ATRX in chromatin assembly and genome architecture during development and disease

2011 ◽  
Vol 89 (5) ◽  
pp. 435-444 ◽  
Author(s):  
Nathalie G. Bérubé
Keyword(s):  
Gene Regulation ◽  
Chromatin Remodeling ◽  
Chromatin Structure ◽  
Higher Order ◽  
Chromatin Assembly ◽  
Genome Architecture ◽  
Chromatin Conformation ◽  
Mammalian Development ◽  
Mitosis And Meiosis

The regulation of genome architecture is essential for a variety of fundamental cellular phenomena that underlie the complex orchestration of mammalian development. The ATP-dependent chromatin remodeling protein ATRX is emerging as a key regulatory component of nucleosomal dynamics and higher order chromatin conformation. Here we provide an overview of the role of ATRX at chromatin and during development, and discuss recent studies exposing a repertoire of ATRX functions at heterochromatin, in gene regulation, and during mitosis and meiosis. Exciting new progress on several fronts suggest that ATRX operates in histone variant deposition and in the modulation of higher order chromatin structure. Not surprisingly, dysfunction or absence of ATRX protein has devastating consequences on embryonic development and leads to human disease.

The role of long non-coding RNAs in chromatin structure and gene regulation: variations on a theme

2008 ◽  
Vol 389 (4) ◽  
pp. 323-331 ◽  
Author(s):  
David Umlauf ◽  
Peter Fraser ◽  
Takashi Nagano
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Chromatin Structure ◽  
Genome Architecture ◽  
Paradoxical Situation ◽  
Intergenic Regions ◽  
Non Coding Rnas ◽  
Variations On A Theme

Abstract Transcriptome studies have uncovered a plethora of non-coding RNAs (ncRNA) in mammals. Most originate within intergenic regions of the genome and recent evidence indicates that some are involved in many different pathways that ultimately act on genome architecture and gene expression. In this review, we discuss the role of well-characterized long ncRNAs in gene regulation pointing to their similarities, but also their differences. We will attempt to highlight a paradoxical situation in which transcription is needed to repress entire chromosomal domains possibly through the action of ncRNAs that create nuclear environments refractory to transcription.

Role of thyroid hormone in hepatic gene regulation, chromatin remodeling, and autophagy

2017 ◽  
Vol 458 ◽  
pp. 160-168 ◽  
Author(s):  
Brijesh Kumar Singh ◽  
Rohit Anthony Sinha ◽  
Kenji Ohba ◽  
Paul Michael Yen
Keyword(s):  
Gene Regulation ◽  
Thyroid Hormone ◽  
Chromatin Remodeling

scholarly journals β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Syed Raza Mahmood ◽  
Xin Xie ◽  
Nadine Hosny El Said ◽  
Tomas Venit ◽  
Kristin C. Gunsalus ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Chromatin Structure ◽  
Genomic Analysis ◽  
Chromatin Accessibility ◽  
Genome Architecture ◽  
Chromatin Remodelers ◽  
3D Genome ◽  
Polycomb Proteins ◽  
Crucial Component ◽  
Development And Differentiation

Abstractβ-actin is a crucial component of several chromatin remodeling complexes that control chromatin structure and accessibility. The mammalian Brahma-associated factor (BAF) is one such complex that plays essential roles in development and differentiation by regulating the chromatin state of critical genes and opposing the repressive activity of polycomb repressive complexes (PRCs). While previous work has shown that β-actin loss can lead to extensive changes in gene expression and heterochromatin organization, it is not known if changes in β-actin levels can directly influence chromatin remodeling activities of BAF and polycomb proteins. Here we conduct a comprehensive genomic analysis of β-actin knockout mouse embryonic fibroblasts (MEFs) using ATAC-Seq, HiC-seq, RNA-Seq and ChIP-Seq of various epigenetic marks. We demonstrate that β-actin levels can induce changes in chromatin structure by affecting the complex interplay between chromatin remodelers such as BAF/BRG1 and EZH2. Our results show that changes in β-actin levels and associated chromatin remodeling activities can not only impact local chromatin accessibility but also induce reversible changes in 3D genome architecture. Our findings reveal that β-actin-dependent chromatin remodeling plays a role in shaping the chromatin landscape and influences the regulation of genes involved in development and differentiation.

Structure and dynamics of the crenarchaeal nucleoid

2013 ◽  
Vol 41 (1) ◽  
pp. 321-325 ◽  
Author(s):  
Rosalie P.C. Driessen ◽  
Remus Th. Dame
Keyword(s):  
Gene Regulation ◽  
Chromatin Structure ◽  
Molecular Properties ◽  
Present Review ◽  
Structure And Dynamics ◽  
Architectural Proteins ◽  
Chromatin Proteins

Crenarchaeal genomes are organized into a compact nucleoid by a set of small chromatin proteins. Although there is little knowledge of chromatin structure in Archaea, similarities between crenarchaeal and bacterial chromatin proteins suggest that organization and regulation could be achieved by similar mechanisms. In the present review, we describe the molecular properties of crenarchaeal chromatin proteins and discuss the possible role of these architectural proteins in organizing the crenarchaeal chromatin and in gene regulation.

scholarly journals The Drosophila Mi-2 Chromatin-Remodeling Factor Regulates Higher-Order Chromatin Structure and Cohesin Dynamics In Vivo

