Chromatin structures condensed by linker histones

2019 ◽  
Vol 63 (1) ◽  
pp. 75-87 ◽  
Author(s):  
Bing-Rui Zhou ◽  
Yawen Bai
Keyword(s):  
Structural Unit ◽  
Linker Histone ◽  
Histone H2a ◽  
Linker Histones ◽  
The Core ◽  
High Order Chromatin Structure ◽  
Core Histones ◽  
Order Structures ◽  
Made In

Abstract In eukaryotic cells, genomic DNA exists in the form of chromatin through association with histone proteins, which consist of four core histone (H2A, H2B, H3, and H4) families and one linker histone (H1) family. The core histones bind to DNA to form the nucleosome, the recurring structural unit of chromatin. The linker histone binds to the nucleosome to form the next structural unit of chromatin, the chromatosome, which occurs dominantly in metazoans. Linker histones also play an essential role in condensing chromatin to form higher order structures. Unlike the core histones in the formation of the nucleosome, the role of linker histone in the formation of the chromatosome and high-order chromatin structure is not well understood. Nevertheless, exciting progress in the structural studies of chromatosomes and nucleosome arrays condensed by linker histones has been made in the last several years. In this mini-review, we discuss these recent experimental results and provide some perspectives for future studies.

A compendium of the histone H1 family of somatic subtypes: An elusive cast of characters and their characteristics

2001 ◽  
Vol 79 (3) ◽  
pp. 289-304 ◽  
Author(s):  
Missag H Parseghian ◽  
Barbara A Hamkalo
Keyword(s):  
Historical Context ◽  
Histone H1 ◽  
General Function ◽  
Linker Histones ◽  
Chromatin Compaction ◽  
The Core ◽  
The Past ◽  
Current State ◽  
Core Histones

The last 35 years has seen a substantial amount of information collected about the somatic H1 subtypes, yet much of this work has been overshadowed by research into highly divergent isoforms of H1, such as H5. Reports from several laboratories in the past few years have begun to call into question some of the traditional views regarding the general function of linker histones and their heterogeneity. Hence, the impression in some circles is that less is known about these ubiquitous nuclear proteins as compared with the core histones. The goal of the following review is to acquaint the reader with the ubiquitous somatic H1s by categorizing them and their characteristics into several classes. The reasons for our current state of misunderstanding is put into a historical context along with recent controversies centering on the role of H1 in the nucleus. Finally, we propose a model that may explain the functional role of H1 heterogeneity in chromatin compaction.Key words: histone H1, linker histones, chromatin organization, chromatin compaction, heat shock.

scholarly journals Site-specific ubiquitylation acts as a regulator of linker histone H1

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Eva Höllmüller ◽  
Simon Geigges ◽  
Marie L. Niedermeier ◽  
Kai-Michael Kammer ◽  
Simon M. Kienle ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Histone H1 ◽  
Linker Histone ◽  
Active Chromatin ◽  
Site Specific ◽  
Linker Histone H1 ◽  
Fundamental Process ◽  
Core Histones ◽  
Wide Scale

AbstractDecoding the role of histone posttranslational modifications (PTMs) is key to understand the fundamental process of epigenetic regulation. This is well studied for PTMs of core histones but not for linker histone H1 in general and its ubiquitylation in particular due to a lack of proper tools. Here, we report on the chemical synthesis of site-specifically mono-ubiquitylated H1.2 and identify its ubiquitin-dependent interactome on a proteome-wide scale. We show that site-specific ubiquitylation of H1 at position K64 modulates interactions with deubiquitylating enzymes and the deacetylase SIRT1. Moreover, it affects H1-dependent chromatosome assembly and phase separation resulting in a more open chromatosome conformation generally associated with a transcriptionally active chromatin state. In summary, we propose that site-specific ubiquitylation plays a general regulatory role for linker histone H1.

scholarly journals The Nuclear Actin-related Protein of Saccharomyces cerevisiae, Act3p/Arp4, Interacts with Core Histones

