Rvb1–Rvb2: essential ATP-dependent helicases for critical complexesThis paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (1) ◽  
pp. 29-40 ◽  
Author(s):  
Jennifer Huen ◽  
Yoshito Kakihara ◽  
Francisca Ugwu ◽  
Kevin L. Y. Cheung ◽  
Joaquin Ortega ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Homo Sapiens ◽  
Peer Review Process ◽  
Cellular Processes ◽  
Damage Repair ◽  
Wide Range ◽  
Chromatin Remodeling Complexes ◽  
Polycomb Repressive Complex 1 ◽  
Brahma Complex ◽  
Regulation Of Growth

Rvb1 and Rvb2 are highly conserved, essential AAA+ helicases found in a wide range of eukaryotes. The versatility of these helicases and their central role in the biology of the cell is evident from their involvement in a wide array of critical cellular complexes. Rvb1 and Rvb2 are components of the chromatin-remodeling complexes INO80, Swr-C, and BAF. They are also members of the histone acetyltransferase Tip60 complex, and the recently identified R2TP complex present in Saccharomyces cerevisiae and Homo sapiens; a complex that is involved in small nucleolar ribonucleoprotein (snoRNP) assembly. Furthermore, in humans, Rvb1 and Rvb2 have been identified in the URI prefoldin-like complex. In Drosophila, the Polycomb Repressive complex 1 contains Rvb2, but not Rvb1, and the Brahma complex contains Rvb1 and not Rvb2. Both of these complexes are involved in the regulation of growth and development genes in Drosophila. Rvbs are therefore crucial factors in various cellular processes. Their importance in chromatin remodeling, transcription regulation, DNA damage repair, telomerase assembly, mitotic spindle formation, and snoRNP biogenesis is discussed in this review.

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 SWR1 Chromatin Remodeling Complex: A Key Transcriptional Regulator in Plants

Cells ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 1621 ◽  
Author(s):  
Mohammad Aslam ◽  
Beenish Fakher ◽  
Bello Hassan Jakada ◽  
Shijiang Cao ◽  
Yuan Qin
Keyword(s):  
Chromatin Remodeling ◽  
Dna Accessibility ◽  
Physiological Processes ◽  
Chromatin Remodeling Complex ◽  
Damage Repair ◽  
Eukaryotic Chromatin ◽  
Chromatin Remodeling Complexes ◽  
Cellular Machinery ◽  
Environmental Responses

The nucleosome is the structural and fundamental unit of eukaryotic chromatin. The chromatin remodeling complexes change nucleosome composition, packaging and positioning to regulate DNA accessibility for cellular machinery. SWI2/SNF2-Related 1 Chromatin Remodeling Complex (SWR1-C) belongs to the INO80 chromatin remodeling family and mainly catalyzes the exchange of H2A-H2B with the H2A.Z-H2B dimer. The replacement of H2A.Z into nucleosomes affects nucleosome stability and chromatin structure. Incorporation of H2A.Z into the chromatin and its physiochemical properties play a key role in transcriptional regulation during developmental and environmental responses. In Arabidopsis, various studies have uncovered several pivotal roles of SWR1-C. Recently, notable progress has been achieved in understanding the role of SWR1-C in plant developmental and physiological processes such as DNA damage repair, stress tolerance, and flowering time. The present article introduces the SWR1-C and comprehensively reviews recent discoveries made in understanding the function of the SWR1 complex in plants.

