The nucleosome-remodeling ATPase ISWI is regulated by poly-ADP-ribosylation.

ATP-dependent nucleosome-remodeling enzymes and covalent modifiers of chromatin set the functional state of chromatin. However, how these enzymatic activities are coordinated in the nucleus is largely unknown. We found that the evolutionary conserved nucleosome-remodeling ATPase ISWI and the poly-ADP-ribose polymerase PARP genetically interact. We present evidence showing that ISWI is target of poly-ADP-ribosylation. Poly-ADP-ribosylation counteracts ISWI function in vitro and in vivo. Our work suggests that ISWI is a physiological target of PARP and that poly-ADP-ribosylation can be a new, important post-translational modification regulating the activity of ATP-dependent nucleosome remodel…

P/CAF-mediated spermidine acetylation regulates histone acetyltransferase activity

Histones and polyamines are important determinants of the chromatin structure. Histones form the core of nucleosome particles and their modification by acetylation of N-terminal tails is involved in chromatin structural changes and transcriptional regulation. Polyamines, including spermidine, are also targets of both cytoplasmic and nuclear acetylation, which in turn alters their affinity for DNA and nucleosomes. Previous studies report the interplay between polyamines metabolism and levels of histone acetylation, but the molecular basis of this effect is still unclear. In this work, we have analyzed the in vitro effect of spermidine on histone H3 acetylation catalyzed by P/CAF, a highly co…

Functional Interaction between ISWI and Covalent Modifiers of Chromatin

Regulation of Chromatin Remodeling through poly-ADP-ribosylation

An RNA Memory Mechanism to Inherit Epigenetic Marks

The Nucleosome Remodeling ATPase ISWI is Regulated by poly-ADP-ribosylation

A MULTI-LAYER MODEL TO STUDY GENOME-SCALE POSITIONS OF NUCLEOSOMES

The positioning of nucleosomes along chromatin has been implicated in the regulation of gene expression in eukaryotic cells, because packaging DNA into nucleosomes affects sequence accessibility. In this paper we propose a new model (called MLM) for the identification of nucleosomes and linker regions across DNA, consisting in a thresholding technique based on cut-set conditions. For this purpose we have defined a method to generate synthetic microarray data fully inspired from the approach that has been used by Yuan et al. Results have shown a good recognition rate on synthetic data, moreover, the $MLM$ shows a good agreement with the recently published method based on Hidden Markov Model …

Multiple roles for ISWI in transcription, chromosome organization and DNA replication.

ISWI functions as the ATPase subunit of multiple chromatin-remodeling complexes. These complexes use the energy of ATP hydrolysis to slide nucleosomes and increase chromatin fluidity, thereby modulating the access of transcription factors and other regulatory proteins to DNA. Here we discuss recent progress toward understanding the biological functions of ISWI, with an emphasis on its roles in transcription, chromosome organization and DNA replication.

Extracellular release of HSP60 from tumor cells occurs via various secretory pathways

Hsp60 is actively secreted by human tumor cells

Background Hsp60, a Group I mitochondrial chaperonin, is classically considered an intracellular chaperone with residence in the mitochondria; nonetheless, in the last few years it has been found extracellularly as well as in the cell membrane. Important questions remain pertaining to extracellular Hsp60 such as how generalized is its occurrence outside cells, what are its extracellular functions and the translocation mechanisms that transport the chaperone outside of the cell. These questions are particularly relevant for cancer biology since it is believed that extracellular chaperones, like Hsp70, may play an active role in tumor growth and dissemination. Methodology/Principal Findings S…

ISWI Regulates Higher-Order Chromatin Structure and Histone H1 Assembly In Vivo

Imitation SWI (ISWI) and other ATP-dependent chromatin-remodeling factors play key roles in transcription and other processes by altering the structure and positioning of nucleosomes. Recent studies have also implicated ISWI in the regulation of higher-order chromatin structure, but its role in this process remains poorly understood. To clarify the role of ISWI in vivo, we examined defects in chromosome structure and gene expression resulting from the loss of Iswi function in Drosophila. Consistent with a broad role in transcriptional regulation, the expression of a large number of genes is altered in Iswi mutant larvae. The expression of a dominant-negative form of ISWI leads to dramatic a…