1999 ◽  
Vol 10 (8) ◽  
pp. 2595-2605 ◽  
Author(s):  
Masahiko Harata ◽  
Yukako Oma ◽  
Shigeki Mizuno ◽  
Yi Wei Jiang ◽  
David J. Stillman ◽  
...  
Keyword(s):  
Nuclear Actin ◽  
Histone H2a ◽  
Related Protein ◽  
The Core ◽  
Core Histones ◽  
Episomal Dna ◽  
Two Hybrid ◽  
Far Western Blot ◽  
Correct Expression

Act3p/Arp4, an essential actin-related protein ofSaccharomyces cerevisiae located within the nucleus, is, according to genetic data, involved in transcriptional regulation. In addition to the basal core structure of the actin family members, which is responsible for ATPase activity, Act3p possesses two insertions, insertions I and II, the latter of which is predicted to form a loop-like structure protruding from beyond the surface of the molecule. Because Act3p is a constituent of chromatin but itself does not bind to DNA, we hypothesized that insertion II might be responsible for an Act3p-specific function through its interaction with some other chromatin protein. Far Western blot and two-hybrid analyses revealed the ability of insertion II to bind to each of the core histones, although with somewhat different affinities. Together with our finding of coimmunoprecipitation of Act3p with histone H2A, this suggests the in vivo existence of a protein complex required for correct expression of particular genes. We also show that a conditionalact3 mutation affects chromatin structure of an episomal DNA molecule, indicating that the putative Act3p complex may be involved in the establishment, remodeling, or maintenance of chromatin structures.

scholarly journals Perfect Timing: Mobile Brain/Body Imaging scaffolds the 4E-cognition research program

2020 ◽  
Author(s):  
Francisco J. Parada ◽  
Alejandra Rossi
Keyword(s):  
Real Life ◽  
Body Imaging ◽  
The Core ◽  
4E Cognition ◽  
Body Dynamics ◽  
Brain And Behavior ◽  
And Behavior ◽  
A Current ◽  
Made In

Recent technological advancements encompassed under the Mobile Brain/Body Imaging (MoBI) framework, have produced exciting new experimental results linking mind, brain, and behavior. The main goal of the MoBI approach is to model brain and body dynamics during every-day, natural, real-life situations. However, even though considerable advances have been made in both hardware and software, technical and analytical conditions are not yet optimal. The MoBI approach is based on attaching synchronized, small, and lightweight neurobehavioral sensors to and around participants during behaviorally-measured structured, semi-structured, and unstructured settings. These sensors have yet to become fully unobtrusive or transparent. Even though a considerable technical and analytical gap still exists, acquisition of brain/body dynamics during real-world situations as well as in virtual, modified, and/or extended laboratory settings has been -in many cases- successful. Nevertheless, even if the technical/analytical gap is breached, novel hypotheses, measures, and experimental paradigms are needed in order to tackle MoBI’s ultimate goal: to model and understand cognition, behavior, and experience as it emerges and unfolds unto and from the world. Such a goal is not completely novel or unique to the MoBI framework; it is at the core of a long-standing scientific and philosophical challenge. The present work starts by briefly reviewing the historical origins of complexity in order to identify three “waves and ripples of complexity” derived from naturalist accounts to the historical brain/body problem. We furthermore argue for a current 4th wave. Finally, we offer the reader what we consider to be the main objective for the MoBI+4E framework in its quest for understanding the functional role of brain/body/world couplings in the emergence of cognition.

Part II Ambit of Protection, 6 Investment

2017 ◽  
Author(s):  
McLachlan Campbell ◽  
Shore Laurence ◽  
Weiniger Matthew
Keyword(s):  
Minority Shareholders ◽  
Central Concept ◽  
Holding Companies ◽  
Host State ◽  
The Core ◽  
Investment Treaties ◽  
Definition Of ◽  
Portfolio Investments ◽  
Made In

Chapter 6 explores the central concept of ‘investment’. It first considers the core question of the definition of ‘investment’ under the ICSID Convention and under investment treaties. It then takes up four important issues: (1) the time when an investment is made in relation to the temporal scope of the treaty protections; (2) the extent to which pre-contract investment may obtain treaty protection; (3) the place of an investment; and (4) the role of host State law in defining ‘investment’. It then analyses a set of problems that arise out of indirect investments: the relation between the losses suffered by a subsidiary in the host State and the investor’s investment; the rights of minority shareholders; claims brought by holding companies; corporate restructuring as a means to gain the advantage of investment treaties; the position of ultimate beneficiaries; and the position of portfolio investments.

