Chromatin remodeling complexes: ATP-dependent machines in action

2005 ◽  
Vol 83 (4) ◽  
pp. 405-417 ◽  
Author(s):  
Cotteka N Johnson ◽  
Nicholas L Adkins ◽  
Philippe Georgel
Keyword(s):  
Chromatin Remodeling ◽  
Atp Hydrolysis ◽  
Nucleosome Remodeling ◽  
Core Histones ◽  
Associated Proteins ◽  
Chromatin Template ◽  
Chromatin Remodeling Complexes ◽  
The Individual ◽  
Insight Into

Since the initial characterization of chromatin remodeling as an ATP-dependent process, many studies have given us insight into how nucleosome-remodeling complexes can affect various nuclear functions. However, the multistep DNA-histone remodeling process has not been completely elucidated. Although new studies are published on a nearly weekly basis, the nature and roles of interactions of the individual SWI/SNF- and ISWI-based remodeling complexes and DNA, core histones, and other chromatin-associated proteins are not fully understood. In addition, the potential changes associated with ATP recruitment and its subsequent hydrolysis have not been fully characterized. This review explores possible mechanisms by which chromatin-remodeling complexes are recruited to specific loci, use ATP hydrolysis to achieve actual remodeling through disruption of DNA-histone interactions, and are released from their chromatin template. We propose possible roles for ATP hydrolysis in a chromatin-release/target-scanning process that offer an alternative to or complement the often overlooked function of delivering the energy required for sliding or dislodging specific subsets of core histones.Key words: chromatin remodeling, SWI/SNF, ISWI, APT hydrolysis.

scholarly journals Identification and Functional Characterization of Protest SWI/SNF and ISWI Complexes

2021 ◽  
Author(s):  
Alejandro Saettone Chipana
Keyword(s):  
Chromatin Remodeling ◽  
Tetrahymena Thermophila ◽  
Affinity Purification ◽  
Functional Characterization ◽  
Peptide Array ◽  
Interacting Proteins ◽  
Silent Chromatin ◽  
Lysine Residues ◽  
Chromatin Remodeling Complexes

The thesis aims to identify and initiate functional characterization of the SWI/SNF and ISWI complexes in Tetrahymena thermophila. Through affinity purification of the conserved subunit Snf5 followed by mass spectrometry (AP-MS), I identified the first SWI/SNF complex in protists. One of the subunits I found is a small bromodomain containing protein named Ibd1. Through AP-MS of Ibd1 I found Ibd1 is versatile and interacts with several additional chromatin remodeling complexes. Bromodomains are known to have affinity for acetylated lysine residues within proteins such as histones. A peptide array experiment suggests that Ibd1 also has affinity for acetylated chromatin. Indirect immunofluorescence (IF) of Ibd1 hints at a role in transcription. My analysis of Tetrahymena Iswi1 shows expression during meiosis, vegetative growth and starvation. IF data shows its localization is consistent with Iswi1 function in mitosis/meiosis or maintenance of silent chromatin. AP-MS of ISW1 discovered several interacting proteins of unknown function.

scholarly journals Comparative Analysis of SWIRM Domain-Containing Proteins in Plants

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Yan Gao ◽  
Songguang Yang ◽  
Lianyu Yuan ◽  
Yuhai Cui ◽  
Keqiang Wu
Keyword(s):  
Chromatin Remodeling ◽  
Essential Role ◽  
Atp Hydrolysis ◽  
Chromatin Modification ◽  
Dna Binding Proteins ◽  
Plant Responses ◽  
Chromosomal Proteins ◽  
Genes Encoding ◽  
Chromatin Remodeling Complexes ◽  
Affect Gene Expression