Connection between histone H2A variants and chromatin remodeling complexesThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 35-50 ◽  
Author(s):  
Mohammed Altaf ◽  
Andréanne Auger ◽  
Marcela Covic ◽  
Jacques Côté
Keyword(s):  
Chromatin Remodeling ◽  
Chromatin Structure ◽  
Cellular Response ◽  
Peer Review Process ◽  
Histone Variants ◽  
Histone H2a ◽  
Chromatin Dynamics ◽  
Recent Developments ◽  
Chromatin Remodeling Complexes ◽  
And Function

The organization of the eukaryotic genome into chromatin makes it inaccessible to the factors required for gene transcription and DNA replication, recombination, and repair. In addition to histone-modifying enzymes and ATP-dependent chromatin remodeling complexes, which play key roles in regulating many nuclear processes by altering the chromatin structure, cells have developed a mechanism of modulating chromatin structure by incorporating histone variants. These variants are incorporated into specific regions of the genome throughout the cell cycle. H2A.Z, which is an evolutionarily conserved H2A variant, performs several seemingly unrelated and even contrary functions. Another H2A variant, H2A.X, plays a very important role in the cellular response to DNA damage. This review summarizes the recent developments in our understanding of the role of H2A.Z and H2A.X in the regulation of chromatin structure and function, focusing on their functional links with chromatin modifying and remodeling complexes.

scholarly journals FBXO32 links ubiquitination to epigenetic reprograming of melanoma cells

2021 ◽  
Author(s):  
Nadia Habel ◽  
Najla El-Hachem ◽  
Frédéric Soysouvanh ◽  
Hanene Hadhiri-Bzioueche ◽  
Serena Giuliano ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Target Gene ◽  
Tumor Development ◽  
Melanoma Cells ◽  
Complex Activity ◽  
Cellular Processes ◽  
Chromatin Remodeling Complex ◽  
Chromatin Remodeling Complexes ◽  
Proliferation And Invasion

AbstractUbiquitination by serving as a major degradation signal of proteins, but also by controlling protein functioning and localization, plays critical roles in most key cellular processes. Here, we show that MITF, the master transcription factor in melanocytes, controls ubiquitination in melanoma cells. We identified FBXO32, a component of the SCF E3 ligase complex as a new MITF target gene. FBXO32 favors melanoma cell migration, proliferation, and tumor development in vivo. Transcriptomic analysis shows that FBXO32 knockdown induces a global change in melanoma gene expression profile. These include the inhibition of CDK6 in agreement with an inhibition of cell proliferation and invasion upon FBXO32 silencing. Furthermore, proteomic analysis identifies SMARC4, a component of the chromatin remodeling complexes BAF/PBAF, as a FBXO32 partner. FBXO32 and SMARCA4 co-localize at loci regulated by FBXO32, such as CDK6 suggesting that FBXO32 controls transcription through the regulation of chromatin remodeling complex activity. FBXO32 and SMARCA4 are the components of a molecular cascade, linking MITF to epigenetics, in melanoma cells.

scholarly journals Chromatin remodeling factor CECR2 forms tissue-specific complexes with CCAR2 and LUZP1

2021 ◽  
Author(s):  
Farshad Niri ◽  
Alaina Terpstra ◽  
Kenji Rowel Quintana Lim ◽  
Heather McDermid
Keyword(s):  
Chromatin Remodeling ◽  
Neural Tube ◽  
Es Cells ◽  
Embryonic Stem ◽  
Neural Tube Closure ◽  
Loss Of Function ◽  
Cellular Processes ◽  
Novel Proteins ◽  
Chromatin Remodeling Complexes ◽  
And Function

Chromatin remodeling complexes alter chromatin structure to control access to DNA and therefore control cellular processes such as transcription, DNA replication, and DNA repair. CECR2 is a chromatin remodeling factor that plays an important role in neural tube closure and reproduction. Loss-of-function mutations in Cecr2 result primarily in the perinatal lethal neural tube defect exencephaly, with non-penetrant mice that survive to adulthood exhibiting subfertility. CECR2 forms a complex with ISWI proteins SMARCA5 and/or SMARCA1, but further information on the structure and function of the complex is not known. We therefore have identified candidate components of the CECR2-containing remodeling factor (CERF) complex in embryonic stem (ES) cells through mass spectroscopy. Both SMARCA5 and SMARCA1 were confirmed to be present in CERF complexes in ES cells and testis. However, novel proteins CCAR2 and LUZP1 are CERF components in ES cells but not testis. This tissue specificity in mice suggests these complexes may also have functional differences. Furthermore, LUZP1, loss of which is also associated with exencephaly, appears to play a role in stabilizing the CERF complex in ES cells. Keywords: CECR2, LUZP1, CCAR2, Chromatin remodeling factor, Neural tube defects

