Publications

2020

1. NAT COMMUN

   RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

   Bonetti, Alessandro, Agostini, Federico, Suzuki, Ana Maria, Hashimoto, Kosuke, Pascarella, Giovanni, Gimenez, Juliette, Roos, Leonie, Nash, Alex J, Ghilotti, Marco, Cameron, Christopher J F, Valentine, Matthew, Medvedeva, Yulia A., Noguchi, Shuhei, Agirre, Eneritz, Kashi, Kaori, Samudyata, , Luginbühl, Joachim, Cazzoli, Riccardo, Agrawal, Saumya, Luscombe, Nicholas M., Blanchette, Mathieu, Kasukawa, Takeya, Hoon, Michiel, Arner, Erik, Lenhard, Boris, Plessy, Charles, Castelo-Branco, Gonçalo, Orlando, Valerio, and Carninci, Piero

   Nature Communications 2020

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   Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. To investigate the function of such RNAs, methods to massively map the genomic interacting sites of multiple transcripts have been developed; however, these methods have some limitations. Here, we introduce RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), a technology that maps genome-wide RNA–chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation-based methodology that reduces the bias for nascent transcription, while increasing genomic coverage and unique mapping rate efficiency compared with existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type–specific RNA-chromatin interactions, and highlights the role of transcription in the establishment of chromatin structure.

2. BIORXIV

   Intergenic RNA mainly derives from nascent transcripts of known genes

   Agostini, Federico, Zagalak, Julian A, Attig, Jan, Ule, Jernej, Luscombe, Nicholas M, Federico, Agostini, Julian, Zagalak, Jan, Attig, Jernej, Ule, and M, Luscombe Nicholas

   bioRxiv 2020

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   Background: Eukaryotic genomes undergo pervasive transcription, leading to the production of many types of stable and unstable RNAs. Transcription is not restricted to regions with annotated gene features but includes almost any genomic context. Currently, the source and function of most RNAs originating from intergenic regions in the human genome remains unclear. Results: We hypothesised that many intergenic RNA can be ascribed to the presence of as-yet unannotated genes or the 'fuzzy' transcription of known genes that extends beyond the annotated boundaries. To elucidate the contributions of these two sources, we assembled a dataset of >2.5 billion publicly available RNA-seq reads across 5 human cell lines and multiple cellular compartments to annotate transcriptional units in the human genome. About 80% of transcripts from unannotated intergenic regions can be attributed to the fuzzy transcription of existing genes; the remaining transcripts originate mainly from putative long non-coding RNA loci that are rarely spliced. We validated the transcriptional activity of these intergenic RNA using independent measurements, including transcriptional start sites, chromatin signatures, and genomic occupancies of RNA polymerase II in various phosphorylation states. We also analysed the nuclear localisation and sensitivities of intergenic transcripts to nucleases to illustrate that they tend to be rapidly degraded either 'on-chromatin' by XRN2 or 'off-chromatin' by the exosome. Conclusions: We provide a curated atlas of intergenic RNAs that distinguishes between alternative processing of well annotated genes from independent transcriptional units based on the combined analysis of chromatin signatures, nuclear RNA localisation and degradation pathways.

3. NAT BIOTECHNOL

   GPSeq reveals the radial organization of chromatin in the cell nucleus

   Girelli, Gabriele, Custodio, Joaquin, Kallas, Tomasz, Agostini, Federico, Wernersson, Erik, Spanjaard, Bastiaan, Mota, Ana, Kolbeinsdottir, Solrun, Gelali, Eleni, Crosetto, Nicola, and Bienko, Magda

   Nature Biotechnology 2020

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   With the exception of lamina-associated domains, the radial organization of chromatin in mammalian cells remains largely unexplored. Here we describe genomic loci positioning by sequencing (GPSeq), a genome-wide method for inferring distances to the nuclear lamina all along the nuclear radius. GPSeq relies on gradual restriction digestion of chromatin from the nuclear lamina toward the nucleus center, followed by sequencing of the generated cut sites. Using GPSeq, we mapped the radial organization of the human genome at 100-kb resolution, which revealed radial patterns of genomic and epigenomic features and gene expression, as well as A and B subcompartments. By combining radial information with chromosome contact frequencies measured by Hi-C, we substantially improved the accuracy of whole-genome structure modeling. Finally, we charted the radial topography of DNA double-strand breaks, germline variants and cancer mutations and found that they have distinctive radial arrangements in A and B subcompartments. We conclude that GPSeq can reveal fundamental aspects of genome architecture.

