Chromatin Remodeling Mechanisms Research Articles

Stress-Mediated Alterations in Chromatin Architecture Correlate with Down-Regulation of a Gene Encoding 60S rpL32 in Rice

Several ribosomal proteins are down-regulated at the translational, post-transcriptional and transcriptional level in response to abiotic stress, resulting in retardation of growth and productivity in various plants. However, transcriptional mechanisms associated with the stress-mediated down-regulation of such genes have not been well studied. Recently, we reported salt-responsive transcriptional down-regulation of a gene encoding 60S ribosomal protein L32, rpL32_8.1, in rice. In the present work, chromatin remodeling mechanisms associated with down-regulation of this gene under salt stress have been studied. The data obtained from the sodium bisulfite sequencing of a genomic region containing portions of the promoter and 5'-untranslated region of rpL32_8.1 exclude a role for DNA methylation in this down-regulation event. Fine mapping of the first nucleosome after the transcription start site (TSS) revealed its occupancy over the TSS to a greater extent under salt stress than that observed in a controlled environment, possibly causing a hindrance to transcription initiation during its down-regulation. Using chromatin immunoprecipitation, it was observed that histone modifications that are generally associated with highly active genes were markedly reduced under stress conditions at the 5' end region of this gene under salt stress. By applying a modified chromatin conformation capture (mCCC) technique, promoter-terminator interaction was detected for this gene under control conditions. The efficiency of this interaction was diminished under salt stress. This work indicates that the stress-responsive transcriptional down-regulation of rpL32_8.1 is accompanied by alterations in nucleosome positioning, histone modification and gene looping, but not DNA methylation.

BRCA/FA and NFκB signaling: mechanisms of chromatin remodeling and chemical resistance

BRCA/FA and NFκB signaling: mechanisms of chromatin remodeling and chemical resistance

Valproate Alters Dopamine Signaling in Association with Induction of Par-4 Protein Expression

Chromatin remodeling through histone modifications has emerged as a key mechanism in the pathophysiology of psychiatric disorders. Valproate (VPA), a first-line medication for bipolar disorder, is known to have histone deacetylase (HDAC) inhibitor activity, but the relationship between its efficacy as a mood stabilizer and HDAC inhibitory activity is unclear. Here we provide evidence that prostate apoptosis response-4 (Par-4), an intracellular binding partner of dopamine D2 receptors (DRD2), plays a role in mediating the effectiveness of VPA. We found that chronic VPA treatment enhanced the expression of Par-4 in cultured neurons and adult mouse brains. This Par-4 induction phenomenon occurred at the transcriptional level and was correlated with an increase in histone H3 and H4 acetylation of the Par-4 promoter regions. Furthermore, chronic VPA treatment potentiated the suppression of the cAMP signaling cascade upon dopamine stimulation, which was blocked by sulpiride treatment. These results indicate that VPA potentiates DRD2 activity by enhancing Par-4 expression via a chromatin remodeling mechanism.

Chromatin modification and remodelling: a regulatory landscape for the control of Arabidopsis defence responses upon pathogen attack

Due to their sessile lifestyle, plants have to cope with an ever-changing environment and to defend themselves against a multitude of biotic aggressors that compromise their development and reproduction. Responses to various biotic stresses largely depend on the plant's capacity to modulate rapidly and specifically its transcriptome. In a stress type-dependent manner, external signals are translocated into the nucleus to activate transcription factors, resulting in the increased expression of particular sets of defence-related genes. Among mechanisms of transcriptional regulation, chromatin remodelling accomplished through the activity of histone-modifying enzymes and ATP-dependent chromatin-remodelling complexes is emerging as a key process in the orchestration of plant biotic stress responses. In this review, we summarize and discuss roles that chromatin-remodelling mechanisms may play in regulating Arabidopsis defence responses.

