To function effectively proteins must avoid aberrant aggregation, and hence they are expected to be expressed at concentrations safely below their solubility limits. By analyzing proteome-wide mass ...spectrometry data of Caenorhabditis elegans, however, we show that the levels of about three-quarters of the nearly 4,000 proteins analyzed in adult animals are close to their intrinsic solubility limits, indeed exceeding them by about 10% on average. We next asked how aging and functional self-assembly influence these solubility limits. We found that despite the fact that the total quantity of proteins within the cellular environment remains approximately constant during aging, protein aggregation sharply increases between days 6 and 12 of adulthood, after the worms have reproduced, as individual proteins lose their stoichiometric balances and the cellular machinery that maintains solubility undergoes functional decline. These findings reveal that these proteins are highly prone to undergoing concentration-dependent phase separation, which on aging is rationalized in a decrease of their effective solubilities, in particular for proteins associated with translation, growth, reproduction, and the chaperone system.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2000 coronaviruses and computed >100 000 human protein interactions ...with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genomic regions display different degrees of conservation. SARS-CoV-2 domain encompassing nucleotides 22 500-23 000 is conserved both at the sequence and structural level. The regions upstream and downstream, however, vary significantly. This part of the viral sequence codes for the Spike S protein that interacts with the human receptor angiotensin-converting enzyme 2 (ACE2). Thus, variability of Spike S is connected to different levels of viral entry in human cells within the population. Our predictions indicate that the 5' end of SARS-CoV-2 is highly structured and interacts with several human proteins. The binding proteins are involved in viral RNA processing, include double-stranded RNA specific editases and ATP-dependent RNA-helicases and have strong propensity to form stress granules and phase-separated assemblies. We propose that these proteins, also implicated in viral infections such as HIV, are selectively recruited by SARS-CoV-2 genome to alter transcriptional and post-transcriptional regulation of host cells and to promote viral replication.
is a lncRNA overexpressed in several epithelial cancers and strongly correlated with invasion. This lncRNA was proven a pivotal element of the epithelial-to-mesenchymal transition (EMT), a ...transdifferentiation process triggering metastasis. Snail, master inducer of EMT, requires
to recruit EZH2 on specific epithelial target genes (i.e.,
, and
) and cause their repression. Here, we designed a
deletion mutant form, named
-
, including the putative Snail-binding domain but depleted of the EZH2-binding domain.
-
acted as a dominant negative of the endogenous
. In both murine and human tumor cells,
-
impaired the ability of
to bind Snail and, in turn, trigger H3K27me3/EZH2-mediated repression of Snail epithelial target genes. Notably,
-
expression was proven to reduce cellular motility, invasiveness, anchorage-independent growth, and responsiveness to TGFβ-induced EMT. These data provide evidence on a lncRNA-based strategy to effectively impair the function of a master EMT-transcriptional factor. SIGNIFICANCE: This study defines an innovative RNA-based strategy to interfere with a pivotal function of the tumor-related lncRNA
, comprising a dominant negative mutant that was computationally designed and that impairs epithelial-to-mesenchymal transition.
One of the challenges in the healthcare sector is making accurate forecasts across insurance years for claims reserve. Healthcare claims present huge variability and heterogeneity influenced by ...random decisions of the courts and intrinsic characteristics of the damaged parties, which makes traditional methods for estimating reserves inadequate. We propose a new methodology to estimate claim reserves in the healthcare insurance system based on generalized linear models using the Overdispersed Poisson distribution function. In this context, we developed a method to estimate the parameters of the quasi-likelihood function using a Gauss–Newton algorithm optimized through a genetic algorithm. The genetic algorithm plays a crucial role in glimpsing the position of the global minimum to ensure a correct convergence of the Gauss–Newton method, where the choice of the initial guess is fundamental. This methodology is applied as a case study to the healthcare system of the Tuscany region. The results were validated by comparing them with state-of-the-art measurement of the confidence intervals of the Overdispersed Poisson distribution parameters with better outcomes. Hence, local healthcare authorities could use the proposed and improved methodology to allocate resources dedicated to healthcare and global management.