4. NAT PROTOC

   Genome-wide detection of DNA double-strand breaks by in-suspension BLISS

   Bouwman, Britta A. M., Agostini, Federico, Garnerone, Silvano, Petrosino, Giuseppe, Gothe, Henrike J., Sayols, Sergi, Moor, Andreas E., Itzkovitz, Shalev, Bienko, Magda, Roukos, Vassilis, and Crosetto, Nicola

   Nature Protocols 2020

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   sBLISS (in-suspension breaks labeling in situ and sequencing) is a versatile and widely applicable method for identification of endogenous and induced DNA double-strand breaks (DSBs) in any cell type that can be brought into suspension. sBLISS provides genome-wide profiles of the most consequential DNA lesion implicated in a variety of pathological, but also physiological, processes. In sBLISS, after in situ labeling, DSB ends are linearly amplified, followed by next-generation sequencing and DSB landscape analysis. Here, we present a step-by-step experimental protocol for sBLISS, as well as a basic computational analysis. The main advantages of sBLISS are (i) the suspension setup, which renders the protocol user-friendly and easily scalable; (ii) the possibility of adapting it to a high-throughput or single-cell workflow; and (iii) its flexibility and its applicability to virtually every cell type, including patient-derived cells, organoids, and isolated nuclei. The wet-lab protocol can be completed in 1.5 weeks and is suitable for researchers with intermediate expertise in molecular biology and genomics. For the computational analyses, basic-to-intermediate bioinformatics expertise is required.

2019

1. NAT COMMUN

   iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture

   Gelali, Eleni, Girelli, Gabriele, Matsumoto, Masahiro, Wernersson, Erik, Custodio, Joaquin, Mota, Ana, Schweitzer, Maud, Ferenc, Katalin, Li, Xinge, Mirzazadeh, Reza, Agostini, Federico, Schell, John P., Lanner, Fredrik, Crosetto, Nicola, and Bienko, Magda

   Nature Communications 2019

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   DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells. At present, there is a lack of free resources of DNA FISH probes and probe design tools which can be readily applied. Here, we describe iFISH, an open-source repository currently comprising 380 DNA FISH probes targeting multiple loci on the human autosomes and chromosome X, as well as a genome-wide database of optimally designed oligonucleotides and a freely accessible web interface (http://ifish4u.org) that can be used to design DNA FISH probes. We individually validate 153 probes and take advantage of our probe repository to quantify the extent of intermingling between multiple heterologous chromosome pairs, showing a much higher extent of intermingling in human embryonic stem cells compared to fibroblasts. In conclusion, iFISH is a versatile and expandable resource, which can greatly facilitate the use of DNA FISH in research and diagnostics.

2018

1. EMBO J

   No way out: when RNA elements promote nuclear retention

   Agostini, Federico, Ule, Jernej, and Zagalak, Julian A

   The EMBO Journal 2018
2. CELL

   Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing

   Attig, Jan, Agostini, Federico, Gooding, Clare, Chakrabarti, Anob M, Singh, Aarti, Haberman, Nejc, Zagalak, Julian A, Emmett, Warren, Smith, Christopher W.J., Luscombe, Nicholas M, and Ule, Jernej

   Cell 2018

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   Long mammalian introns make it challenging for the RNA processing machinery to identify exons accurately. We find that LINE-derived sequences (LINEs) contribute to this selection by recruiting dozens of RNA-binding proteins (RBPs) to introns. This includes MATR3, which promotes binding of PTBP1 to multivalent binding sites within LINEs. Both RBPs repress splicing and 3′ end processing within and around LINEs. Notably, repressive RBPs preferentially bind to evolutionarily young LINEs, which are located far from exons. These RBPs insulate the LINEs and the surrounding intronic regions from RNA processing. Upon evolutionary divergence, changes in RNA motifs within LINEs lead to gradual loss of their insulation. Hence, older LINEs are located closer to exons, are a common source of tissue-specific exons, and increasingly bind to RBPs that enhance RNA processing. Thus, LINEs are hubs for the assembly of repressive RBPs and also contribute to the evolution of new, lineage-specific transcripts in mammals.