Quantitative Analysis of the Chromatin Proteome in Disease Reveals Remodeling Principles and Identifies High Mobility Group Protein B2 as a Regulator of Hypertrophic Growth

A fundamental question in biology is how genome-wide changes in gene expression are enacted in response to a finite stimulus. Recent studies have mapped changes in nucleosome localization, determined the binding preferences for individual transcription factors, and shown that the genome adopts a nonrandom structure in vivo. What remains unclear is how global changes in the proteins bound to DNA alter chromatin structure and gene expression. We have addressed this question in the mouse heart, a system in which global gene expression and massive phenotypic changes occur without cardiac cell division, making the mechanisms of chromatin remodeling centrally important. To determine factors controlling genomic plasticity, we used mass spectrometry to measure chromatin-associated proteins. We have characterized the abundance of 305 chromatin-associated proteins in normal cells and measured changes in 108 proteins that accompany the progression of heart disease. These studies were conducted on a high mass accuracy instrument and confirmed in multiple biological replicates, facilitating statistical analysis and allowing us to interrogate the data bioinformatically for modules of proteins involved in similar processes. Our studies reveal general principles for global shifts in chromatin accessibility: altered linker to core histone ratio; differing abundance of chromatin structural proteins; and reprogrammed histone post-translational modifications. Using small interfering RNA-mediated loss-of-function in isolated cells, we demonstrate that the non-histone chromatin structural protein HMGB2 (but not HMGB1) suppresses pathologic cell growth in vivo and controls a gene expression program responsible for hypertrophic cell growth. Our findings reveal the basis for alterations in chromatin structure necessary for genome-wide changes in gene expression. These studies have fundamental implications for understanding how global chromatin remodeling occurs with specificity and accuracy, demonstrating that isoform-specific alterations in chromatin structural proteins can impart these features.

Non-coding RNAs in retinal development.

Retinal development is dependent on an accurately functioning network of transcriptional and translational regulators. Among the diverse classes of molecules involved, non-coding RNAs (ncRNAs) play a significant role. Members of this family are present in the cell as transcripts, but are not translated into proteins. MicroRNAs (miRNAs) are small ncRNAs that act as post-transcriptional regulators. During the last decade, they have been implicated in a variety of biological processes, including the development of the nervous system. On the other hand, long-ncRNAs (lncRNAs) represent a different class of ncRNAs that act mainly through processes involving chromatin remodeling and epigenetic mechanisms. The visual system is a prominent model to investigate the molecular mechanisms underlying neurogenesis or circuit formation and function, including the differentiation of retinal progenitor cells to generate the seven principal cell classes in the retina, pathfinding decisions of retinal ganglion cell axons in order to establish the correct connectivity from the eye to the brain proper, and activity-dependent mechanisms for the functionality of visual circuits. Recent findings have associated ncRNAs in several of these processes and uncovered a new level of complexity for the existing regulatory mechanisms. This review summarizes and highlights the impact of ncRNAs during the development of the vertebrate visual system, with a specific focus on the role of miRNAs and a synopsis regarding recent findings on lncRNAs in the retina.

Downstream and Intermediate Interactions of Synovial Sarcoma-Associated Fusion Oncoproteins and Their Implication for Targeted Therapy

Synovial sarcoma (SS), an aggressive type of soft tissue tumor, occurs mostly in adolescents and young adults. The origin and molecular mechanism of the development of SS remain only partially known. Over 90% of SS cases are characterized by the t(X;18)(p11.2;q11.2) translocation, which results mainly in the formation of SS18-SSX1 or SS18-SSX2 fusion genes. In recent years, several reports describing direct and indirect interactions of SS18-SSX1/SSX2 oncoproteins have been published. These reports suggest that the fusion proteins particularly affect the cell growth, cell proliferation, TP53 pathway, and chromatin remodeling mechanisms, contributing to SS oncogenesis. Additional research efforts are required to fully explore the protein-protein interactions of SS18-SSX oncoproteins and the pathways that are regulated by these partnerships for the development of effective targeted therapy.

Chromatin remodelling: why, when & how?

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Epigenetic repressor-like genes are differentially regulated during grapevine (Vitis vinifera L.) development

Grapevine sexual reproduction involves a seasonal separation between inflorescence primordia (flowering induction) and flower development. We hypothesized that a repression mechanism implicating epigenetic changes could play a role in the seasonal separation of these two developmental processes in grapevine. Therefore, the expression of five grapevine genes with homology to the Arabidopsis epigenetic repressor genes FERTILIZATION INDEPENDENT ENDOSPERM (FIE), EMBRYONIC FLOWER 2 (EMF2), CURLY LEAF (CLF), MULTICOPY SUPPRESSOR OF IRA 1 (MSI1) and SWINGER (SWN) was analyzed during the development of buds and vegetative and reproductive organs. During bud development, the putative grapevine epigenetic repressor genes VvCLF, VvEMF2, VvMSI1, VvSWN and VvFIE are mainly expressed in latent buds at the flowering induction period, but also detected during bud burst and inflorescence/flower development. The overlapping expression patterns of grapevine PcG-like genes in buds suggest that chromatin remodeling mechanisms could be operating during grapevine bud development for controlling processes such as seasonal flowering, dormancy and bud burst. Furthermore, the expression of grapevine PcG-like genes was also detected in fruits and vegetative organs, suggesting that epigenetic changes could be at the basis of the regulation of various proliferation-differentiation cell transitions that occur during grapevine development.