A Drosophila model to study the human multysistemic disease Williams Beuren sindrome

The Activity of the Nucleosome Remodeling ATPase ISWI is Regulated by poly-ADP-ribosylation

Flow Cytometry and Karyotype Analysis ofD. melanogasterEye Disc Cells

The developing Drosophila eye-antennal disc is a particularly suited system for the genetic and cellular studies of complex biological processes. Methods to analyze Drosophila eye discs by flow cytometry are mainly based on the dissociation of tissues with trypsin. Dissociation operated by trypsin is very effective, though it causes a lot of stress to live cells often compromising the use of treated cells for further analyses. Here, we report a method to produce dissociated eye-disc cells that retain cell-membrane markers and that can be used for flow cytometry and cytological analysis of mitotic chromosomes. The method described is a great complementing tool for the cellular characterizati…

Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila

RNA interference (RNAi) pathways have evolved as important modulators of gene expression that operate in the cytoplasm by degrading RNA target molecules through the activity of short (21-30 nucleotide) RNAs1-6. RNAi components have been reported to have a role in the nucleus, as they are involved in epigenetic regulation and heterochromatin formation(7-10). However, although RNAi-mediated post-transcriptional gene silencing is well documented, the mechanisms of RNAi-mediated transcriptional gene silencing and, in particular, the role of RNAi components in chromatin dynamics, especially in animal multicellular organisms, are elusive. Here we show that the key RNAi components Dicer 2 (DCR2) a…

The Poly-ADP-Ribose Polymerase PARP Modulates the Activity of the Nucleosome Remodeling ATPase ISWI

Poly-ADP-Ribose (PAR) as an epigenetic flag

Epigenetics is the study of hereditable chromatin modifications, such as DNA methylation, histone modifications, and nucleosome-remodelling, which occur without alterations to the DNA sequence. The establishment of different epigenetic states in eukaryotes depends on regulatory mechanisms that induce structural changes in chromatin in response to environmental and cellular cues. Two classes of enzymes modulate chromatin accessibility: chromatin-covalent modifiers and ATP-dependent chromatin remodelling complexes. The first class of enzymes catalyzes covalent modifications of DNA as well as the amino- and carboxy-terminal tails of histones, while the second uses the energy of ATP hydrolysis …

EXTRACELLULAR RELEASE OF HSP60 FROM TUMOR CELLS

A Dominant Modifiers Screen for Suppressors of ISWI Function

Functional Regulation of the Nucleosome Remodeling ATPase ISWI by PARP

Functional Interaction between the Nucleosome Remodeling Factor ISWI and the Hsr-omega non-coding RNA

Use of anthocyans as in vivo pH indicators for higher eukaryotes

The Odyssey of Hsp60 from Tumor Cells to Other Destinations Includes Plasma Membrane-Associated Stages and Golgi and Exosomal Protein-Trafficking Modalities

BACKGROUND: In a previous work we showed for the first time that human tumor cells secrete Hsp60 via exosomes, which are considered immunologically active microvesicles involved in tumor progression. This finding raised questions concerning the route followed by Hsp60 to reach the exosomes, its location in them, and whether Hsp60 can be secreted also via other mechanisms, e.g., by the Golgi. We addressed these issues in the work presented here. PRINCIPAL FINDINGS: We found that Hsp60 localizes in the tumor cell plasma membrane, is associated with lipid rafts, and ends up in the exosomal membrane. We also found evidence that Hsp60 localizes in the Golgi apparatus and its secretion is prevent…

The Nucleosome Remodeling ATPase ISWI is Regulated by poly-ADP-ribosylation

Hsp60 secretion and migration from cancer cells: a proposal for a multistage pathway

Functional Interaction between Remodelers and Covalent Modifiers of Chromatin

Exosome Involvment in Hsp60 secretion by tumor cells.

