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117 results on '"Cigliano, Riccardo Aiese"'

3. Development of a roadmap for action on the application of Omics and associated Bioinformatics Approaches in Risk Assessment.

Author

Radio, Santiago, Di Marsico, Marco, Bersani, Costanza, Malinverni, Roberto, Casacuberta, Josep, Corpetti, Chiara, Cigliano, Riccardo Aiese, and Sanseverino, Walter

Subjects
FOOD safety, RISK assessment, GOVERNMENT agencies, BIOINFORMATICS, POSSIBILITY
Abstract

The implementation of omics technologies and associated bioinformatics approaches hold significant promise for generating additional evidence for food and feed risk assessments thereby enhancing the European Food Safety Authority (EFSA) capacity to deliver scientific opinions and guidance documents in the future. To explore this possibility, EFSA launched a Call for the development of a roadmap to identify the main actions needed for a wider use of Omics in future risk assessments. To address this objective, this action roadmap outlines six project proposals. These proposals are based on a comprehensive mapping of the state‐of‐the‐art omics and associated bioinformatics technologies in research, EFSA's activities as well as current and planned activities from other relevant regulatory bodies and organisations. The outlined recommendations also address some of the identified main knowledge gaps and highlight the added value that further investments in the different food & feed safety scientific domains could bring. In addition, the work in this roadmap addresses some key challenges and blockers that might hinder a wider integration of omics in risk assessment and leverages on the opportunities for cooperation with external stakeholders. Finally, this roadmap provides suggestions on how EFSA may more broadly and effectively engage with relevant stakeholders in the use of omics technologies and associated bioinformatics approaches in regulatory science. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Caratterizzazione del microbiota fecale del suino Nero Siciliano dopo una dieta a base di siero di latte liquido.

Author

Tardiolo, Giuseppe, Romeo, Orazio, Zumbo, Alessandro, Di Marsico, Marco, Sutera, Anna Maria, Cigliano, Riccardo Aiese, Paytuví, Andreu, and D’Alessandro, Enrico

Abstract

Copyright of Summa, Animali da Reddito is the property of Point Veterinaire Italie s.r.l. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2024

7. The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

Author

Aversano, Riccardo, Contaldi, Felice, Ercolano, Maria Raffaella, Grosso, Valentina, Iorizzo, Massimo, Tatino, Filippo, Xumerle, Luciano, Molin, Alessandra Dal, Avanzato, Carla, Ferrarini, Alberto, Delledonne, Massimo, Sanseverino, Walter, Cigliano, Riccardo Aiese, Capella-Gutierrez, Salvador, Gabaldón, Toni, Frusciante, Luigi, Bradeen, James M., and Carputo, Domenico

Published
2015

14. Mitochondrial DNA is a frequent target of HBV integration

Author

Giosa, Domenico, primary, Lombardo, Daniele, additional, Musolino, Cristina, additional, Chines, Valeria, additional, Raffa, Giuseppina, additional, Tocco, Francesca Casuscelli di, additional, D’Aliberti, Deborah, additional, Caminiti, Giuseppe, additional, Saitta, Carlo, additional, Alibrandi, Angela, additional, Cigliano, Riccardo Aiese, additional, Romeo, Orazio, additional, Navarra, Giuseppe, additional, Raimondo, Giovanni, additional, and Pollicino, Teresa, additional

Published
2022
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15. A high-throughput viral integration sequencing method reveals that mitochondrial DNA is frequently targeted by HBV integration

Author

Giosa, Domenico, primary, Lombardo, Daniele, additional, Musolino, Cristina, additional, Chines, Valeria, additional, Raffa, Giuseppina, additional, D’aliberti, Deborah, additional, di Tocco, Francesca Casuscelli, additional, Saitta, Carlo, additional, Cigliano, Riccardo Aiese, additional, Romeo, Orazio, additional, Alibrandi, Angela, additional, Navarra, Giuseppe, additional, Raimondo, Giovanni, additional, and Pollicino, Teresa, additional

Published
2022
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17. Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation

Author

Varotto, Serena, Varotto, Serena, Krugman, Tamar, Cigliano, Riccardo Aiese, Kashkush, Khalil, Kondić-Špika, Ankica, Aravanopoulos, Fillipos A., Pradillo, Monica, Consiglio, Federica, Aversano, Riccardo, Pecinka, Ales, Miladinović, Dragana, Varotto, Serena, Varotto, Serena, Krugman, Tamar, Cigliano, Riccardo Aiese, Kashkush, Khalil, Kondić-Špika, Ankica, Aravanopoulos, Fillipos A., Pradillo, Monica, Consiglio, Federica, Aversano, Riccardo, Pecinka, Ales, and Miladinović, Dragana

Abstract

Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desired traits in plant germplasms and subsequently incorporating them into cultivars. Epigenetic diversity may provide an additional layer of variation within CWR and can contribute novel epialleles for key traits for crop improvement. There is emerging evidence that epigenetic variants of functional and/or agronomic importance exist in CWR gene pools. This provides a rationale for the conservation of epigenotypes of interest, thus contributing to agrobiodiversity preservation through conservation and (epi)genetic monitoring. Concepts and techniques of classical and modern breeding should consider integrating recent progress in epigenetics, initially by identifying their association with phenotypic variations and then by assessing their heritability and stability in subsequent generations. New tools available for epigenomic analysis offer the opportunity to capture epigenetic variation and integrate it into advanced (epi)breeding programmes. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers, such as epiQTLs.