Involvement of a Toxoplasma gondii Chromatin Remodeling Complex Ortholog in Developmental Regulation

The asexual cycle of the parasite Toxoplasma gondii has two developmental stages: a rapidly replicating form called a tachyzoite and a slow growing cyst form called a bradyzoite. While the importance of ATP-independent histone modifications for gene regulation in T. gondii have been demonstrated, ATP-dependent chromatin remodeling pathways have not been examined. In this study we characterized C9, an insertional mutant showing reduced expression of bradyzoite differentiation marker BAG1, in cultured human fibroblasts. This mutant contains an insertion in the gene encoding TgRSC8, which is homologous to the Saccharomyces cerevisiae proteins Rsc8p (remodel the structure of chromatin complex subunit 8) and Swi3p (switch/sucrose non-fermentable [SWI/SNF]) of ATP-dependent chromatin-remodeling complexes. In the C9 mutant, TgRSC8 is the downstream open reading frame on a dicistronic transcript. Though protein was expressed from the downstream gene of the dicistron, TgRSC8 levels were decreased in C9 from those of wild-type parasites, as determined by western immunoblot and flow cytometry. As TgRSC8 localized to the parasite nucleus, we postulated a role in gene regulation. Transcript levels of several markers were assessed by quantitative PCR to test this hypothesis. The C9 mutant displayed reduced steady state transcript levels of bradyzoite-induced genes BAG1, LDH2, SUSA1, and ENO1, all of which were significantly increased with addition of TgRSC8 to the mutant. Transcript levels of some bradyzoite markers were unaltered in C9, or unable to be increased by complementation with TgRSC8, indicating multiple pathways control bradyzoite-upregulated genes. Together, these data suggest a role for TgRSC8 in control of bradyzoite-upregulated gene expression. Thus chromatin remodeling, by both ATP-independent and dependent mechanisms, is an important mode of gene regulation during stage differentiation in parasites.

Determinants of nucleosome organization in primary human cells

Nucleosomes are the basic packaging units of chromatin, modulating accessibility of regulatory proteins to DNA and thus influencing eukaryotic gene regulation. Elaborate chromatin remodeling mechanisms have evolved that govern nucleosome organization at promoters, regulatory elements, and other functional regions in the genome1. Analyses of chromatin landscape have uncovered a variety of mechanisms, including DNA sequence preferences, that can influence nucleosome positions2–4. To identify major determinants of nucleosome organization in the human genome, we utilized deep sequencing to map nucleosome positions in three primary human cell types and in vitro. A majority of the genome exhibited substantial flexibility of nucleosome positions while a small fraction showed reproducibly positioned nucleosomes. Certain sites that position in vitro can anchor the formation of nucleosomal arrays that have cell type-specific spacing in vivo. Our results unveil an interplay of sequence-based nucleosome preferences and non-nucleosomal factors in determining nucleosome organization within mammalian cells.

Signaling from the cytoplasm to the nucleus in striatal medium-sized spiny neurons.

Striatal medium-sized spiny neurons (MSNs) receive massive glutamate inputs from the cerebral cortex and thalamus and are a major target of dopamine projections. Interaction between glutamate and dopamine signaling is crucial for the control of movement and reward-driven learning, and its alterations are implicated in several neuropsychiatric disorders including Parkinson’s disease and drug addiction. Long-lasting forms of synaptic plasticity are thought to depend on transcription of gene products that alter the structure and/or function of neurons. Although multiple signal transduction pathways regulate transcription, little is known about signal transmission between the cytoplasm and the nucleus of striatal neurons and its regulation. Here we review the current knowledge of the signaling cascades that target the nucleus of MSNs, most of which are activated by cAMP and/or Ca2+. We outline the mechanisms by which signals originating at the plasma membrane and amplified in the cytoplasm are relayed to the nucleus, through the regulation of several protein kinases and phosphatases and transport through the nuclear pore. We also summarize the identified mechanisms of transcription regulation and chromatin remodeling in MSNs that appear to be important for behavioral adaptations, and discuss their relationships with epigenetic regulation.