White alleles Suppress Position Effect Variegation

A Drosophila Model to Study the Human Multisystemic Disease Williams-Beuren Syndrome

Studying Nucleosomes Positioning by a Multi-Layer Model

Eukaryotic DNA is packaged into a highly compact and dynamic structure called chromatin. While this packaging allows the cell to organize a large and complex genome in the nucleus, it can also block the access of transcription factors and other proteins to DNA. Nucleosomes are the fundamental repeating units of eukaryotic chromatin. Nucleosome position can be regulated in vivo by multi-subunit chromatin remodeling complexes, and their position can influence gene expression in eukaryotic cells. Alterations in chromatin structure, and hence in nucleosome organization, can result in a variety of diseases, including cancer, highlighting the need to achieve a better understanding of the molecula…

Loss of the Sin3A/Rpd3 Histone De-Acetylase Complex Causes Polytene Chromosome Telomeric Fusions

Functional Interaction between the Nucleosome Remodeling Factor ISWI and Covalent Modifiers of Chromatin

Functional Interaction between the Nucleosome Remodeling Factor ISWI and the Hsrω non-coding RNA

A multi-layer method to study genome-scale positions of nucleosomes

AbstractThe basic unit of eukaryotic chromatin is the nucleosome, consisting of about 150 bp of DNA wrapped around a protein core made of histone proteins. Nucleosomes position is modulated in vivo to regulate fundamental nuclear processes. To measure nucleosome positions on a genomic scale both theoretical and experimental approaches have been recently reported. We have developed a new method, Multi-Layer Model (MLM), for the analysis of nucleosome position data obtained with microarray-based approach. The MLM is a feature extraction method in which the input data is processed by a classifier to distinguish between several kinds of patterns. We applied our method to simulated-synthetic and…

Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures

In the quest for a mathematical measure able to capture and shed light on the dual notions of information and complexity in biosequences, Hazen et al. have introduced the notion of Functional Information (FI for short). It is also the result of earlier considerations and findings by Szostak and Carothers et al. Based on the experiments by Charoters et al., regarding FI in RNA binding activities, we decided to study the relation existing between FI and classic measures of complexity applied on protein-DNA interactions on a genome-wide scale. Using classic complexity measures, i.e, Shannon entropy and Kolmogorov Complexity as both estimated by data compression, we found that FI applied to pro…

Loss of the Sin3A/Rpd3 Histone De-Acetylase Complex Causes Telomeric Fusions

A Protein Nuclear Extract fromD. melanogasterLarval Tissues

Preparation of protein nuclear extracts is often the first step to study in vitro biological processes occurring in the nucleus of the eukaryotic cell. Nuclear extracts have been extensively used in different model organisms to identify and study protein function in nuclei. Drosophila embryos can be collected in large quantities and have been the source of choice for the production of protein nuclear extracts. However, most of Drosophila in vivo studies on protein function are conducted in larval tissues. Here we report a new method to produce highly stable large-scale protein nuclear extracts from whole Drosophila larvae that are suited for a variety of biochemical analyses.

Epigenetics: More than Genetics

Regulation of ISWI chromatin remodelling activity.

The packaging of the eukaryotic genome into chromatin facilitates the storage of the genetic information within the nucleus, but prevents the access to the underlying DNA sequences. Structural changes in chromatin are mediated by several mechanisms. Among them, ATP-dependent remodelling complexes belonging to ISWI family provides one of the best examples that eukaryotic cells evolved to finely regulate these changes. ISWI-containing complexes use the energy derived from ATP hydrolysis to rearrange nucleosomes on chromatin in order to favour specific nuclear reactions. The combination of regulatory nuclear factors associated with the ATPase subunit as well as its modulation by specific histo…

Immunolocalization of Poly ADP-Ribose on Drosophila Polytene Chromosomes

Poly ADP-ribosylation (PARylation) is a posttranslational protein modification catalyzed by poly -ADP-ribose polymerases (PARPs). Poly ADP-ribose metabolism is involved in a wide range of biological processes, such as maintenance of genome stability, transcriptional regulation, energy metabolism, and programed cell death. Recently, chromatin components, including histones, have been shown to be targets of PARylation. Unlike mammals, which have several PARP-encoded genes, the model organism Drosophila melanogaster has only one PARP gene, highly related to mammalian PARP1. These features make flies a great model system to study PARP biology. Commercially available antibodies recognizing this …

Genome-wide identification of chromatin binding sites of the ISWI nucleosome remodeler

Un Modello in Drosophila per Studiare la Sindrome di Williams-Beuren

A genetic screen to identify ISWI antagonists in Drosophila melanogaster

Chromatin remodeling regulation by small molecules and metabolites.

