Comparative Analysis of SWIRM Domain-Containing Proteins in Plants

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.

Download Full-text

Specialization of the chromatin remodeler RSC to mobilize partially-unwrapped nucleosomes

eLife ◽

10.7554/elife.58130 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 1

Author(s):

Alisha Schlichter ◽

Margaret M Kasten ◽

Timothy J Parnell ◽

Bradley R Cairns

Keyword(s):

Ribosomal Protein ◽

Chromatin Remodeling ◽

Dna Sequences ◽

Dna Binding Proteins ◽

Ribosomal Protein Genes ◽

Expression Of Genes ◽

Chromatin Remodeling Complexes ◽

Hmg Protein ◽

Better Than

SWI/SNF-family chromatin remodeling complexes, such as S. cerevisiae RSC, slide and eject nucleosomes to regulate transcription. Within nucleosomes, stiff DNA sequences confer spontaneous partial unwrapping, prompting whether and how SWI/SNF-family remodelers are specialized to remodel partially-unwrapped nucleosomes. RSC1 and RSC2 are orthologs of mammalian PBRM1 (polybromo) which define two separate RSC sub-complexes. Remarkably, in vitro the Rsc1-containing complex remodels partially-unwrapped nucleosomes much better than does the Rsc2-containing complex. Moreover, a rsc1Δ mutation, but not rsc2Δ, is lethal with histone mutations that confer partial unwrapping. Rsc1/2 isoforms both cooperate with the DNA-binding proteins Rsc3/30 and the HMG protein, Hmo1, to remodel partially-unwrapped nucleosomes, but show differential reliance on these factors. Notably, genetic impairment of these factors strongly reduces the expression of genes with wide nucleosome-deficient regions (e.g., ribosomal protein genes), known to harbor partially-unwrapped nucleosomes. Taken together, Rsc1/2 isoforms are specialized through composition and interactions to manage and remodel partially-unwrapped nucleosomes.

Download Full-text

Chromatin remodeling complexes: ATP-dependent machines in action

Biochemistry and Cell Biology ◽

10.1139/o05-115 ◽

2005 ◽

Vol 83 (4) ◽

pp. 405-417 ◽

Cited By ~ 50

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.

Download Full-text

Structure and Function of ATP-Dependent Chromatin Remodeling Complexes in Human Cancer

Blood ◽

10.1182/blood-2019-121033 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. SCI-48-SCI-48

Author(s):

Cigall Kadoch

Keyword(s):

Chromatin Remodeling ◽

Developmental Disorders ◽

Human Cancer ◽

Malignant Rhabdoid Tumor ◽

Advisory Committees ◽

Sequencing Studies ◽

Genes Encoding ◽

Therapeutic Development ◽

Chromatin Remodeling Complexes ◽

And Function

Dr. Cigall Kadoch will discuss how recent exome-and genome-wide sequencing studies in human cancers have unmasked a striking frequency of mutations in the genes encoding subunits of the mammalian SWI/SNF (mSWI/SNF) family of ATP-dependent chromatin remodeling complexes. Her laboratory uses biochemistry, structural biology, systems biology, and genomics-based approaches to define the mechanisms of chromatin and gene regulation carried out by the mSWI/SNF family of chromatin regulators. Specifically, they have studied rare, genetically well-defined pediatric cancers including synovial sarcoma, Ewing sarcoma, malignant rhabdoid tumor and others, all of which involve mSWI/SNF complex perturbations as critical drivers of their oncogenic programs. These studies have informed the diverse mechanisms underlying mSWI/SNF complex targeting and function in a wide array of cancers (including hematologic cancers) and developmental disorders and have provided new foundations for therapeutic development. Disclosures Kadoch: Foghorn Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

Download Full-text

SWR1C catalyzes H2A.Z deposition by coupling ATPase activity to the nucleosome acidic patch

10.1101/2021.12.08.471801 ◽

2021 ◽

Author(s):

Nathan Gioacchini ◽

Craig L Peterson

Keyword(s):

Atpase Activity ◽

Exchange Reaction ◽

Chromatin Remodeling ◽

Essential Role ◽

Atp Hydrolysis ◽

Histone H2a ◽

Rich Region ◽

Biochemical Assays ◽

Nucleosomal Histone ◽

Exchange Activity

The SWR1C chromatin remodeling enzyme catalyzes the ATP-dependent exchange of nucleosomal histone H2A for the histone variant H2A.Z, a key variant involved in a multitude of nuclear functions. How the 14-subunit SWR1C engages the nucleosomal substrate remains largely unknown. Numerous studies on the ISWI, CHD1, and SWI/SNF families of chromatin remodeling enzymes have demonstrated an essential role for the nucleosomal acidic patch for remodeling activity, however a role for this nucleosomal epitope in nucleosome editing by SWR1C has not been tested. Here, we employ a variety of biochemical assays to demonstrate an essential role for the nucleosomal acidic patch in the H2A.Z exchange reaction. Nucleosomes lacking acidic patch residues retain the ability to stimulate the ATPase activity of SWR1C, implicating a role in coupling the energy of ATP hydrolysis to H2A/H2B dimer eviction. A conserved arginine-rich region within the Swc5 subunit is identified that interacts with the acidic patch and is found to be essential for dimer exchange activity. Together these findings provide new insights into how SWR1C engages its nucleosomal substrate to promote efficient H2A.Z deposition.