An epigenetic chromatin remodeling role for NFATc1 in transcriptional regulation of growth and survival genes in diffuse large B-cell lymphomas

AbstractThe nuclear factor of activated T cells (NFAT) family of transcription factors functions as integrators of multiple signaling pathways by binding to chromatin in combination with other transcription factors and coactivators to regulate genes central for cell growth and survival in hematopoietic cells. Recent experimental evidence has implicated the calcineurin/NFAT signaling pathway in the pathogenesis of various malignancies, including diffuse large B-cell lymphoma (DLBCL). However, the molecular mechanism(s) underlying NFATc1 regulation of genes controlling lymphoma cell growth and survival is still unclear. In this study, we demonstrate that the transcription factor NFATc1 regulates gene expression in DLBCL cells through a chromatin remodeling mechanism that involves recruitment of the SWItch/Sucrose NonFermentable chromatin remodeling complex ATPase enzyme SMARCA4 (also known as Brahma-related gene 1) to NFATc1 targeted gene promoters. The NFATc1/Brahma-related gene 1 complex induces promoter DNase I hypersensitive sites and recruits other transcription factors to the active chromatin site to regulate gene transcription. Targeting NFATc1 with specific small hairpin RNA inhibits DNase I hypersensitive site formation and down-regulates target gene expression. Our data support a novel epigenetic control mechanism for the transcriptional regulation of growth and survival genes by NFATc1 in the pathophysiology of DLBCL and suggests that targeting NFATc1 could potentially have therapeutic value.

Commentary: The Year in Circadian Rhythms

The circadian clock orchestrates intrinsic timing in most organisms and controls a large variety of physiological and metabolic programs. In my presentation “The Year in Circadian Rhythms” at the Endocrine Society meeting (San Diego, June 2010) I reviewed some of the recent spectacular developments of the field. The exceptional interest that circadian rhythms have suscitated during the past two decades has caused a remarkable increase in the number of researchers and of committed resources dedicated to the field. This has also generated the promise of potentially novel pharmacological strategies. Indeed, specific molecular pathways of circadian regulation have been recently linked to endocrine and metabolic control, as well as cell cycle and proliferation. Importantly, circadian gene expression involves an important proportion of cellular genes, underscoring the role played by dynamic mechanisms of chromatin remodeling. This suggests that the circadian machinery could have evolved as a privileged molecular interface between cellular metabolism and epigenetic control. (Molecular Endocrinology 24: 2081–2087, 2010)

Commentary: The Year in Circadian Rhythms

The circadian clock orchestrates intrinsic timing in most organisms and controls a large variety of physiological and metabolic programs. In my presentation "The Year in Circadian Rhythms" at the Endocrine Society meeting (San Diego, June 2010) I reviewed some of the recent spectacular developments of the field. The exceptional interest that circadian rhythms have suscitated during the past two decades has caused a remarkable increase in the number of researchers and of committed resources dedicated to the field. This has also generated the promise of potentially novel pharmacological strategies. Indeed, specific molecular pathways of circadian regulation have been recently linked to endocrine and metabolic control, as well as cell cycle and proliferation. Importantly, circadian gene expression involves an important proportion of cellular genes, underscoring the role played by dynamic mechanisms of chromatin remodeling. This suggests that the circadian machinery could have evolved as a privileged molecular interface between cellular metabolism and epigenetic control.

SWI/SNF Has Intrinsic Nucleosome Disassembly Activity that Is Dependent on Adjacent Nucleosomes

The ATP-dependent chromatin remodeling complex SWI/SNF regulates transcription and has been implicated in promoter nucleosome eviction. Efficient nucleosome disassembly by SWI/SNF alone in biochemical assays, however, has not been directly observed. Employing a model system of dinucleosomes rather than mononucleosomes, we demonstrate that remodeling leads to ordered and efficient disassembly of one of the two nucleosomes. An H2A/H2B dimer is first rapidly displaced, and then, in a slower reaction, an entire histone octamer is lost. Nucleosome disassembly by SWI/SNF did not require additional factors such as chaperones or acceptors of histones. Observations in single molecules as well as bulk measurement suggest that a key intermediate in this process is one in which a nucleosome is moved toward the adjacent nucleosome. SWI/SNF recruited by the transcriptional activator Gal4-VP16 preferentially mobilizes the proximal nucleosome and destabilizes the adjacent nucleosome.