The eukaryotic genome is a highly organized nucleoprotein structure comprising of DNA, histones, non-histone proteins, and RNAs, referred to as chromatin. The chromatin exists as a dynamic entity, shuttling between the open and closed forms at specific nuclear regions and loci based on the requirement of the cell. This dynamicity is essential for the various DNA-templated phenomena like transcription, replication, and repair and is achieved through the activity of ATP-dependent chromatin remodeling complexes and covalent modifiers of chromatin. A growing body of data indicates that chromatin enzymatic activities are finely and specifically regulated by a variety of small molecules derived f…

Human Hsp60 with Its Mitochondrial Import Signal Occurs in Solution as Heptamers and Tetradecamers Remarkably Stable over a Wide Range of Concentrations

It has been established that Hsp60 can accumulate in the cytosol in various pathological conditions, including cancer and chronic inflammatory diseases. Part or all of the cytosolic Hsp60 could be naive, namely, bear the mitochondrial import signal (MIS), but neither the structure nor the in solution oligomeric organization of this cytosolic molecule has still been elucidated. Here we present a detailed study of the structure and self-organization of naive cytosolic Hsp60 in solution. Results were obtained by different biophysical methods (light and X ray scattering, single molecule spectroscopy and hydrodynamics) that all together allowed us to assay a wide range of concentrations of Hsp60…

Genetic and Cytological Analysis of Drosophila Chromatin-Remodeling Factors

The Nucleosome Remodeling Factor ISWI Functionally Interacts with the Hsr-ω non-coding RNA

The ISWI chromatin remodeler organizes the hsrω ncRNA-containing omega speckle nuclear compartments.

The complexity in composition and function of the eukaryotic nucleus is achieved through its organization in specialized nuclear compartments. The Drosophila chromatin remodeling ATPase ISWI plays evolutionarily conserved roles in chromatin organization. Interestingly, ISWI genetically interacts with the hsrω gene, encoding multiple non-coding RNAs (ncRNA) essential, among other functions, for the assembly and organization of the omega speckles. The nucleoplasmic omega speckles play important functions in RNA metabolism, in normal and stressed cells, by regulating availability of hnRNPs and some other RNA processing proteins. Chromatin remodelers, as well as nuclear speckles and their assoc…

The histone deacetylase Rpd3 regulates telomeric heterochromatin structure of polytene chromosomes

ICIL: a new ISWI Complex In D.melanogaster Larvae

UbcD1 knock-down increases chromosomes condensation defects caused by loss of ISWI function

La Perdita di Funzione del Complesso di Deacetilazione Istonica Sin3A/Rpd3 Causa Fusioni Telomeriche

Hsp60 from cancer cells can reach near and distant targets: A proposal for a multistage pathway

Cancer cells have means to influence other cells in their vicinity and distant, and in this signal-delivering mechanisms the chaperonin Hsp60 plays a role, which is currently being recognized as potentially crucial for the growth and dissemination of at least certain types of tumors. In order to arrive at its destination, Hsp60, a typical resident of mitochondria in normal and tumor cells, leaves the organelle and reaches the blood. In the latter, Hsp60 can travel and arrive at targets situated far away from its origin. The details of the route followed by Hsp60 and their molecular mechanisms have not yet been fully elucidated. We investigated Hsp60 levels and secretion in normal and tumor …

A Drosophila Model to Study the Human Multisystemic Disease Williams-Beuren Syndrome

A Genetic Screen for Dominant Modifiers of ISWI Reveals Functional Interactions with the SIN3A/RPD3 Complex