Proteasome activator Blm10 regulates transcription especially during aging

2021 ◽  
Vol 22 ◽  
Author(s):  
Yu-Shan Chen ◽  
Xia Han ◽  
Kui Lin ◽  
Tian-Xia Jiang ◽  
Xiao-Bo Qiu
Keyword(s):  
Critical Role ◽  
Regulation Of Gene Expression ◽  
Cellular Aging ◽  
Yeast Cells ◽  
Histone Marks ◽  
Proteasome Activator ◽  
The Core ◽  
Core Histones ◽  
The Stability

Background: Histones are basic elements of the chromatin, and are critical to controlling chromatin structure and transcription. The proteasome activator PA200 promotes the acetylation-dependent proteasomal degradation of the core histones during spermatogenesis, DNA repair, transcription and cellular aging, and maintains the stability of histone marks. Objective: The study aimed to explore whether the yeast ortholog of PA200, Blm10, promotes degradation of the core histones during transcription and regulates transcription especially during aging. Method: Protein degradation assays were performed to detect the role of Blm10 in histone degradation during transcription. mRNA profiles were compared in WT and mutant BY4741 or MDY510 yeast cells by RNA-sequencing. Results: The core histones can be degraded by the Blm10-proteasome in the non-replicating yeast, suggesting that Blm10 promotes the transcription-coupled degradation of the core histones. Blm10 preferentially regulates transcription in aged yeast, especially transcription of genes related to translation, amino acid metabolism and carbohydrate metabolism. Mutations of Blm10 at F2125/N2126 in its putative acetyl-lysine binding region abolished the Blm10-mediated regulation of gene expression. Conclusion: Blm10 promotes degradation of the core histones during transcription and regulates transcription especially during cellular aging, further supporting the critical role of PA200 in maintaining the stability of histone marks from the evolutionary view. These results should provide meaningful insights into the mechanisms underlying aging and the related diseases.

scholarly journals Short Histone H2A Variants: Small in Stature but not in Function

Cells ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 867 ◽  
Author(s):  
Xuanzhao Jiang ◽  
Tatiana A. Soboleva ◽  
David J. Tremethick
Keyword(s):  
Chromatin Structure ◽  
Biochemical Composition ◽  
Histone Variants ◽  
Histone H2a ◽  
The Core ◽  
Unique Protein ◽  
Core Histones ◽  
The Brain ◽  
Fundamental Mechanism ◽  
The Way

The dynamic packaging of DNA into chromatin regulates all aspects of genome function by altering the accessibility of DNA and by providing docking pads to proteins that copy, repair and express the genome. Different epigenetic-based mechanisms have been described that alter the way DNA is organised into chromatin, but one fundamental mechanism alters the biochemical composition of a nucleosome by substituting one or more of the core histones with their variant forms. Of the core histones, the largest number of histone variants belong to the H2A class. The most divergent class is the designated “short H2A variants” (H2A.B, H2A.L, H2A.P and H2A.Q), so termed because they lack a H2A C-terminal tail. These histone variants appeared late in evolution in eutherian mammals and are lineage-specific, being expressed in the testis (and, in the case of H2A.B, also in the brain). To date, most information about the function of these peculiar histone variants has come from studies on the H2A.B and H2A.L family in mice. In this review, we describe their unique protein characteristics, their impact on chromatin structure, and their known functions plus other possible, even non-chromatin, roles in an attempt to understand why these peculiar histone variants evolved in the first place.

scholarly journals MNase Digestion Protection Patterns of the Linker DNA in Chromatosomes