Download Full-text

Specialization of the Chromatin Remodeler RSC to Mobilize Partially-Unwrapped Nucleosomes

10.1101/799361 ◽

2019 ◽

Author(s):

Alisha Schlichter ◽

Margaret M. Kasten ◽

Timothy J. Parnell ◽

Bradley R. Cairns

Keyword(s):

Ribosomal Protein ◽

Chromatin Remodeling ◽

Dna Sequences ◽

Dna Binding Proteins ◽

Ribosomal Protein Genes ◽

Expression Of Genes ◽

Chromatin Remodeling Complexes ◽

Hmg Protein ◽

Better Than

AbstractSWI/SNF-family chromatin remodeling complexes, such as S. cerevisiae RSC, slide and eject nucleosomes to regulate transcription. Within nucleosomes, stiff DNA sequences confer spontaneous partial unwrapping, prompting whether and how SWI/SNF-family remodelers are specialized to remodel partially-unwrapped nucleosomes. RSC1 and RSC2 are orthologs of mammalian PBRM1 (polybromo) which define two separate RSC sub-complexes. Remarkably, in vitro the Rsc1-containing complex remodels partially-unwrapped nucleosomes much better than does the Rsc2-containing complex. Moreover, a rsc1Δ mutation, but not rsc2Δ, is lethal with histone mutations that confer partial unwrapping. Rsc1/2 isoforms both cooperate with the DNA-binding proteins Rsc3/30 and the HMG protein, Hmo1, to remodel partially-unwrapped nucleosomes, but show differential reliance on these factors. Notably, genetic impairment of these factors strongly reduces the expression of genes with wide nucleosome-deficient regions (e.g. ribosomal protein genes), known to harbor partially-unwrapped nucleosomes. Taken together, Rsc1/2 isoforms are specialized through composition and interactions to manage and remodel partially-unwrapped nucleosomes.

Download Full-text

156 DIFFERENTIAL REORGANIZATION OF HISTONE ACETYLATION THROUGH ATP-DEPENDENT REMODELING FACTOR DURING PRONUCLEAR FORMATION IN PORCINE ZYGOTIC CHROMATINS

Reproduction Fertility and Development ◽

10.1071/rdv19n1ab156 ◽

2007 ◽

Vol 19 (1) ◽

pp. 195

Author(s):

G. Wee ◽

D.-B. Koo ◽

J.-S. Kim ◽

B.-S. Song ◽

J.-S. Park ◽

...

Keyword(s):

Histone Acetylation ◽

Chromatin Remodeling ◽

Atp Hydrolysis ◽

Chromatin Modification ◽

Covalent Modification ◽

Sperm Chromatin ◽

Histone H4 ◽

Histone H4 Acetylation ◽

M Phase ◽

Pronuclear Formation

ATP-dependent remodeling complexes and histone acetyltransferase/deacetylase complexes in chromatin modification can be characterized by the use of energy from ATP hydrolysis or covalent modification. But they have similar functions during the transcriptional process. After fertilization, histone acetylation in paternal and maternal chromatin is reprogrammed to obtain transcriptional activity during chromatin remodeling such as decondensation. However, these mechanisms in zygotic chromatin are poorly understood. In the present study, the reorganization process of histone H4 acetylation after fertilization was investigated through co-localization in the nucleus of ATP-dependent remodeling factors and histone acetyltransferases during parental chromatin decondensation. The molecules were monitored by immunofluorescence analysis with specific antibodies directed against AcH4K5, HAT1, P300, Tip60, Brg-1, and Mi-2. Fluorescence signals of Brg-1 and Mi-2 in porcine embryonic fibroblasts and HeLa cells co-localized with chromatin during interphase and M phase, although the Mi-2 signal existed around chromosomes at metaphase. However, Brg-1 and Mi-2 in porcine oocytes did not interact with chromosomes during meiosis, despite their existence in the oocyte cytoplasm. At 6 h after fertilization, signals of Brg-1 and Mi-2 were observed in most parental chromatin and remained until syngamy of the pronuclear stage. In histone acetylation and chromatin remodeling, acetylation of H4K5 was generated from sperm chromatin at 4 h after fertilization and preceded the appearance of Brg-1. Additionally, HAT1 showed stronger intensities compared with P300 and Tip60, correlating with acetylated-H4K5, and also appeared earlier than Brg-1. In contrast to that in sperm chromatin, Brg-1 in maternal chromatin anteceded HAT1. Consequently, paternal chromatin remodeling was completed after histone acetylation, but maternal chromatin remodeling was preceded by histone acetylation. Our findings indicate that paternal and maternal chromatin undergo differential remodeling and reprogramming during pronuclear formation, suggesting that gene expression in the chromatin of each parent may be regulated separately.