Functional antagonism between histone H3K4 demethylases in vivo

Dynamic regulation of histone modifications is critical during development, and aberrant activity of chromatin-modifying enzymes has been associated with diseases such as cancer. Histone demethylases have been shown to play a key role in eukaryotic gene transcription; however, little is known about how their activities are coordinated in vivo to regulate specific biological processes. In Drosophila, two enzymes, dLsd1 (Drosophila ortholog of lysine-specific demethylase 1) and Lid (little imaginal discs), demethylate histone H3 at Lys 4 (H3K4), a residue whose methylation is associated with actively transcribed genes. Our studies show that compound mutation of Lid and dLsd1 results in increa…

ISWI genetically interacts with the hsr-omega ncRNA

Loss of the Sin3A/Rpd3 Histone De-Acetylase Complex Causes Polytene Chromosome Telomeric Fusions

Soppressione della Variegazione per Effetto di Posizione da parte di Alleli white

Chromatin associated RNAi components take part in active transcriptional regulation in Drosophila

Emerging Roles for hnRNPs in post-transcriptional regulation: what can we learn from flies?

Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a highly conserved family of RNA-binding proteins able to associate with nascent RNAs in order to support their localization, maturation and translation. Research over this last decade has remarked the importance of gene regulatory processes at post-transcriptional level, highlighting the emerging roles of hnRNPs in several essential biological events. Indeed, hnRNPs are key factors in regulating gene expression, thus, having a number of roles in many biological pathways. Moreover, failure of the activities catalysed by hnRNPs affects various biological processes and may underlie several human diseases including cancer, diabetes and neur…

The nucleosome remodeling factor ISWI functionally interacts with an evolutionarily conserved network of cellular factors

Abstract ISWI is an evolutionarily conserved ATP-dependent chromatin remodeling factor playing central roles in DNA replication, RNA transcription, and chromosome organization. The variety of biological functions dependent on ISWI suggests that its activity could be highly regulated. Our group has previously isolated and characterized new cellular activities that positively regulate ISWI in Drosophila melanogaster. To identify factors that antagonize ISWI activity we developed a novel in vivo eye-based assay to screen for genetic suppressors of ISWI. Our screen revealed that ISWI interacts with an evolutionarily conserved network of cellular and nuclear factors that escaped previous genetic…

Loss of ISWI in Drosophila immaginal discs causes cell cycle defects

UbcD1 is a Histone H2B Ubiquitin-Conjugating Enzyme Essential for Global Chromatin Structure and Gene Expression Regulation

UbcD1: from telomere capping to global chromatin regulation

Emerging roles of hnRNP's in postranscriptional regulation: what can we learn from flies ?

Circulating exosomal Hsp60 as a new marker of colon cancer.

New Fly Food for Drosophila melanogaster

Genetic identification of a network of factors that functionally interact with the nucleosome remodeling ATPase ISWI.

Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function. However, much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and transcription. The evolutionarily conserved ATP-dependent chromatin-remodeling factor ISWI plays essential roles in chromosome organization, DNA replication, and transcription regulation. To gain insight into regulation and mechanism of action of ISWI, we conducted an unbiased genetic screen to identify factors with which it interacts in vivo. We found that ISWI interacts with a network o…

The histone deacetylase Rpd3 regulates the heterochromatin structure of Drosophila telomeres

Telomeres are specialized structures at the end of eukaryotic chromosomes that are required to preserve genome integrity, chromosome stability and nuclear architecture. Telomere maintenance and function are established epigenetically in several eukaryotes. However, the exact chromatin enzymatic modifications regulating telomere homeostasis are poorly understood. In Drosophila melanogaster, telomere length and stability are maintained through the retrotransposition of specialized telomeric sequences and by the specific loading of protecting capping proteins, respectively. Here, we show that the loss of the essential and evolutionarily conserved histone deacetylase Rpd3, the homolog of mammal…

