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 collectively named proteinopathies. Here, we show that TBPH (TAR DNA-binding protein-43 homolog), the Drosophila ortholog of human TDP-43 TAR DNA-binding protein-43, interacts with the arcRNA hsrω and with hsrω-associated hnRNPs. Additionally, we found that the loss of the omega speckles remodeler ISWI (Imitation SWI) changes the TBPH sub-cellular localization to drive a TBPH cytoplasmic accumulation. Our results, hence, identify TBPH as a new component of omega speckles and highlight a role of chromatin remodelers in hnRNPs nuclear compartmentalization.

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 conserved histone acetyltransferase (HAT) (E.C. 2.3.1.48). We have observed that spermidine at very low concentrations activates P/CAF, while it has an inhibitory effect at concentrations higher than 4M. In addition, the in vitro bimodal effect of spermidine on histone H3 acetylation was also distinctly observed in vivo on polytene chromosomes of Drosophila melanogaster. We also performed kinetic studies indicating that the activating effect of low spermidine concentrations on P/CAF-HAT activity is based on its involvement as a substrate for P/CAF to produce N-8-acetylspermidine that is able in turn to increase the enzyme activity up to four fold.

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. Our data suggest a general new unexpected level of gene expression control mediated by homologous RNA molecules in the context of heterochromatic genes.

MOTIVATIONThanks 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.RESULTSWe contribute to close this important methodological gap between the two models by providing three very simple formulas for the sequence specific one. They are all based on well-known formulas in Computer Science and Bioinformatics, and they give different quantifications of how complex a sequence is. In view of how remarkably well they perform, it is very surprising that measures of sequence complexity have not even been considered as candidates to close the mentioned gap. We provide experimental evidence that the intrinsic level of combinatorial organization and information-theoretic content of subsequences within a genome are strongly correlated to the level of DNA encoded nucleosome organization discovered by Kaplan et al Our results establish an important connection between the intrinsic complexity of subsequences in a genome and the intrinsic, i.e. DNA encoded, nucleosome organization of eukaryotic genomes. It is a first step towards a mathematical characterization of this latter 'encoding'.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online.CONTACTfutro@us.ibm.com.

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 naïve, 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 naïve 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. We found that Naïve Hsp60 in aqueous solution is assembled in very stable heptamers and tetradecamers at all concentrations assayed, without any trace of monomer presence.

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) and lung fibroblast (HFL-1) cells, in vitro, showed Hsp10 in the nucleus, before and after CSE exposure; (iii) CSE stimulation did not increase the levels of Hsp10 but did elicit qualitative changes as indicated by molecular weight and isoelectric point shifts; and (iv) Hsp10 nuclear levels increased after CSE stimulation in HFL-1, indicating cytosol to nucleus migration, and although Hsp10 did not bind DNA, it bound a DNA-associated protein.

It is currently accepted that the human Hsp60 resides and works not only in the mitochondria, the canonical residence, but also outside it. It is also known that Hsp60 although coded by a nuclear gene is synthesized in the cytosol and includes an N-terminal mitochondrial import signal (MIS), which directs the polypeptide toward the inside of the organelle where the MIS is removed. Therefore, there are at least two functional types of Hsp60, with and without MIS, the former in the cytosol the latter inside the mitochondria. A key question is: how do these two forms of Hsp60 differ beyond the fact that while one has MIS the other lacks it? How presence or absence of MIS affects the ability of Hsp60 to form oligomers, which are considered important for chaperoning peptides and assist them to reach a native state? We report here our initial observations on this issue. Typically, in the mitochondria, Hsp60 forms ring-shaped heptamers, two of which associate to build a barrel-shaped tetradecamer, the functional chaperoning complex. It is not known if the cytosolic Hsp60 with its MIS, also forms hepta- and tetradecamers. A clarification of this issue will most likely shed light on the physiological functions of extramitochondrial Hsp60, and also on its pathogenic role in Hsp60 chaperonopathies. Consequently, we compared recombinant Hsp60 bearing the MIS with the prokaryotic ortholog GroEL, which under normal conditions forms functional double-ring tetradecamers. Characteristic hydrodynamic sizes of the oligomeric complex for both systems were investigated by small angle X-ray (SAXS) and static and dynamic light scattering (SLS and DLS) in solution under similar physicochemical conditions. High Performance Liquid Chromatography (HPLC) and blue native polyacrylamide-gel electrophoresis were used to further clarify the equilibrium between the different oligomeric species of the two proteins over a wide range of concentrations. Hsp60 with MIS formed hepta- and tetradecamers similarly to GroEL. Oligomerization was dependent on concentration for GroEL and Hsp60, but for the latter, formation of larger oligomers, e.g., tetradecamers, required higher concentrations than the former.