Chromatin-remodeling complexes affect gene expression by using the energy of ATP hydrolysis to locally disrupt or alter the association of histones with DNA. SWIRM (Swi3p, Rsc8p, and Moira) domain is an alpha-helical domain of about 85 residues in chromosomal proteins. SWIRM domain-containing proteins make up large multisubunit complexes by interacting with other chromatin modification factors and may have an important function in plants. However, little is known about SWIRM domain-containing proteins in plants. In this study, 67 SWIRM domain-containing proteins from 6 plant species were identified and analyzed. Plant SWIRM domain proteins can be divided into three distinct types: Swi-type, LSD1-type, and Ada2-type. Generally, the SWIRM domain forms a helix-turn-helix motif commonly found in DNA-binding proteins. The genes encoding SWIRM domain proteins inOryza sativaare widely expressed, especially in pistils. In addition,OsCHB701andOsHDMA701were downregulated by cold stress, whereasOsHDMA701andOsHDMA702were significantly induced by heat stress. These observations indicate that SWIRM domain proteins may play an essential role in plant development and plant responses to environmental stress.

scholarly journals The characterization of amphibian nucleoplasmins yields new insight into their role in sperm chromatin remodeling

BMC Genomics ◽  
2006 ◽  
Vol 7 (1) ◽  
Author(s):  
Lindsay J Frehlick ◽  
José María Eirín-López ◽  
Erin D Jeffery ◽  
Donald F Hunt ◽  
Juan Ausió
Keyword(s):  
Chromatin Remodeling ◽  
Sperm Chromatin ◽  
Insight Into

scholarly journals CHD4-NURD controls spermatogonia survival and differentiation

2019 ◽  
Author(s):  
Rodrigo O. de Castro ◽  
Victor Goitea ◽  
Luciana Previato ◽  
Agustin Carbajal ◽  
Courtney T. Griffin ◽  
...  
Keyword(s):  
Germ Cell ◽  
Cell Survival ◽  
Chromatin Remodeling ◽  
Male Gamete ◽  
Stem Cell Population ◽  
Nurd Complex ◽  
Nucleosome Remodeling ◽  
Testis Development ◽  
Expression Of Genes ◽  
Chromatin Remodeling Complexes

AbstractTestis development and sustained germ cell production in adults rely on the establishment of spermatogonia stem cells and their proper differentiation into mature gametes. Control of these processes involves not only promoting the expression of genes required for cell survival and differentiation but also repressing other cell fates. This level of transcriptional control requires chromatin-remodeling complexes that restrict or promote transcription machinery. Here, we investigated the roles of the NUcleosome Remodeling and Deacetylase (NURD) complex during spermatogenesis. Our cellular and biochemical analyses revealed differential expression and composition of NURD subunits in gametocytes at different stages of testis development. Germ cell-specific deletion of the NURD catalytic component CHD4, but not CHD3, resulted in arrested early gamete development due to failed cell survival of the undifferentiated spermatogonia stem cell population. Genome-wide CHD4 chromatin localization and transcriptomic analyses revealed that CHD4 binds the promoters and regulates the expression of genes involved in spermatogonia cell survival and differentiation. These results uncover the requirements of CHD4 in mammalian gonad development, and point to unique roles for the NURD complex with respect to other chromatin remodelers during gamete development.Significance StatementGametogenesis is a fundamental developmental program required for sustained fertility and survival of all sexually reproducing species. The developing male gamete undergoes numerous cell divisions and developmental stage transitions that are carefully monitored by epigenetic mechanisms. One prominent mechanism is directed by chromatin remodeling complexes, which modify chromatin structure and thereby control fundamental cellular processes such as gene transcription. In this work, we focused in understanding the role of CHD4 and CHD3 proteins, catalytic subunits of the NURD chromatin-remodeling complex, in mouse gametogenesis. We find that CHD4 has an essential function in gametogenesis, with an absolute requirement for survival of spermatogonia populations in the developing testis. This is accompanied by CHD4-mediated transcriptional regulation of genes important for spermatogonia survival, and differentiation.

scholarly journals Identification and Characterization of Tomato SWI3-Like Proteins: Overexpression of SlSWIC Increases the Leaf Size in Transgenic Arabidopsis