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2239
Author(s):  
Chang-Hui Shen ◽  
James Allan
Keyword(s):  
Globin Gene ◽  
Linker Histone ◽  
Computational Studies ◽  
Core Particle ◽  
Linker Histones ◽  
Dna Accessibility ◽  
The Core ◽  
Mnase Digestion ◽  
Recent Developments ◽  
Nucleosomal Structure

The compact nucleosomal structure limits DNA accessibility and regulates DNA-dependent cellular activities. Linker histones bind to nucleosomes and compact nucleosomal arrays into a higher-order chromatin structure. Recent developments in high throughput technologies and structural computational studies provide nucleosome positioning at a high resolution and contribute to the information of linker histone location within a chromatosome. However, the precise linker histone location within the chromatin fibre remains unclear. Using monomer extension, we mapped core particle and chromatosomal positions over a core histone-reconstituted, 1.5 kb stretch of DNA from the chicken adult β-globin gene, after titration with linker histones and linker histone globular domains. Our results show that, although linker histone globular domains and linker histones display a wide variation in their binding affinity for different positioned nucleosomes, they do not alter nucleosome positions or generate new nucleosome positions. Furthermore, the extra ~20 bp of DNA protected in a chromatosome is usually symmetrically distributed at each end of the core particle, suggesting linker histones or linker histone globular domains are located close to the nucleosomal dyad axis.

scholarly journals A glitch in the snitch: the role of linker histone H1 in shaping the epigenome in normal and diseased cells

Open Biology ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 210124
Author(s):  
Ankita Saha ◽  
Yamini Dalal
Keyword(s):  
Transcription Factors ◽  
New Technologies ◽  
Harry Potter ◽  
Linker Histone ◽  
Chromatin Organization ◽  
Linker Histones ◽  
Positively Charged

Histone H1s or the linker histones are a family of dynamic chromatin compacting proteins that are essential for higher-order chromatin organization. These highly positively charged proteins were previously thought to function solely as repressors of transcription. However, over the last decade, there is a growing interest in understanding this multi-protein family, finding that not all variants act as repressors. Indeed, the H1 family members appear to have distinct affinities for chromatin and may potentially affect distinct functions. This would suggest a more nuanced contribution of H1 to chromatin organization. The advent of new technologies to probe H1 dynamics in vivo , combined with powerful computational biology, and in vitro imaging tools have greatly enhanced our knowledge of the mechanisms by which H1 interacts with chromatin. This family of proteins can be metaphorically compared to the Golden Snitch from the Harry Potter series, buzzing on and off several regions of the chromatin, in combat with competing transcription factors and chromatin remodellers, thereby critical to the epigenetic endgame on short and long temporal scales in the life of the nucleus. Here, we summarize recent efforts spanning structural, computational, genomic and genetic experiments which examine the linker histone as an unseen architect of chromatin fibre in normal and diseased cells and explore unanswered fundamental questions in the field.

scholarly journals Remodeling sperm chromatin in Xenopus laevis egg extracts: the role of core histone phosphorylation and linker histone B4 in chromatin assembly.

1994 ◽  
Vol 126 (3) ◽  
pp. 591-601 ◽  
Author(s):  
S Dimitrov ◽  
M C Dasso ◽  
A P Wolffe
Keyword(s):  
Xenopus Laevis ◽  
Sperm Nucleus ◽  
Linker Histone ◽  
Core Histone ◽  
Sperm Chromatin ◽  
Histone Phosphorylation ◽  
Egg Extracts ◽  
Core Histones ◽  
Histone Octamers

We find that the remodeling of the condensed Xenopus laevis sperm nucleus into the paternal pronucleus in egg extracts is associated with phosphorylation of the core histones H2A, H2A.X and H4, and uptake of a linker histone B4 and a HMG 2 protein. Histone B4 is required for the assembly of chromatosome structures in the pronucleus. However neither B4 nor core histone phosphorylation are required for the assembly of spaced nucleosomal arrays. We suggest that the spacing of nucleosomal arrays is determined by interaction between adjacent histone octamers under physiological assembly conditions.

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