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 neurodegenerative syndromes. In this review, we summarize some of hnRNPs' roles in the model organism Drosophila melanogaster, particularly focusing on their participation in all aspects of post-transcriptional regulation as well as their conserved role and involvement in the aetiology of human pathologies.

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 histone modifications, specializes the nuclear function of each ISWI-containing complex. Here we review the different ways by which ISWI enzymatic activity can be modulated and regulated in the nucleus of eukaryotic cells.

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. Moreover, Suv4-20h KO mice develop muscular dystrophy signs. Finally, we identify the FRG1/Suv4-20h1 target Eid3 as a novel myogenic inhibitor that contributes to the muscle differentiation defects. Our study suggests a novel role of FRG1 as epigenetic regulator of muscle differentiation and indicates that Suv4-20h1 has a gene-specific function in myogenesis.

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 prevented by an inhibitor of this organelle. Conclusions/Significance We propose a multistage process for the translocation of Hsp60 from the inside to the outside of the cell that includes a combination of protein traffic pathways and, ultimately, presence of the chaperonin in the circulating blood. The new information presented should help in designing future strategies for research and for developing diagnostic-monitoring means useful in clinical oncology.

Nucleosome organization in eukaryotic genomes has a deep impact on gene function. Although progress has been recently made in the identification of various concurring factors influencing nucleosome positioning, it is still unclear whether nucleosome positions are sequence dictated or determined by a random process. It has been postulated for a long time that,in the proximity of TSS, a barrier determines the position of the +1 nucleosome and then geometric constraints alter the random positioning process determining nucleosomal phasing. Such a pattern fades out as one moves away from the barrier to become again a random positioning process. Although this statistical model is widely accepted,the molecular nature of the barrier is still unknown. Moreover,we are far from the identification of a set of sequence rules able:to account for the genome-wide nucleosome organization;to explain the nature of the barriers on which the statistical mechanism hinges;to allow for a smooth transition from sequence-dictated to statistical positioning and back. We show that sequence complexity,quantified via various methods, can be the rule able to at least partially account for all the above.In particular, we have conducted our analyses on 4 high resolution nucleosomal maps of the model eukaryotes and found that nucleosome depleted regions can be well distinguished from nucleosome enriched regions by sequence complexity measures.In particular, (a) the depleted regions are less complex than the enriched ones, (b) around TSS complexity measures alone are in striking agreement with in vivo nucleosome occupancy,in particular precisely indicating the positions of the +1 and -1 nucleosomes. Those findings indicate that the intrinsic richness of subsequences within sequences plays a role in nucleosomal formation in genomes, and that sequence complexity constitutes the molecular nature of nucleosome barrier.

Hsp60 can be released by tumor cells to promote growth. Hsp60 exits mitochondria, reaches the blood and distant targets by mechanisms not yet understood. We determined Hsp60 levels and secretion in normal and tumor cell lines in cell lysates, medium, exosomes, membranes, lipid rafts, and other materials, by ultracentrifugation, electrophoresis, Western blotting, ELISA, EM, and enzymatic tests. Exosomes were purified and characterized by EM and by presence of ALIX, Hsp90, Hsp70, ATPase, and AChE. The tumor, not the normal cells secreted Hsp60, in the absence of cell death, involving lipid rafts‐exosome pathways; Hsp60 associated with lipid‐rafts and cell and exosomal membranes. A working model predicts: Hsp60 gets in the cytosol from mitochondria or from synthesis in the cytosol without entering the organelle, arrives at the cell membrane and binds lipid rafts and, through lipid‐raft mediated endocytosis, is included in early endosomes and then in multivesicular bodies and, lastly, in exosomes for secretion. Hsp60 in exosomes may then reach components of the innate immune system and trigger inflammation; endothelial cells to elicit neoangiogenesis; and other tumor cells to block apoptosis and promote cancer survival.

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 mammalian HDAC1, causes aberrant telomeric fusions on polytene chromosome ends. Remarkably, these telomere fusion defects are associated with a marked decrease of histone H4 acetylation, as well as an accumulation of heterochromatic epigenetic marks at telomeres, including histone H3K9 trimethylation and the heterochromatic protein HP2. Our work suggests that Drosophila telomere structure is epigenetically regulated by the histone deacetylase Rpd3.