PLoS Genetics ◽  
2012 ◽  
Vol 8 (8) ◽  
pp. e1002878 ◽  
Author(s):  
Barbara Fasulo ◽  
Renate Deuring ◽  
Magdalena Murawska ◽  
Maria Gause ◽  
Kristel M. Dorighi ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Chromatin Structure ◽  
Higher Order

scholarly journals MeCP2 and Chromatin Compartmentalization

Cells ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 878 ◽  
Author(s):  
Annika Schmidt ◽  
Hui Zhang ◽  
M. Cristina Cardoso
Keyword(s):  
Transcriptional Regulation ◽  
Rett Syndrome ◽  
Chromatin Structure ◽  
Binding Protein ◽  
Higher Order ◽  
Functional Domains ◽  
Genome Architecture

Methyl-CpG binding protein 2 (MeCP2) is a multifunctional epigenetic reader playing a role in transcriptional regulation and chromatin structure, which was linked to Rett syndrome in humans. Here, we focus on its isoforms and functional domains, interactions, modifications and mutations found in Rett patients. Finally, we address how these properties regulate and mediate the ability of MeCP2 to orchestrate chromatin compartmentalization and higher order genome architecture.

scholarly journals The role of aTp-dependent chromatin remodeling factors in chromatin assembly in vivo

2019 ◽  
Vol 23 (2) ◽  
pp. 160-167
Author(s):  
Iu. A. Il’ina ◽  
A. Yu. Konev
Keyword(s):  
Dna Repair ◽  
Chromatin Remodeling ◽  
Molecular Motor ◽  
Chromatin Assembly ◽  
Histone Chaperones ◽  
Nucleosome Assembly ◽  
Male Pronucleus ◽  
Histone Exchange

Chromatin assembly is a fundamental process essential for chromosome duplication subsequent to DNA replication. In addition, histone removal and incorporation take place constantly throughout the cell cycle in the course of DNA-utilizing processes, such as transcription, damage repair or recombination. In vitro studies have revealed that nucleosome assembly relies on the combined action of core histone chaperones and ATP-utilizing molecular motor proteins such as ACF or CHD1. Despite extensive biochemical characterization of ATP-dependent chromatin assembly and remodeling factors, it has remained unclear to what extent nucleosome assembly is an ATP-dependent process in vivo. Our original and published data about the functions of ATP-dependent chromatin assembly and remodeling factors clearly demonstrated that these proteins are important for nucleosome assembly and histone exchange in vivo. During male pronucleus reorganization after fertilization CHD1 has a critical role in the genomescale, replication-independent nucleosome assembly involving the histone variant H3.3. Thus, the molecular motor proteins, such as CHD1, function not only in the remodeling of existing nucleosomes but also in de novo nucleosome assembly from DNA and histones in vivo. ATP-dependent chromatin assembly and remodeling factors have been implicated in the process of histone exchange during transcription and DNA repair, in the maintenance of centromeric chromatin and in the loading and remodeling of nucleosomes behind a replication fork. Thus, chromatin remodeling factors are involved in the processes of both replication-dependent and replication-independent chromatin assembly. The role of these proteins is especially prominent in the processes of large-scale chromatin reorganization; for example, during male pronucleus formation or in DNA repair. Together, ATP-dependent chromatin assembly factors, histone chaperones and chromatin modifying enzymes form a “chromatin integrity network” to ensure proper maintenance and propagation of chromatin landscape.

scholarly journals The ISWI Chromatin-Remodeling Protein Is Required for Gene Expression and the Maintenance of Higher Order Chromatin Structure In Vivo

2000 ◽  
Vol 5 (2) ◽  
pp. 355-365 ◽  
Author(s):  
Renate Deuring ◽  
Laura Fanti ◽  
Jennifer A Armstrong ◽  
Melinda Sarte ◽  
Ophelia Papoulas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Remodeling ◽  
Chromatin Structure ◽  
Higher Order

scholarly journals The Role of Chromatin Structure in Gene Regulation of the Human Malaria Parasite

2017 ◽  
Vol 33 (5) ◽  
pp. 364-377 ◽  
Author(s):  
Gayani Batugedara ◽  
Xueqing M. Lu ◽  
Evelien M. Bunnik ◽  
Karine G. Le Roch
Keyword(s):  
Gene Regulation ◽  
Chromatin Structure ◽  
Malaria Parasite ◽  
Human Malaria Parasite ◽  
Human Malaria

scholarly journals ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Sharon E Torigoe ◽  
Ashok Patel ◽  
Mai T Khuong ◽  
Gregory D Bowman ◽  
James T Kadonaga
Keyword(s):  
Chromatin Remodeling ◽  
Motor Proteins ◽  
Chromatin Assembly ◽  
Histone Chaperones ◽  
Nucleosome Assembly ◽  
Periodic Arrays ◽  
Combined Action ◽  
The Relationship ◽  
Nucleosome Arrays

Chromatin assembly involves the combined action of ATP-dependent motor proteins and histone chaperones. Because motor proteins in chromatin assembly also function as chromatin remodeling factors, we investigated the relationship between ATP-driven chromatin assembly and chromatin remodeling in the generation of periodic nucleosome arrays. We found that chromatin remodeling-defective Chd1 motor proteins are able to catalyze ATP-dependent chromatin assembly. The resulting nucleosomes are not, however, spaced in periodic arrays. Wild-type Chd1, but not chromatin remodeling-defective Chd1, can catalyze the conversion of randomly-distributed nucleosomes into periodic arrays. These results reveal a functional distinction between ATP-dependent nucleosome assembly and chromatin remodeling, and suggest a model for chromatin assembly in which randomly-distributed nucleosomes are formed by the nucleosome assembly function of Chd1, and then regularly-spaced nucleosome arrays are generated by the chromatin remodeling activity of Chd1. These findings uncover an unforeseen level of specificity in the role of motor proteins in chromatin assembly.

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