Download Full-text

ARID1A loss in neuroblastoma promotes the adrenergic-to-mesenchymal transition by regulating enhancer-mediated gene expression

Science Advances ◽

10.1126/sciadv.aaz3440 ◽

2020 ◽

Vol 6 (29) ◽

pp. eaaz3440 ◽

Cited By ~ 4

Author(s):

Hui Shi ◽

Ting Tao ◽

Brian J. Abraham ◽

Adam D. Durbin ◽

Mark W. Zimmerman ◽

...

Keyword(s):

Gene Expression ◽

Chromatin Remodeling ◽

Neuroblastoma Cells ◽

Tumor Development ◽

Mesenchymal Cell ◽

Drug Resistant ◽

Zebrafish Model ◽

Mesenchymal Transition ◽

Genes Encoding ◽

Chromatin Remodeling Complexes

Mutations in genes encoding SWI/SNF chromatin remodeling complexes are found in approximately 20% of all human cancers, with ARID1A being the most frequently mutated subunit. Here, we show that disruption of ARID1A homologs in a zebrafish model accelerates the onset and increases the penetrance of MYCN-driven neuroblastoma by increasing cell proliferation in the sympathoadrenal lineage. Depletion of ARID1A in human NGP neuroblastoma cells promoted the adrenergic-to-mesenchymal transition with changes in enhancer-mediated gene expression due to alterations in the genomic occupancies of distinct SWI/SNF assemblies, BAF and PBAF. Our findings indicate that ARID1A is a haploinsufficient tumor suppressor in MYCN-driven neuroblastoma, whose depletion enhances tumor development and promotes the emergence of the more drug-resistant mesenchymal cell state.

Download Full-text

ATP-Dependent Chromatin Remodeling Complex in the Lineage Specification of Mesenchymal Stem Cells

Stem Cells International ◽

10.1155/2020/8839703 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Wen Du ◽

Daimo Guo ◽

Wei Du

Keyword(s):

Stem Cells ◽

Mesenchymal Stem Cells ◽

Chromatin Remodeling ◽

Cardiac Tissue ◽

Gene Expression Regulation ◽

Atp Hydrolysis ◽

Transcriptional Level ◽

Lineage Specification ◽

Chromatin Remodelers ◽

Chromatin Remodeling Complexes

Mesenchymal stem cells (MSCs) present in multiple tissues can self-renew and differentiate into multiple lineages including the bone, cartilage, muscle, cardiac tissue, and connective tissue. Key events, including cell proliferation, lineage commitment, and MSC differentiation, are ensured by precise gene expression regulation. ATP-dependent chromatin alteration is one form of epigenetic modifications that can regulate the transcriptional level of specific genes by utilizing the energy from ATP hydrolysis to reorganize chromatin structure. ATP-dependent chromatin remodeling complexes consist of a variety of subunits that together perform multiple functions in self-renewal and lineage specification. This review highlights the important role of ATP-dependent chromatin remodeling complexes and their different subunits in modulating MSC fate determination and discusses the proposed mechanisms by which ATP-dependent chromatin remodelers function.

Download Full-text

Cardiac enriched BAF chromatin remodeling complex subunit Baf60c regulates gene expression programs essential for heart development and function

10.1101/184143 ◽

2017 ◽

Author(s):

Xin Sun ◽

Swetansu K. Hota ◽

Yu-Qing Zhou ◽

Stefanie Novak ◽

Dario Miguel-Perez ◽

...

Keyword(s):

Gene Expression ◽

Chromatin Remodeling ◽

Heart Development ◽

Gene Networks ◽

Contractile Function ◽

Conditional Deletion ◽

Genes Encoding ◽

Organ Specific ◽

Chromatin Remodeling Complexes ◽

And Function

AbstractHow gene networks controlling organ-specific properties are modulated by chromatin remodeling complexes is not well understood. Baf60c (Smarcd3) encodes a cardiac-enriched subunit of the SWI/SNF-like BAF chromatin complex. Its role throughout heart development is not fully understood. We show that constitutive loss of Baf60c leads to embryonic cardiac hypoplasia and pronounced cardiac dysfunction. Conditional deletion of Baf60c in cardiomyocytes results in postnatal dilated cardiomyopathy with impaired contractile function. Baf60c regulates a gene expression program that includes genes encoding contractile proteins, modulators of sarcomere function, and cardiac metabolic genes. Many of the genes deregulated in Baf60c null embryos are targets of the MEF2/SRF co-factor Myocardin (MYOCD). In a yeast two-hybrid screen we identify MYOCD as a BAF60c interacting factor; we show that BAF60c and MYOCD directly and functionally interact. We conclude that Baf60c is essential for coordinating a program of gene expression that regulates the fundamental functional properties of cardiomyocytes.

Download Full-text