Published
2022

19. Early Alpine occupation backdates westward human migration in Late Glacial Europe

Author

Bortolini, Eugenio, Pagani, Luca, Oxilia, Gregorio, Posth, Cosimo, Fontana, Federica, Badino, Federica, Saupe, Tina, Montinaro, Francesco, Margaritora, Davide, Romandini, Matteo, Lugli, Federico, Papini, Andrea, Boggioni, Marco, Perrini, Nicola, Oxilia, Antonio, Cigliano, Riccardo Aiese, Barcelona, Rosa, Visentin, Davide, Fasser, Nicolò, Arrighi, Simona, Figus, Carla, Marciani, Giulia, Silvestrini, Sara, Bernardini, Federico, Menghi Sartorio, Jessica C., Fiorenza, Luca, Cecchi, Jacopo Moggi, Tuniz, Claudio, Kivisild, Toomas, Gianfrancesco, Fernando, Peresani, Marco, Scheib, Christiana L., Talamo, Sahra, D’Esposito, Maurizio, and Benazzi, Stefano

Published
2021
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23. GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5′ and 3′ ends of its target genes

Author

Ruggieri, Valentino, Alexiou, Konstantinos, Morata, Jordi, Argyris, Jason, Pujol, Marta, Yano, Ryoichi, Nonaka, Satoko, Ezura, Hiroshi, Cigliano, Riccardo Aiese, Sanseverino, Walter, Puigdomenech, Pere, Casacuberta, Josep, Kirienko, Anna, Porozov, Yuri, Malkov, Nikita, Akhtemova, Gulnara, Le Signor, Christine, Thompson, Richard, Saffray, Christine, Dalmais, Marion, Tikhonovich, Igor, Dolgikh, Elena, Boucheham, Anouar, Sommard, Vivien, Zehraoui, Farida, Batouche, Mohamed, Israeli, David, Tahi, Fariza, Jacob, Pierre, Avni, Adi, Ligerot, Yasmine, De Saint Germain, Alexandre, Waldie, Tanya, Kadakia, Nikita, Pillot, Jean-Paul, Prigge, Michael, Aubert, Gregoire, Leyser, Ottoline, Estelle, Mark, Debellé, Frederic, Rameau, Catherine, GOUZY, Jerome, Badouin, Hélène, Lemainque, Arnaud, Vergne, Philippe, Moja, Sandrine, Choisne, Nathalie, Pont, Caroline, Carrere, Sebastien, Caissard, Jean-Claude, Couloux, Arnaud, Cottret, Ludovic, Aury, Jean-Marc, Szécsi, Judit, Madoui, Mohammed-Amin, Yang, Shu-Hua, Piola, Florence, Larrieu, Antoine, Perez, Magali, Labadie, Karine, Perrier, Lauriane, govetto, Benjamin, LABROUSSE, Yoan, Villand, Priscilla, Bardoux, Claudia, Boltz, Véronique, Lopez-Roques, Celine, Heitzler, Pascal, Vernoux, Teva, Quesneville, Hadi, Boualem, Adnane, Liu, Chang, Le Bris, Manuel, Salse, Jerome, Baudino, Sylvie, Wincker, Patrick, François, Léa, Verdenaud, Marion, Fu, Xiaopeng, Ruleman, Darcy, Dubois, Annick, Vandenbussche, Michiel, Raymond, Olivier, Just, Jérémy, Bendahmane, Mohammed, Giner, Ana, Pascual, Laura, Bourgeois, Michael, Gyetvai, Gabor, Rios, Pablo, Picó, Belén, Troadec, Christelle, Bendahmane, Abdel, Garcia-Mas, Jordi, MARTIN-HERNANDEZ, Ana Montserrat, Kim, Soonkap, Piquerez, Sophie, Ramirez-Prado, Juan, Mastorakis, Emmanouil, Veluchamy, Alaguraj, Latrasse, David, Manza-Mianza, Deborah, Brik-Chaouche, Rim, Huang, Ying, Rodriguez-Granados, Natalia, Concia, Lorenzo, Blein, Thomas, Citerne, Sylvie, Bendahmane, Abdelhafid, Bergounioux, Catherine, Crespi, Martin, Mahfouz, Magdy, Raynaud, Cécile, Hirt, Heribert, Ntoukakis, Vardis, BENHAMED, Moussa, Centre for Research in Agricultural Genomics (CRAG), IRTA, Center for Research in Agricultural Genomics, University of Tsukuba, Sequentia Biotech SL, LAboratoire PLasma et Conversion d'Energie (LAPLACE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), All-Russia Research Institute for Agricultural Microbiology, University Salah Boubnider Constantine 3, Laboratoire d'Informatique de Paris-Nord (LIPN), Université Sorbonne Paris Cité (USPC)-Institut Galilée-Université Paris 13 (UP13)-Centre National de la Recherche Scientifique (CNRS), LIRE laboratory, Constantine, University of Constantine, GENETHON 3, Université Paris Saclay (COmUE), Tel Aviv University [Tel Aviv], Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Sainsbury Laboratory, University of Cambridge [UK] (CAM), University of California [San Diego] (UC San Diego), University of California, Laboratoire de chimie organique et organométallique (LCOO), Université Sciences et Technologies - Bordeaux 1-Centre National de la Recherche Scientifique (CNRS), Division of Biology [La Jolla], University of California-University of California, UMR 0441 INRA / CNRS : Laboratoire de Biologie moléculaire des relations plantes-microorganismes, Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Sexe et évolution, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (LBVPAM), Université Jean Monnet [Saint-Étienne] (UJM), Unité de Recherche Génomique Info (URGI), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Département de chirurgie, CRLCC Val d'Aurelle - Paul Lamarque, Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Centre for Plant Integrative Biology [Nothingham] (CPIB), University of Nottingham, UK (UON), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), GeT PlaGe, Genotoul, Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sun Yat-Sen University [Guangzhou] (SYSU), Institut Méditerranéen d'Ecologie et de Paléoécologie (IMEP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS), Huazhong Agricultural University, Division of Biology [Pasadena], California Institute of Technology (CALTECH), Unité de recherche Génétique et amélioration des fruits et légumes (GAFL), Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Universitat Politecnica de Valencia (UPV), Institute of Agrifood Research and Technology (IRTA), Institut de Recerca i Tecnologia Agroalimentaries, King Abdullah University of Science and Technology (KAUST), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), School of Economics and Management [Beijing] (BUAA), Beihang University, Institut de biotechnologie des plantes (IBP), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Warwick [Coventry], AgroParisTech, and ANR-18-CE20-0015,EPICLIPSE,Dynamique des marques épigénétiques dans les cellules hôtes infectées et subversion de l'épigénome par le pathogène.(2018)