scholarly journals Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1884
Author(s):  
Galina Smolikova ◽  
Ksenia Strygina ◽  
Ekaterina Krylova ◽  
Tatiana Leonova ◽  
Andrej Frolov ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Seed Germination ◽  
Chromatin Remodeling ◽  
Hormonal Regulation ◽  
Seed Maturation ◽  
Post Translational Modifications ◽  
Epigenetic Methylation ◽  
Chromatin Remodeling Complexes ◽  
Abscisic Acid Insensitive3 ◽  
Polycomb Repressive Complex 1

Transition from seed to seedling is one of the critical developmental steps, dramatically affecting plant growth and viability. Before plants enter the vegetative phase of their ontogenesis, massive rearrangements of signaling pathways and switching of gene expression programs are required. This results in suppression of the genes controlling seed maturation and activation of those involved in regulation of vegetative growth. At the level of hormonal regulation, these events are controlled by the balance of abscisic acid and gibberellins, although ethylene, auxins, brassinosteroids, cytokinins, and jasmonates are also involved. The key players include the members of the LAFL network—the transcription factors LEAFY COTYLEDON1 and 2 (LEC 1 and 2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (FUS3), as well as DELAY OF GERMINATION1 (DOG1). They are the negative regulators of seed germination and need to be suppressed before seedling development can be initiated. This repressive signal is mediated by chromatin remodeling complexes—POLYCOMB REPRESSIVE COMPLEX 1 and 2 (PRC1 and PRC2), as well as PICKLE (PKL) and PICKLE-RELATED2 (PKR2) proteins. Finally, epigenetic methylation of cytosine residues in DNA, histone post-translational modifications, and post-transcriptional downregulation of seed maturation genes with miRNA are discussed. Here, we summarize recent updates in the study of hormonal and epigenetic switches involved in regulation of the transition from seed germination to the post-germination stage.

The molecular basis of chromatin dynamics during nucleotide excision repairThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 265-272 ◽  
Author(s):  
Ling Zhang ◽  
Kristi Jones ◽  
Feng Gong
Keyword(s):  
Chromatin Remodeling ◽  
Molecular Basis ◽  
Excision Repair ◽  
Peer Review Process ◽  
Critical Role ◽  
Chromatin Dynamics ◽  
Nucleotide Excision ◽  
Chromatin Remodeling Complexes

The assembly of DNA into chromatin in eukaryotic cells affects all DNA-related cellular activities, such as replication, transcription, recombination, and repair. Rearrangement of chromatin structure during nucleotide excision repair (NER) was discovered more than 2 decades ago. However, the molecular basis of chromatin dynamics during NER remains undefined. Pioneering studies in the field of gene transcription have shown that ATP-dependent chromatin-remodeling complexes and histone-modifying enzymes play a critical role in chromatin dynamics during transcription. Similarly, recent studies have demonstrated that the SWI/SNF chromatin-remodeling complex facilitates NER both in vitro and in vivo. Additionally, histone acetylation has also been linked to the NER of ultraviolet light damage. In this article, we will discuss the role of these identified chromatin-modifying activities in NER.

scholarly journals Yeast Isw1p Forms Two Separable Complexes In Vivo

2003 ◽  
Vol 23 (1) ◽  
pp. 80-91 ◽  
Author(s):  
Jay C. Vary, ◽  
Vamsi K. Gangaraju ◽  
Jun Qin ◽  
Carolyn Church Landel ◽  
Charles Kooperberg ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcriptional Regulation ◽  
Chromatin Remodeling ◽  
Elevated Temperatures ◽  
Cellular Processes ◽  
Biochemical Assays ◽  
Associated Proteins ◽  
Chromatin Remodeling Complexes ◽  
Specific Activities