SIN3A genetically and physically interacts with ISWI

Chromatin remodeling disease: a functional link with poly-ADP-Ribosylation

ISWI Functionally Interacts with the SIN3A/RPD3 Complex

INDICATORI DI PH IN VIVO CONTENENTI ANTOCIANI E LORO USO

Chromatin remodeling redulation by small molecules and metabolites

UbcD1: from telomere capping to global heterochromatin regulation

Regulation of ISWI-family of chromatin remodelling Complexes

The packaging of DNA into chromatin facilitates the storage of the genetic information within the nucleus but prevents the access to the underlying sequences. The evolutionarily conserved ISWI family of ATP-dependent chromatin remodelling complexes provide one of the regulatory mechanisms that eukaryotic cells have evolved to induce structural changes to chromatin. All ISWI-containing complexes use the energy derived from ATP hydrolysis in order to rearrange nucleosomes on chromatin to carry specific nuclear reactions. The combination of associated proteins with the ATPase subunit as well as specific histone modifications specialize the nuclear function of each ISWI-containing complex. Here…

A new epigenetic cross-talk links effete and iswi in determining chromatin structure

The intrinsic combinatorial organization and information theoretic content of a sequence are correlated to the DNA encoded nucleosome organization of eukaryotic genomes

Abstract Motivation: Thanks to research spanning nearly 30 years, two major models have emerged that account for nucleosome organization in chromatin: statistical and sequence specific. The first is based on elegant, easy to compute, closed-form mathematical formulas that make no assumptions of the physical and chemical properties of the underlying DNA sequence. Moreover, they need no training on the data for their computation. The latter is based on some sequence regularities but, as opposed to the statistical model, it lacks the same type of closed-form formulas that, in this case, should be based on the DNA sequence only. Results: We contribute to close this important methodological gap …

A conserved role for the mitochondrial citrate transporter Sea/SLC25A1 in the maintenance of chromosome integrity.

Histone acetylation plays essential roles in cell cycle progression, DNA repair, gene expression and silencing. Although the knowledge regarding the roles of acetylation of histone lysine residues is rapidly growing, very little is known about the biochemical pathways providing the nucleus with metabolites necessary for physiological chromatin acetylation. Here, we show that mutations in the scheggia (sea)-encoded Sea protein, the Drosophila ortholog of the human mitochondrial citrate carrier Solute carrier 25 A1 (SLC25A1), impair citrate transport from mitochondria to the cytosol. Interestingly, inhibition of sea expression results in extensive chromosome breakage in mitotic cells and indu…

Functional Interaction between the Nucleosome Remodeling Factor ISWI and the Hsrω non-coding RNA

Trans-Reactivation: A New Epigenetic Phenomenon Underlying Transcriptional Reactivation of Silenced Genes

In order to study the role played by cellular RNA pools produced by homologous genomic loci in defining the transcriptional state of a silenced gene, we tested the effect of non-functional alleles of the white gene in the presence of a functional copy of white, silenced by heterochromatin. We found that non-functional alleles of white, unable to produce a coding transcript, could reactivate in trans the expression of a wild type copy of the same gene silenced by heterochromatin. This new epigenetic phenomenon of transcriptional trans-reactivation is heritable, relies on the presence of homologous RNA’s and is affected by mutations in genes involved in post-transcriptional gene silencing. Ou…

Hsp10 nuclear localization and changes in lung cells response to cigarette smoke suggest novel roles for this chaperonin

Heat-shock protein (Hsp)10 is the co-chaperone for Hsp60 inside mitochondria, but it also resides outside the organelle. Variations in its levels and intracellular distribution have been documented in pathological conditions, e.g. cancer and chronic obstructive pulmonary disease (COPD). Here, we show that Hsp10 in COPD undergoes changes at the molecular and subcellular levels in bronchial cells from human specimens and derived cell lines, intact or subjected to stress induced by cigarette smoke extract (CSE). Noteworthy findings are: (i) Hsp10 occurred in nuclei of epithelial and lamina propria cells of bronchial mucosa from non-smokers and smokers; (ii) human bronchial epithelial (16HBE) a…

The acetylation of spermidine catalyzed by P/CAF regulates its acetyltransferase activity versus histones

Transcriptional regulation in eukaryotes occurs within a chromatin setting and is strongly inhibited by nucleosomal barriers imposed by histone proteins. Among the well-known covalent modifications of chromatin, the reversible acetylation of specific lysine residues of histones, catalyzed by several acetyltransferase and deacetylases, has been linked to many biological processes including transcriptional regulation. Indeed, many transcriptional coactivators possess histone acetyltransferase (HAT) activity (1). Functional interactions between HAT and polyamines have been previously reported. In particular, it has been shown that polyamines facilitate oligomerization of nucleosomal arrays in …

