modifications that can modify the gene expression without changing the DNA sequence. The most common epigenetic alternations consist of DNA methylation and histone modifications. How these changes lead to asthmatic phenotype or promote the asthma features, in particular by immune pathways regulation, is an understudied topic. Since external effects, like exposure to tobacco smoke, air pollution, and drugs, influence both asthma development and the epigenome, elucidating the role of epigenetic changes in asthma is of great importance. This review presents available evidence on the epigenetic process that drives asthma genes and pathways, with a particular focus on DNA methylation, histone methylation, and acetylation. We gathered and assessed studies conducted in this field over the past two decades. Our study examined asthma in different aspects and also shed light on the limitations and the important factors involved in the outcomes of the studies. To date, most of the studies in this area have been carried out on DNA methylation. Therefore, the need for diagnostic and therapeutic applications through this molecular process calls for more research on the histone modifications in this disease.

scholarly journals The dynamics of deforestation and reforestation in a developing economy

2021 ◽  
pp. 1-22
Author(s):  
Julien Wolfersberger ◽  
Gregory S. Amacher ◽  
Philippe Delacote ◽  
Arnaud Dragicevic
Keyword(s):  
Critical Role ◽  
Environmental Benefits ◽  
Secondary Forests ◽  
Developing Economy ◽  
Forest Types ◽  
Institutional Reforms ◽  
Land Title ◽  
Shed Light

Abstract We develop a model of optimal land allocation in a developing economy that features three possible land uses: agriculture, primary and secondary forests. The distinction between those forest types reflects their different contributions in terms of public goods. In our model, reforestation is costly because it undermines land title security. Using the forest transition concept, we study long-term land-use change and explain important features of cumulative deforestation across countries. Our results shed light on the speed at which net deforestation ends, on the effect of tenure costs in this process, and on composition in steady state. We also present a policy analysis that emphasizes the critical role of institutional reforms addressing the costs of both deforestation and tenure in order to promote a transition. We find that focusing only on net forest losses can be misleading since late transitions may yield, upon given conditions, a higher level of environmental benefits.

scholarly journals Reorganisation of chromatin during erythroid differentiation

2019 ◽  
Vol 23 (1) ◽  
pp. 95-99
Author(s):  
A. A. Khabarova ◽  
A. S. Ryzhkova ◽  
N. R. Battulin
Keyword(s):  
Chromatin Structure ◽  
Molecular Mechanisms ◽  
Critical Role ◽  
Erythroid Differentiation ◽  
Gene Activity ◽  
Nuclear Space ◽  
Specific Cell ◽  
Cell Type ◽  
Differentiation Potential

A totipotent zygote has unlimited potential for differentiation into all cell types found in an adult organism. During ontogenesis proliferating and maturing cells gradually lose their differentiation potential, limiting the spectrum of possible developmental transitions to a specific cell type. Following the initiation of the developmental program cells acquire specific morphological and functional properties. Deciphering the mechanisms that coordinate shifts in gene expression revealed a critical role of three-dimensional chromatin structure in the regulation of gene activity during lineage commitment. Several levels of DNA packaging have been recently identified using chromosome conformation capture based techniques such a Hi-C. It is now clear that chromatin regions with high transcriptional activity assemble into Mb-scale compartments in the nuclear space, distinct from transcriptionally silent regions. More locally chromatin is organized into topological domains, serving as functionally insulated units with cell type – specific regulatory loop interactions. However, molecular mechanisms establishing and maintaining such 3D organization are yet to be investigated. Recent focus on studying chromatin reorganization accompanying cell cycle progression and cellular differentiation partially explained some aspects of 3D genome folding. Throughout erythropoiesis cells undergo a dramatic reorganization of the chromatin landscape leading to global nuclear condensation and transcriptional silencing, followed by nuclear extrusion at the final stage of mammalian erythropoiesis. Drastic changes of genome architecture and function accompanying erythroid differentiation seem to be an informative model for studying the ways of how genome organization and dynamic gene activity are connected. Here we summarize current views on the role of global rearrangement of 3D chromatin structure in erythroid differentiation.

Epigenetic analysis of human embryonic carcinoma cells during retinoic acid-induced neural differentiation

2010 ◽  
Vol 88 (3) ◽  
pp. 527-538 ◽  
Author(s):  
Maryam Shahhoseini ◽  
Adeleh Taei ◽  
Narges Zare Mehrjardi ◽  
Ghasem Hosseini Salekdeh ◽  
Hossein Baharvand
Keyword(s):  
Cell Culture ◽  
Stem Cell ◽  
Retinoic Acid ◽  
Histone Modifications ◽  
Chromatin Structure ◽  
Neural Differentiation ◽  
Stem Cell Differentiation ◽  
Histone Variants ◽  
Global Changes ◽  
Dependent Manner

Differentiation of stem cells from a pluripotent to a committed state involves global changes in genome expression patterns, critically determined by chromatin structure and interactions of chromatin-binding proteins. The dynamics of chromatin structure are tightly regulated by multiple epigenetic mechanisms such as histone modifications and the incorporation of histone variants. In the current work, we induced neural differentiation of a human embryonal carcinoma stem cell line, NTERA2/NT2, by retinoic acid (RA) treatment, primarily according to two different methods of adherent cell culture (rosette formation) and suspension cell culture (EB formation) conditions, and histone modifications and variations were compared through these processes. Western blot analysis of histone extracts showed significant changes in the acetylation and methylation patterns of histone H3, and expression level of the histone variant H2A.Z, after RA treatment in both protocols. Using chromatin immunoprecipitation (ChIP) coupled with real-time PCR, it was shown that these epigenetic changes occurred on the regulatory regions of 4 marker genes (Oct4, Nanog, Nestin, and Pax6) in a culture condition dependent manner. This report demonstrates the dynamic interplay of histone modification and variation in regulating the gene expression profile, during stem cell differentiation and under different culture conditions.

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