ATP-dependent chromatin remodeling complex and its function in regulating chromatin structure

The highly condensed chromatin prevents binding of transcription factors and cofactors to DNA. Therefore, it is crucial to relief the repressive environment for transcription through chromatin remodeling activities. Recently, it is widely accepted that chromatin remodeling is carried out by at least two mechanisms: ATP-dependent chromatin remodeling complex and covalent modifications of histone tails by histone modification complexes. This paper reviews the mechanisms of chromatin remodeling through ATP-dependent chromatin remodeling complex and how the two complexes work together to modify the chromatin structure and regulate the function of transcription mechanism according to recent studies.

The structure and function of ATP‐dependent chromatin remodeling complexes

ATP‐dependent chromatin remodelers are key regulators of the epigenome and have important roles in transcription, replication, repair and recombination of DNA. These remodelers all have the basic ability to translocate along DNA in an ATP‐dependent manner. The remodelers use this activity in various ways to reorganize chromatin fibers through nucleosome mobilization, histone exchange, and/or nucleosome disassembly. The interactions with chromatin of three of the four major families of ATP‐dependent chromatin remodelers are examined to find some of their fundamental differences. The subunits and protein domains that bind nucleosomes have been mapped. The mechanism of chromatin remodeling has been studied using a variety of techniques to capture the intermediate states and to map changes in protein‐DNA and protein‐protein interactions. Deletion and point mutagenesis of protein domains have further delineated the functional role of particular domains in chromatin remodeling both in vitro and in vivo and has provided additional insights into the mechanism of chromatin remodeling. Three basic models for chromatin remodeling will be presented that account for some of the diversity among chromatin remodelers.

Mechanism of Chromatin Remodeling and Recovery During Passage of RNA Polymerase II

Transcription of eukaryotic genes by RNA polymerase II (Pol II) is typically accompanied by nucleosome survival and minimal exchange of histones H3/H4. The mechanism of survival and recovery of chromatin structure remains obscure. In our recent studies we have shown how transcription through chromatin by Pol II is uniquely coupled with nucleosome survival. Structural modeling and functional analysis of the intermediates of transcription through a nucleosome was conducted. When Pol II approaches the area of strong DNA‐histone interactions, a small intranucleosomal DNA loop (zero‐size or Ø‐loop) containing transcribing enzyme is formed. During formation of the Ø‐loop, the recovery of DNA‐histone interactions behind Pol II is tightly coupled with their disruption ahead of the enzyme. This coupling is a distinct feature of the Pol II‐type mechanism that allows further transcription through the nucleosome, prevents nucleosome translocation and minimizes displacement of H3/H4 histones from DNA during enzyme passage.

Rapid Elimination of the Histone Variant MacroH2A from Somatic Cell Heterochromatin after Nuclear Transfer

Oocytes contain a maternal store of the histone variant MacroH2A, which is eliminated from zygotes shortly after fertilization. Preimplantation embryos then execute three cell divisions without MacroH2A before the onset of embryonic MacroH2A expression at the 16-cell stage. During subsequent development, MacroH2A is expressed in most cells, where it is assembled into facultative heterochromatin. Because differentiated cells contain heterochromatin rich in MacroH2A, we investigated the fate of MacroH2A during somatic cell nuclear transfer (SCNT). The results show that MacroH2A is rapidly eliminated from the chromosomes of transplanted somatic cell nuclei by a process in which MacroH2A is first stripped from chromosomes, and then degraded. Furthermore, MacroH2A is eliminated from transplanted nuclei by a mechanism requiring intact microtubules and nuclear envelope break down. Preimplantation SCNT embryos express endogenous MacroH2A once they reach the morula stage, similar to the timing observed in embryos produced by natural fertilization. We also show that the ability to reprogram somatic cell heterochromatin by SCNT is tied to the developmental stage of recipient cell cytoplasm because enucleated zygotes fail to support depletion of MacroH2A from transplanted somatic nuclei. Together, the results indicate that nuclear reprogramming by SCNT utilizes the same chromatin remodeling mechanisms that act upon the genome immediately after fertilization.