2019 ◽  
Vol 20 (20) ◽  
pp. 5121 ◽  
Author(s):  
Zhongyi Zhao ◽  
Tao Li ◽  
Xiuling Peng ◽  
Keqiang Wu ◽  
Songguang Yang
Keyword(s):  
Chromatin Remodeling ◽  
Transgenic Arabidopsis ◽  
Expression Patterns ◽  
Cold Treatment ◽  
Leaf Size ◽  
Localization Analysis ◽  
Chromatin Remodeling Complexes ◽  
Mating Type Switching ◽  
Identification And Characterization

As the subunits of the SWI/SNF (mating-type switching (SWI) and sucrose nonfermenting (SNF)) chromatin-remodeling complexes (CRCs), Swi3-like proteins are crucial to chromatin remodeling in yeast and human. Growing evidence indicate that AtSWI3s are also essential for development and response to hormones in Arabidopsis. Nevertheless, the biological functions of Swi3-like proteins in tomato (Solanum lycopersicum) have not been investigated. Here we identified four Swi3-like proteins from tomato, namely SlSWI3A, SlSWI3B, SlSWI3C, and SlSWI3D. Subcellular localization analysis revealed that all SlSWI3s are localized in the nucleus. The expression patterns showed that all SlSWI3s are ubiquitously expressed in all tissues and organs, and SlSWI3A and SlSWI3B can be induced by cold treatment. In addition, we found that SlSWI3B can form homodimers with itself and heterodimers with SlSWI3A and SlSWI3C. SlSWI3B can also interact with SlRIN and SlCHR8, two proteins involved in tomato reproductive development. Overexpression of SlSWI3C increased the leaf size in transgenic Arabidopsis with increased expression of GROWTH REGULATING FACTORs, such as GRF3, GRF5, and GRF6. Taken together, our results indicate that SlSWI3s may play important roles in tomato growth and development.

scholarly journals Structure of theArabidopsisTOPLESS corepressor provides insight into the evolution of transcriptional repression

2017 ◽  
Vol 114 (30) ◽  
pp. 8107-8112 ◽  
Author(s):  
Raquel Martin-Arevalillo ◽  
Max H. Nanao ◽  
Antoine Larrieu ◽  
Thomas Vinos-Poyo ◽  
David Mast ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Transcriptional Repression ◽  
Site Directed Mutagenesis ◽  
Crystallographic Structure ◽  
Hormone Signaling ◽  
Chromatin Remodeling Complexes ◽  
Insight Into ◽  
Similar Domain

Transcriptional repression involves a class of proteins called corepressors that link transcription factors to chromatin remodeling complexes. In plants such asArabidopsis thaliana, the most prominent corepressor is TOPLESS (TPL), which plays a key role in hormone signaling and development. Here we present the crystallographic structure of theArabidopsisTPL N-terminal region comprising the LisH and CTLH (C-terminal to LisH) domains and a newly identified third region, which corresponds to a CRA domain. Comparing the structure of TPL with the mammalian TBL1, which shares a similar domain structure and performs a parallel corepressor function, revealed that the plant TPLs have evolved a new tetramerization interface and unique and highly conserved surface for interaction with repressors. Using site-directed mutagenesis, we validated those surfaces in vitro and in vivo and showed that TPL tetramerization and repressor binding are interdependent. Our results illustrate how evolution used a common set of protein domains to create a diversity of corepressors, achieving similar properties with different molecular solutions.

The basic structure of chromatin

2019 ◽  
pp. 7-16
Author(s):  
John C. Lucchesi
Keyword(s):  
Dna Replication ◽  
Chromatin Remodeling ◽  
Functional State ◽  
Basic Structure ◽  
Chromatin Fiber ◽  
Damage Repair ◽  
Core Histones ◽  
Chromatin Remodeling Complexes ◽  
Degree Of Condensation ◽  
Active Genes