2015

1. PHD THESIS

   Predictions of RNA-binding ability and aggregation propensity of proteins

   Agostini, Federico

   2015

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   RNA-binding proteins (RBPs) control the fate of a multitude of coding and non-coding transcripts. Formation of ribonucleoprotein (RNP) complexes fine-tunes regulation of post-transcriptional events and influences gene expression. Recently, it has been observed that non-canonical proteins with RNA-binding ability are enriched in structurally disordered and low-complexity regions that are generally involved in functional and dysfunctional associations. Therefore, it is possible that interactions with RNA protect unstructured protein domains from aberrant associations or aggregation. Nevertheless, the mechanisms that prevent protein aggregation and the role of RNA in such processes are not well understood. In this work, I will describe algorithms that I have developed to predict protein solubility and to estimate the ability of proteins and transcripts to interact. I will illustrate applications of computational methods and show how they can be integrated with high throughput approaches. The overarching goal of my work is to provide experimentalists with tools that facilitate the investigation of regulatory mechanisms controlling protein homeostasis.

2014

1. BIOINFORMATICS

   The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities

   Klus, Petr, Bolognesi, Benedetta, Agostini, Federico, Marchese, Domenica, Zanzoni, Andreas, and Tartaglia, Gian Gaetano

   Bioinformatics 2014

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   Motivation: The recent shift towards high-throughput screening is posing new challenges for the interpretation of experimental results. Here we propose the cleverSuite approach for large-scale characterization of protein groups. Description: The central part of the cleverSuite is the cleverMachine (CM), an algorithm that performs statistics on protein sequences by comparing their physico-chemical propensities. The second element is called cleverClassifier and builds on top of the models generated by the CM to allow classification of new datasets. Results: We applied the cleverSuite to predict secondary structure properties, solubility, chaperone requirements and RNA-binding abilities. Using cross-validation and independent datasets, the cleverSuite reproduces experimental findings with great accuracy and provides models that can be used for future investigations. Availability: The intuitive interface for dataset exploration, analysis and prediction is available at http://s.tartaglialab.com/clever_suite.

2. MOL BIOSYST

   Discovery of protein–RNA networks

   Cirillo, Davide, Livi, Carmen Maria, Agostini, Federico, and Tartaglia, Gian Gaetano

   Mol. BioSyst. 2014

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   Coding and non-coding RNAs associate with proteins to perform important functions in the cell. Protein–RNA complexes are essential components of the ribosomal and spliceosomal machinery; they are involved in epigenetic regulation and form non-membrane-bound aggregates known as granules. Despite the functional importance of ribonucleoprotein interactions, the precise mechanisms of macromolecular recognition are still poorly understood. Here, we present the latest developments in experimental and computational investigation of protein–RNA interactions. We compare performances of different algorithms and discuss how predictive models allow the large-scale investigation of ribonucleoprotein associations. Specifically, we focus on approaches to decipher mechanisms regulating the activity of transcripts in protein networks. Finally, the catRAPID omics express method is introduced for the analysis of protein–RNA expression networks.

3. BBA-PROTEINS PROTEOM

   Molecular landscape of the interaction between the urease accessory proteins UreE and UreG

   Merloni, Anna, Dobrovolska, Olena, Zambelli, Barbara, Agostini, Federico, Bazzani, Micaela, Musiani, Francesco, and Ciurli, Stefano

   Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2014

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   Urease, the most efficient enzyme so far discovered, depends on the presence of nickel ions in the catalytic site for its activity. The transformation of inactive apo-urease into active holo-urease requires the insertion of two Ni(II) ions in the substrate binding site, a process that involves the interaction of four accessory proteins named UreD, UreF, UreG and UreE. This study, carried out using calorimetric and NMR-based structural analysis, is focused on the interaction between UreE and UreG from Sporosarcina pasteurii, a highly ureolytic bacterium. Isothermal calorimetric protein–protein titrations revealed the occurrence of a binding event between SpUreE and SpUreG, entailing two independent steps with positive cooperativity (Kd1 = 42 ± 9 \muM; Kd2 = 1.7 ± 0.3 \muM). This was interpreted as indicating the formation of the (UreE)2(UreG)2 hetero-oligomer upon binding of two UreG monomers onto the pre-formed UreE dimer. The molecular details of this interaction were elucidated using high-resolution NMR spectroscopy. The occurrence of SpUreE chemical shift perturbations upon addition of SpUreG was investigated and analyzed to establish the protein–protein interaction site. The latter appears to involve the Ni(II) binding site as well as mobile portions on the C-terminal and the N-terminal domains. Docking calculations based on the information obtained from NMR provided a structural basis for the protein–protein contact site. The high sequence and structural similarity within these protein classes suggests a generality of the interaction mode among homologous proteins. The implications of these results on the molecular details of the urease activation process are considered and analyzed.