ABSTRACT There are several classes of ATP-dependent chromatin remodeling complexes, which modulate the structure of chromatin to regulate a variety of cellular processes. The budding yeast, Saccharomyces cerevisiae, encodes two ATPases of the ISWI class, Isw1p and Isw2p. Previously Isw1p was shown to copurify with three other proteins. Here we identify these associated proteins and show that Isw1p forms two separable complexes in vivo (designated Isw1a and Isw1b). Biochemical assays revealed that while both have equivalent nucleosome-stimulated ATPase activities, Isw1a and Isw1b differ in their abilities to bind to DNA and nucleosomal substrates, which possibly accounts for differences in specific activities in nucleosomal spacing and sliding. In vivo, the two Isw1 complexes have overlapping functions in transcriptional regulation of some genes yet distinct functions at others. In addition, these complexes show different contributions to cell growth at elevated temperatures.

scholarly journals The Roles of Hippo Signaling Transducers Yap and Taz in Chromatin Remodeling

Cells ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 502 ◽  
Author(s):  
Ryan E. Hillmer ◽  
Brian A. Link
Keyword(s):  
Chromatin Remodeling ◽  
Transcriptional Control ◽  
Target Genes ◽  
Hippo Signaling ◽  
Major Pathway ◽  
Nucleosome Remodeling ◽  
Cellular Processes ◽  
Disease States ◽  
Chromatin Remodeling Complexes ◽  
Dna Packing

Hippo signaling controls cellular processes that ultimately impact organogenesis and homeostasis. Consequently, disease states including cancer can emerge when signaling is deregulated. The major pathway transducers Yap and Taz require cofactors to impart transcriptional control over target genes. Research into Yap/Taz-mediated epigenetic modifications has revealed their association with chromatin-remodeling complex proteins as a means of altering chromatin structure, therefore affecting accessibility and activity of target genes. Specifically, Yap/Taz have been found to associate with factors of the GAGA, Ncoa6, Mediator, Switch/sucrose nonfermentable (SWI/SNF), and Nucleosome Remodeling and Deacetylase (NuRD) chromatin-remodeling complexes to alter the accessibility of target genes. This review highlights the different mechanisms by which Yap/Taz collaborate with other factors to modify DNA packing at specific loci to either activate or repress target gene transcription.

scholarly journals WSTF does it all: a multifunctional protein in transcription, repair, and replicationThis paper is one of a selection of papers published in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2011 ◽  
Vol 89 (1) ◽  
pp. 12-23 ◽  
Author(s):  
Chris Barnett ◽  
Jocelyn E. Krebs
Keyword(s):  
Chromatin Remodeling ◽  
Peer Review Process ◽  
Vitamin D Metabolism ◽  
Multifunctional Protein ◽  
Molecular Events ◽  
Chromatin Remodeling Complexes ◽  
A Subunit ◽  
Histone Kinase ◽  
Polymerase I ◽  
Selection Of

Williams syndrome transcription factor (WSTF) has emerged as an incredibly versatile nuclear protein. WSTF and the ATP-dependent chromatin remodeling complexes in which it exists, WINAC, WICH, and B-WICH, have been studied in a variety of organisms. This research has revealed roles for WSTF in a number of diverse molecular events. WSTF function includes chromatin assembly, RNA polymerase I and III gene regulation, vitamin D metabolism, and DNA repair. In addition to functioning as a subunit of several ATP-dependent chromatin remodeling complexes, WSTF binds specifically to acetylated histones and is itself a histone kinase as well as a target of phosphorylation. This review will describe the three known WSTF-containing complexes and discuss their various roles as well as mechanisms of regulating WSTF activity.

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