Identifying human proteins that interact with SARS-CoV-2 genome is important to understand its replication and to identify therapeutic strategies. Recent studies have unveiled protein interactions of ...SARS-COV-2 in different cell lines and through a number of high-throughput approaches. Here, we carried out a comparative analysis of four experimental and one computational studies to characterize the interactions of SARS-CoV-2 genomic RNA. Although hundreds of interactors have been identified, only twenty-one appear in all the experiments and show a strong propensity to bind. This set of interactors includes stress granule forming proteins, pre-mRNA regulators and elements involved in the replication process. Our calculations indicate that DDX3X and several editases bind the 5' end of SARS-CoV-2, a regulatory region previously reported to attract a large number of proteins. The small overlap among experimental datasets suggests that SARS-CoV-2 genome establishes stable interactions only with few interactors, while many proteins bind less tightly. In analogy to what has been previously reported for
non-coding RNA, we propose a mechanism of phase separation through which SARS-CoV-2 progressively sequesters human proteins hijacking the host immune response.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive single-stranded RNA virus, engages in complex interactions with host cell proteins throughout its life cycle. While these ...interactions enable the host to recognize and inhibit viral replication, they also facilitate essential viral processes such as transcription, translation, and replication. Many aspects of these virus-host interactions remain poorly understood. Here, we employed the catRAPID algorithm and utilized the RNA-protein interaction detection coupled with mass spectrometry technology to predict and validate the host proteins that specifically bind to the highly structured 5′ and 3′ terminal regions of the SARS-CoV-2 RNA. Among the interactions identified, we prioritized pseudouridine synthase PUS7, which binds to both ends of the viral RNA. Using nanopore direct RNA sequencing, we discovered that the viral RNA undergoes extensive post-transcriptional modifications. Modified consensus regions for PUS7 were identified at both terminal regions of the SARS-CoV-2 RNA, including one in the viral transcription regulatory sequence leader. Collectively, our findings offer insights into host protein interactions with the SARS-CoV-2 UTRs and highlight the likely significance of pseudouridine synthases and other post-transcriptional modifications in the viral life cycle. This new knowledge enhances our understanding of virus-host dynamics and could inform the development of targeted therapeutic strategies.
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Using proteomic approaches and in silico predictions, we identified the human host proteins interacting with the terminal regions of SARS-CoV-2 genome. Among these is PUS7, an enzyme converting uridine into pseudouridine. Nanopore sequencing confirmed that viral RNAs contained modified PUS7 consensus sequences, suggesting a role for PUS7 in the virus biology.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Abstract
Motivation
RNA structure is difficult to predict in vivo due to interactions with enzymes and other molecules. Here we introduce CROSSalive, an algorithm to predict the single- and ...double-stranded regions of RNAs in vivo using predictions of protein interactions.
Results
Trained on icSHAPE data in presence (m6a+) and absence of N6 methyladenosine modification (m6a-), CROSSalive achieves cross-validation accuracies between 0.70 and 0.88 in identifying high-confidence single- and double-stranded regions. The algorithm was applied to the long non-coding RNA Xist (17 900 nt, not present in the training) and shows an Area under the ROC curve of 0.83 in predicting structured regions.
Availability and implementation
CROSSalive webserver is freely accessible at http://service.tartaglialab.com/new_submission/crossalive
Supplementary information
Supplementary data are available at Bioinformatics online.
•The paper analyses the access to digital health services in the elderly.•A positive correlation is highlighted between the propensity to use and educational qualification.•Actual use is affected by ...regional government decisions on the tools applied.•‘Gender' and 'civil status' are not significant in accessing digital health services.
The Covid-19 pandemic has provided a major innovative thrust to public services regarding their digitization to continue providing an effective response to the population's needs and to reduce management costs. However, there has been a partial lack of those welfare policies that can provide an adequate response to the elderly segment of the population, which is most affected by the introduction of new technologies into the public sphere.
This study analyses the digital gap in health in the elderly living in remote areas of Italy and investigates the use of digital devices for health purposes. It compares the use of digital solutions for health with people's common digital competencies and their willingness to use them. A descriptive analysis of the sample was constructed to verify the different responses of the elderly by age, gender, educational qualification, and geographic area. Furthermore, regression analyses have been conducted to test whether there is any dependent effect among the elderly's characteristics or geographic areas.
The results highlight the existence of a potential digital health gap among the elderly in remote areas of Italy both due to infrastructural issues and the lack of digital skills. The latter are positively correlated with educational qualification, such that it is also possible to highlight differences between age groups analysed and shape future welfare policies to reduce digital inequality.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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•Single-stranded elements enriched in stress granules and P-bodies are disordered.•RNAs enriched in disorder form many contacts with RNAs.•Proteins enriched in disorder bind to ...disordered RNAs.
Condensation, or liquid-like phase separation, is a phenomenon indispensable for the spatiotemporal regulation of molecules within the cell. Recent studies indicate that the composition and molecular organization of phase-separated organelles such as Stress Granules (SGs) and Processing Bodies (PBs) are highly variable and dynamic. A dense contact network involving both RNAs and proteins controls the formation of SGs and PBs and an intricate molecular architecture, at present poorly understood, guarantees that these assemblies sense and adapt to different stresses and environmental changes. Here, we investigated the physico-chemical properties of SGs and PBs components and studied the architecture of their interaction networks. We found that proteins and RNAs establishing the largest amount of contacts in SGs and PBs have distinct properties and intrinsic disorder is enriched in all protein-RNA, protein-protein and RNA-RNA interaction networks. The increase of disorder in proteins is accompanied by an enrichment in single-stranded regions of RNA binding partners. Our results suggest that SGs and PBs quickly assemble and disassemble through dynamic contacts modulated by unfolded domains of their components.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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