Regulation of Chromatin Remodeling through poly-ADP-ribosylation

Loss of the Sin3A/Rpd3 Histone De-Acetylase Complex Causes Telomeric Fusions

A Genetic Screen for Enhancers of ISWI Reveals Interactions between the Nucleosome Stimulated ATPase ISWI and Covalent Modifiers of Chromatin

Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISWI

The evolutionarily conserved ATP-dependent nucleosome remodelling factor ISWI can space nucleosomes affecting a variety of nuclear processes. In Drosophila, loss of ISWI leads to global transcriptional defects and to dramatic alterations in higher-order chromatin structure, especially on the male X chromosome. In order to understand if chromatin condensation and gene expression defects, observed in ISWI mutants, are directly correlated with ISWI nucleosome spacing activity, we conducted a genome-wide survey of ISWI binding and nucleosome positioning in wild-type and ISWI mutant chromatin. Our analysis revealed that ISWI binds both genic and intergenic regions. Remarkably, we found that ISWI…

Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISWI.

The evolutionarily conserved ATP-dependent nucleosome remodelling factor ISWI can space nucleosomes affecting a variety of nuclear processes. In Drosophila, loss of ISWI leads to global transcriptional defects and to dramatic alterations in higher-order chromatin structure, especially on the male X chromosome. In order to understand if chromatin condensation and gene expression defects, observed in ISWI mutants, are directly correlated with ISWI nucleosome spacing activity, we conducted a genome-wide survey of ISWI binding and nucleosome positioning in wild-type and ISWI mutant chromatin. Our analysis revealed that ISWI binds both genic and intergenic regions. Remarkably, we found that ISWI…

Loss of ISWI Function in Drosophila Nuclear Bodies Drives Cytoplasmic Redistribution of Drosophila TDP-43

Over the past decade, evidence has identified a link between protein aggregation, RNA biology, and a subset of degenerative diseases. An important feature of these disorders is the cytoplasmic or nuclear aggregation of RNA-binding proteins (RBPs). Redistribution of RBPs, such as the human TAR DNA-binding 43 protein (TDP-43) from the nucleus to cytoplasmic inclusions is a pathological feature of several diseases. Indeed, sporadic and familial forms of amyotrophic lateral sclerosis (ALS) and fronto-temporal lobar degeneration share as hallmarks ubiquitin-positive inclusions. Recently, the wide spectrum of neurodegenerative diseases characterized by RBPs functions’ alteration and loss was coll…

White alleles Suppress Position Effect Variegation

A new Multi-Layers Method to Analyze Gene Expression

In the paper a new Multi-Layers approach (called Multi-Layers Model MLM) for the analysis of stochastic signals and its application to the analysis of gene expression data is presented. It consists in the generation of sub-samples from the input signal by applying a threshold technique based on cut-set optimal conditions. The MLM has been applied on synthetic and real microarray data for the identification of particular regions across DNA called nucleosomes and linkers. Nucleosomes are the fundamental repeating subunits of all eukaryotic chromatin, and their positioning provides useful information regarding the regulation of gene expression in eukaryotic cells. Results have shown a good rec…

FSHD muscular dystrophy region gene 1 binds Suv4-20h1 histone methyltransferase and impairs myogenesis.

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant myopathy with a strong epigenetic component. It is associated with deletion of a macrosatellite repeat leading to over-expression of the nearby genes. Among them, we focused on FSHD region gene 1 (FRG1) since its over-expression in mice, Xenopus laevis and Caenorhabditis elegans, leads to muscular dystrophy-like defects, suggesting that FRG1 plays a relevant role in muscle biology. Here we show that, when over-expressed, FRG1 binds and interferes with the activity of the histone methyltransferase Suv4-20h1 both in mammals and Drosophila. Accordingly, FRG1 over-expression or Suv4-20h1 knockdown inhibits myogenesis. Moreov…