4. BIOINFORMATICS

   ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli

   Agostini, Federico, Cirillo, Davide, Livi, C. M., Delli Ponti, Riccardo, and Tartaglia, G. G.

   Bioinformatics 2014

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   Summary: Here we introduce ccSOL omics, a webserver for large-scale calculations of protein solubility. Our method allows (i) proteome-wide predictions; (ii) identification of soluble fragments within each sequences; (iii) exhaustive single-point mutation analysis. Results: Using coil/disorder, hydrophobicity, hydrophilicity, β-sheet and α-helix propensities, we built a predictor of protein solubility. Our approach shows an accuracy of 79% on the training set (36 990 Target Track entries). Validation on three independent sets indicates that ccSOL omics discriminates soluble and insoluble proteins with an accuracy of 74% on 31 760 proteins sharing \textless30% sequence similarity. Availability and Implementation: ccSOL omics can be freely accessed on the web at http://s.tartaglialab.com/page/ccsol_group. Documentation and tutorial are available at http://s.tartaglialab.com/static_files/shared/tutorial_ccsol_omics.html.

5. BMC GENOMICS

   SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences

   Agostini, Federico, Cirillo, Davide, Ponti, Riccardo, and Tartaglia, Gian

   BMC Genomics 2014

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   Background: The large amount of data produced by high-throughput sequencing poses new computational challenges. In the last decade, several tools have been developed for the identification of transcription and splicing factor binding sites. Results: Here, we introduce the SeAMotE (Sequence Analysis of Motifs Enrichment) algorithm for discovery of regulatory regions in nucleic acid sequences. SeAMotE provides (i) a robust analysis of high-throughput sequence sets, (ii) a motif search based on pattern occurrences and (iii) an easy-to-use web-server interface. We applied our method to recently published data including 351 chromatin immunoprecipitation (ChIP) and 13 crosslinking immunoprecipitation (CLIP) experiments and compared our results with those of other well-established motif discovery tools. SeAMotE shows an average accuracy of 80% in finding discriminative motifs and outperforms other methods available in literature. Conclusions: SeAMotE is a fast, accurate and flexible algorithm for the identification of sequence patterns involved in protein-DNA and protein-RNA recognition. The server can be freely accessed at http://s.tartaglialab.com/ new_submission/seamote.

6. GENOME BIOL

   Constitutive patterns of gene expression regulated by RNA-binding proteins

   Cirillo, Davide, Marchese, Domenica, Agostini, Federico, Livi, Carmen, Botta-Orfila, Teresa, and Tartaglia, Gian

   Genome Biology 2014

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   Background: RNA-binding proteins regulate a number of cellular processes, including synthesis, folding, translocation, assembly and clearance of RNAs. Recent studies have reported that an unexpectedly large number of proteins are able to interact with RNA, but the partners of many RNA-binding proteins are still uncharacterized.Results: We combined prediction of ribonucleoprotein interactions, based on catRAPID calculations, with analysis of protein and RNA expression profiles from human tissues. We found strong interaction propensities for both positively and negatively correlated expression patterns. Our integration of in silico and ex vivo data unraveled two major types of protein-RNA interactions, with positively correlated patterns related to cell cycle control and negatively correlated patterns related to survival, growth and differentiation. To facilitate the investigation of protein-RNA interactions and expression networks, we developed the catRAPID express web server.Conclusions: Our analysis sheds light on the role of RNA-binding proteins in regulating proliferation and differentiation processes, and we provide a data exploration tool to aid future experimental studies. \textcopyright 2014 Cirillo et al.; licensee BioMed Central Ltd.

2013

1. WIREs

   Predictions of protein-RNA interactions

   Cirillo, Davide, Agostini, Federico, and Tartaglia, Gian Gaetano

   Wiley Interdisciplinary Reviews: Computational Molecular Science 2013

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   Ribonucleoprotein interactions play important roles in a wide variety of cellular processes, ranging from transcriptional and posttranscriptional regulation of gene expression to host defense against pathogens. High throughput experiments to identify RNA–protein interactions provide information about the complexity of interaction networks, but require time and considerable efforts. Thus, there is need for reliable computational methods for predicting ribonucleoprotein interactions. In this review, we discuss a number of approaches that have been developed to predict the ability of proteins and RNA molecules to associate.