Subjects
0106 biological sciences, Transcription, Genetic, AcademicSubjects/SCI00010, [SDV]Life Sciences [q-bio], Arabidopsis, Biology, Genes, Plant, 01 natural sciences, Histones, 03 medical and health sciences, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Homeostasis, Plant Immunity, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Epigenetics, Promoter Regions, Genetic, QH426, ComputingMilieux_MISCELLANEOUS, Histone Acetyltransferases, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Arabidopsis Proteins, Lysine, Gene regulation, Chromatin and Epigenetics, Acetylation, Biotic stress, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Cell biology, Chromatin, enzymes and coenzymes (carbohydrates), Histone, Acetyltransferase, Transcription Coactivator, biology.protein, 5' Untranslated Regions, Salicylic Acid, 010606 plant biology & botany
Abstract

The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes even though GCN5 binding did not systematically correlate with gene activation. Here, we explored the mechanism through which GCN5 controls transcription. First, we fine-mapped its GCN5 binding sites genome-wide and then used several global methodologies (ATAC-seq, ChIP-seq and RNA-seq) to assess the effect of GCN5 loss-of-function on the expression and epigenetic regulation of its target genes. These analyses provided evidence that GCN5 has a dual role in the regulation of H3K14ac levels in their 5′ and 3′ ends of its target genes. While the gcn5 mutation led to a genome-wide decrease of H3K14ac in the 5′ end of the GCN5 down-regulated targets, it also led to an increase of H3K14ac in the 3′ ends of GCN5 up-regulated targets. Furthermore, genome-wide changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac at both 5′ and 3′ ends, providing evidence for a molecular link between the depositions of these two histone modifications. To understand the biological relevance of these regulations, we showed that GCN5 participates in the responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs. Hence, our results demonstrate that GCN5, through the modulation of H3K14ac levels on its targets, controls the balance between biotic and abiotic stress responses and is a master regulator of plant-environmental interactions.