In cells, DNA is associated with histones, non-histone proteins and RNA in a complex referred to as chromatin. Four different types of histones form octamers (nucleosomes), around which DNA is wrapped yielding a chromatin fiber with the configuration of “beads on a string.” Disassembly, followed by reassembly, of this structure occurs during DNA replication, damage repair and transcription. Core histones are replication-coupled; variants are replication-independent. Positioning of nucleosomes on the chromatin fiber is mediated by chromatin remodeling complexes and reflects the functional state of various regions along the fiber. Various biophysical methods have been utilized to study the physical association of nucleosomes and DNA. Chromatin can be differentiated on the basis of the activity of the genes that are present in a given region. Heterochromatin represents repressed or inactive regions of the genome and exhibits a greater degree of condensation than euchromatin, which refers to more unwound regions where active genes are located. The two types of chromatin are present in different nuclear locations.

scholarly journals Differential Targeting of Two Distinct SWI/SNF-Related Drosophila Chromatin-Remodeling Complexes

2004 ◽  
Vol 24 (8) ◽  
pp. 3077-3088 ◽  
Author(s):  
Lisette Mohrmann ◽  
Karin Langenberg ◽  
Jeroen Krijgsveld ◽  
Arnoud J. Kal ◽  
Albert J. R. Heck ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Polytene Chromosomes ◽  
Distribution Patterns ◽  
Human Cells ◽  
Genome Wide ◽  
Larval Salivary Gland ◽  
Associated Proteins ◽  
Chromatin Remodeling Complexes ◽  
Distinct Distribution

ABSTRACT The SWI/SNF family of ATP-dependent chromatin-remodeling factors plays a central role in eukaryotic transcriptional regulation. In yeast and human cells, two subclasses have been recognized: one comprises yeast SWI/SNF and human BAF, and the other includes yeast RSC and human PBAF. Therefore, it was puzzling that Drosophila appeared to contain only a single SWI/SNF-type remodeler, the Brahma (BRM) complex. Here, we report the identification of two novel BRM complex-associated proteins: Drosophila Polybromo and BAP170, a conserved protein not described previously. Biochemical analysis established that Drosophila contains two distinct BRM complexes: (i) the BAP complex, defined by the presence of OSA and the absence of Polybromo and BAP170, and (ii) the PBAP complex, containing Polybromo and BAP170 but lacking OSA. Determination of the genome-wide distributions of OSA and Polybromo on larval salivary gland polytene chromosomes revealed that BAP and PBAP display overlapping but distinct distribution patterns. Both complexes associate predominantly with regions of open, hyperacetylated chromatin but are largely excluded from Polycomb-bound repressive chromatin. We conclude that, like yeast and human cells, Drosophila cells express two distinct subclasses of the SWI/SNF family. Our results support a close reciprocity of chromatin regulation by ATP-dependent remodelers and histone-modifying enzymes.

Solid-State Carbon-13 NMR Studies of Vulcanized Elastomers. VII. Sulfur-Vulcanized Cis-1,4 Polybutadiene at 75.5 Mhz

1989 ◽  
Vol 62 (5) ◽  
pp. 908-927 ◽  
Author(s):  
R. S. Clough ◽  
J. L. Koenig
Keyword(s):  
Solid State ◽  
Nmr Spectroscopy ◽  
Chemical Shifts ◽  
Chemical Information ◽  
Chemical Probes ◽  
Nmr Studies ◽  
Nmr Characterization ◽  
The Individual ◽  
Insight Into

Abstract Solid-state C-13 NMR spectroscopy provides a wealth of chemical information concerning sulfur-vulcanized cis-l,4-polybutadiene. New resonances which appear upon curing have chemical shifts which are expected for crosslink and cyclic structures. The DEPT experiment with MAS worked well for the polybutadiene vulcanizate in the solid state. DEPT is very useful as an aid in the assignment of structures to resonances. The new resonances can be assigned to more than one type of structure given only chemical shift and DEPT information. Swelling measurements indicate the majority of the resonances are due to cyclics. Further work involving C-13 NMR characterization of polybutadiene vulcanizates treated with chemical probes and vulcanizates cured with organic accelerators should provide insight into the specific structures responsible for the individual resonances.

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