2. NAR

   Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein

   Zanzoni, Andreas, Marchese, Domenica, Agostini, Federico, Bolognesi, Benedetta, Cirillo, Davide, Botta-Orfila, Maria, Livi, Carmen Maria, Rodriguez-Mulero, Silvia, and Tartaglia, Gian Gaetano

   Nucleic Acids Research 2013

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   Previous evidence indicates that a number of proteins are able to interact with cognate mRNAs. These autogenous associations represent important regulatory mechanisms that control gene expression at the translational level. Using the catRAPID approach to predict the propensity of proteins to bind to RNA, we investigated the occurrence of autogenous associations in the human proteome. Our algorithm correctly identified binding sites in well-known cases such as thymidylate synthase, tumor suppressor P53, synaptotagmin-1, serine/ariginine-rich splicing factor 2, heat shock 70 kDa, ribonucleic particle-specific U1A and ribosomal protein S13. In addition, we found that several other proteins are able to bind to their own mRNAs. A large-scale analysis of biological pathways revealed that aggregation-prone and structurally disordered proteins have the highest propensity to interact with cognate RNAs. These findings are substantiated by experimental evidence on amyloidogenic proteins such as TAR DNA-binding protein 43 and fragile X mental retardation protein. Among the amyloidogenic proteins, we predicted that Parkinson’s disease-related α-synuclein is highly prone to interact with cognate transcripts, which suggests the existence of RNA-dependent factors in its function and dysfunction. Indeed, as aggregation is intrinsically concentration dependent, it is possible that autogenous interactions play a crucial role in controlling protein homeostasis. \textcopyright 2013 The Author(s).

3. NAR

   X-inactivation: quantitative predictions of protein interactions in the Xist network

   Agostini, Federico, Cirillo, Davide, Bolognesi, Benedetta, and Tartaglia, Gian Gaetano

   Nucleic Acids Research 2013

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   The transcriptional silencing of one of the female X-chromosomes is a finely regulated process that requires accumulation in cis of the long non-coding RNA X-inactive-specific transcript (Xist) followed by a series of epigenetic modifications. Little is known about the molecular machinery regulating initiation and maintenance of chromosomal silencing. Here, we introduce a new version of our algorithm catRAPID to investigate Xist associations with a number of proteins involved in epigenetic regulation, nuclear scaffolding, transcription and splicing processes. Our method correctly identifies binding regions and affinities of protein interactions, providing a powerful theoretical framework for the study of X-chromosome inactivation and other events mediated by ribonucleoprotein associations. \textcopyright 2012 The Author(s). Published by Oxford University Press.

4. BIOINFORMATICS

   catRAPID omics: a web server for large-scale prediction of protein-RNA interactions

   Agostini, Federico, Zanzoni, Andreas, Klus, Petr, Marchese, Domenica, Cirillo, Davide, and Tartaglia, Gian Gaetano

   Bioinformatics 2013

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   Summary: Here we introduce catRAPID omics, a server for largescale calculations of protein-RNA interactions. Our web server allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences without size restriction; (iii) analysis of nucleic acid binding regions in proteins; and (iv) detection of RNA motifs involved in protein recognition. Results: We developed a web server to allow fast calculation of ribonucleoprotein associations in Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae and Xenopus tropicalis (custom libraries can be also generated). The catRAPID omics was benchmarked on the recently published RNA interactomes of Serine/arginine-rich splicing factor 1 (SRSF1), Histone-lysine N-methyltransferase EZH2 (EZH2), TAR DNA-binding protein 43 (TDP43) and RNAbinding protein FUS (FUS) as well as on the protein interactomes of U1/U2 small nucleolar RNAs, X inactive specific transcript (Xist) repeat A region (RepA) and Crumbs homolog 3 (CRB3) 3′-untranslated region RNAs. Our predictions are highly significant (P\textless0.05) and will help the experimentalist to identify candidates for further validation. \textcopyright The Author 2013. Published by Oxford University Press. All rights reserved.

5. RNA

   Neurodegenerative diseases: Quantitative predictions of protein-RNA interactions

   Cirillo, Davide, Agostini, Federico, Klus, Petr, Marchese, Domenica, Rodriguez, Silvia, Bolognesi, Benedetta, and Tartaglia, Gian Gaetano

   RNA 2013

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   Increasing evidence indicates that RNA plays an active role in a number of neurodegenerative diseases. We recently introduced a theoretical framework, catRAPID, to predict the binding ability of protein and RNA molecules. Here, we use catRAPID to investigate ribonucleoprotein interactions linked to inherited intellectual disability, amyotrophic lateral sclerosis, Creutzfeuld-Jakob, Alzheimer’s, and Parkinson’s diseases. We specifically focus on (1) RNA interactions with fragile X mental retardation protein FMRP; (2) protein sequestration caused by CGG repeats; (3) noncoding transcripts regulated by TAR DNA-binding protein 43 TDP-43; (4) autogenous regulation of TDP-43 and FMRP; (5) iron-mediated expression of amyloid precursor protein APP and α-synuclein; (6) interactions between prions and RNA aptamers. Our results are in striking agreement with experimental evidence and provide new insights in processes associated with neuronal function and misfunction. Copyright \textcopyright 2013 RNA Society.

2012

1. JMB

   Sequence-Based Prediction of Protein Solubility

   Agostini, Federico, Vendruscolo, Michele, and Tartaglia, Gian Gaetano

   Journal of Molecular Biology 2012

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   In order to investigate the relationship between the thermodynamics and kinetics of protein aggregation, we compared the solubility of proteins with their aggregation rates. We found a significant correlation between these two quantities by considering a database of protein solubility values measured using an in vitro reconstituted translation system containing about 70% of Escherichia coli proteins. The existence of such correlation suggests that the thermodynamic stability of the native states of proteins relative to the aggregate states is closely linked with the kinetic barriers that separate them. In order to create the possibility of conducting computational studies at the proteome level to investigate further this concept, we developed a method of predicting the solubility of proteins based on their physicochemical properties. \textcopyright 2011 Elsevier Ltd. All rights reserved.

2. CELL REP

   DnaK Functions as a Central Hub in the E. coli Chaperone Network

   Calloni, Giulia, Chen, Taotao, Schermann, Sonya M., Chang, Hung-chun, Genevaux, Pierre, Agostini, Federico, Tartaglia, Gian Gaetano, Hayer-Hartl, Manajit, and Hartl, F. Ulrich

   Cell Reports 2012

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   Cellular chaperone networks prevent potentially toxic protein aggregation and ensure proteome integrity. Here, we used Escherichia coli as a model to understand the organization of these networks, focusing on the cooperation of the DnaK system with the upstream chaperone Trigger factor (TF) and the downstream GroEL. Quantitative proteomics revealed that DnaK interacts with at least ∼700 mostly cytosolic proteins, including ∼180 relatively aggregation-prone proteins that utilize DnaK extensively during and after initial folding. Upon deletion of TF, DnaK interacts increasingly with ribosomal and other small, basic proteins, while its association with large multidomain proteins is reduced. DnaK also functions prominently in stabilizing proteins for subsequent folding by GroEL. These proteins accumulate on DnaK upon GroEL depletion and are then degraded, thus defining DnaK as a central organizer of the chaperone network. Combined loss of DnaK and TF causes proteostasis collapse with disruption of GroEL function, defective ribosomal biogenesis, and extensive aggregation of large proteins. \textcopyright 2012 The Authors.

2011

1. NAT METHODS

   Predicting protein associations with long noncoding RNAs

   Bellucci, Matteo, Agostini, Federico, Masin, Marianela, and Tartaglia, Gian Gaetano

   Nature Methods 2011

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   Only a small fraction of the human transcriptome (∼1%) encodes proteins1, but a large portion of transcripts is long noncoding RNAs (lncRNAs) and is an unexplored component of mammalian genomes2. Here we introduce a method to perform large-scale predictions of protein-RNA associations. Our algorithm, ’fast predictions of RNA and protein interactions and domains at the Center for Genomic Regulation, Barcelona, Catalonia’ (catRAPID), evaluates the interaction propensities of polypeptide and nucleotide chains using their physicochemical properties. The algorithm is freely available at http://big.crg.cat/gene_function_and_evolution/services/catrapid.

2. ANGEW CHEM INT EDIT

   Disulfide Bonds Reduce the Toxicity of the Amyloid Fibrils Formed by an Extracellular Protein

   Mossuto, Maria F., Bolognesi, Benedetta, Guixer, Bernat, Dhulesia, Anne, Agostini, Federico, Kumita, Janet R., Tartaglia, Gian G., Dumoulin, Mireille, Dobson, Christopher M., and Salvatella, Xavier

   Angewandte Chemie International Edition 2011

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   In a stable condition: Disulfide bonds stabilize folded proteins primarily by decreasing the entropic cost of folding. Such cross-links also reduce toxic aggregation by favoring the formation of highly structured amyloid fibrils (see picture). It is suggested that disulfide bonds in extracellular proteins were selected by evolutionary pressures because they decrease the propensity to form toxic aggregates. Copyright \textcopyright 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.