Published
2020
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24. Genomics tools in the cloud: the new frontier in omics data analysis

Author

Universitat Politècnica de Catalunya. Facultat de Matemàtiques i Estadística, Cigliano, Riccardo Aiese, Sanseverino, Walter, Barcelona Cabeza, Rosa, Universitat Politècnica de Catalunya. Facultat de Matemàtiques i Estadística, Cigliano, Riccardo Aiese, Sanseverino, Walter, and Barcelona Cabeza, Rosa

Abstract

Substantial technological advancements in next generation sequencing (NGS) have revolutionized the genomic field. Over the last years, the speed and throughput of NGS technologies have increased while their costs have decreased, allowing us to achieve base-by-base interrogation of the human genome in an efficient and affordable way. All these advances have led to a growing application of NGS technologies in clinical practice to identify the genomics variations and their relationship with certain diseases. However, there is still the need to improve data accessibility, processing and interpretation due to both the huge amount of data generated by these sequencing technologies and the large number of tools available to process it. In addition to a large number of algorithms for variant discovery, each type of variation and data requires the use of a specific algorithm. Therefore, a solid background in bioinformatics is required to be able to select the most suitable algorithm in each case but also to be able to execute them successfully. On that basis, the aim of this project is to facilitate the processing of sequencing data for variant identification and interpretation for non-bioinformaticians. All this by creating high-performance workflows with a strong scientific basis, while remaining accessible and easy to use, as well as a simple and highly intuitive platform for data interpretation. An exhaustive bibliographic review has been carried out where the best existing algorithm has been selected to create automatic pipelines for the discovery of germline short variants (SNPs and indels) and germline structural variants (SVs), including both CNVs and chromosomal rearrangements, from modern human DNA. In addition to creating variant discovery pipelines, a pipeline has been implemented for in silico optimization of CNV detection from WES and TS data (isoCNV). This optimization pipeline has been shown to increase the sensitivity of CNV discovery using only NGS data. Su, Los avances tecnológicos en la secuenciación de próxima generación (NGS) han revolucionado el campo de la genómica. El aumento de velocidad y rendimiento de las tecnologías NGS de los últimos años junto con la reducción de su coste ha permitido interrogar base por base el genoma humano de una manera eficiente y asequible. Todos estos avances han permitido incrementar el uso de las tecnologías NGS en la práctica clínica para la identificación de variaciones genómicas y su relación con determinadas enfermedades. Sin embargo, sigue siendo necesario mejorar la accesibilidad, el procesamiento y la interpretación de los datos debido a la enorme cantidad de datos generados y a la gran cantidad de herramientas disponibles para procesarlos. Además de la gran cantidad de algoritmos disponibles para el descubrimiento de variantes, cada tipo de variación y de datos requiere un algoritmo específico. Por ello, se requiere una sólida formación en bioinformática tanto para poder seleccionar el algoritmo más adecuado como para ser capaz de ejecutarlo correctamente. Partiendo de esa base, el objetivo de este proyecto es facilitar el procesamiento de datos de secuenciación para la identificación e interpretación de variantes para los no bioinformáticos. Todo ello mediante la creación de flujos de trabajo de alto rendimiento y con una sólida base científica, sin dejar de ser accesibles y fáciles de utilizar, así como de una plataforma sencilla y muy intuitiva para la interpretación de datos. Se ha realizado una exhaustiva revisión bibliográfica donde se han seleccionado los mejores algoritmos con los que crear flujos de trabajo automáticos para el descubrimiento de variantes cortas germinales (SNPs e indels) y variantes estructurales germinales (SV), incluyendo tanto CNV como reordenamientos cromosómicos, de ADN humano moderno. Además de crear flujos de trabajo para el descubrimiento de variantes, se ha implementado un flujo para la optimización in silico de la detección de CNV a parti, Postprint (published version)

Published
2021

25. Early Alpine occupation backdates westward human migration in Late Glacial Europe

Author

Bortolini, Eugenio, primary, Pagani, Luca, additional, Oxilia, Gregorio, additional, Posth, Cosimo, additional, Fontana, Federica, additional, Badino, Federica, additional, Saupe, Tina, additional, Montinaro, Francesco, additional, Margaritora, Davide, additional, Romandini, Matteo, additional, Lugli, Federico, additional, Papini, Andrea, additional, Boggioni, Marco, additional, Perrini, Nicola, additional, Oxilia, Antonio, additional, Cigliano, Riccardo Aiese, additional, Barcelona, Rosa, additional, Visentin, Davide, additional, Fasser, Nicolò, additional, Arrighi, Simona, additional, Figus, Carla, additional, Marciani, Giulia, additional, Silvestrini, Sara, additional, Bernardini, Federico, additional, Sartorio, Jessica C. Menghi, additional, Fiorenza, Luca, additional, Moggi Cecchi, Jacopo, additional, Tuniz, Claudio, additional, Kivisild, Toomas, additional, Gianfrancesco, Fernando, additional, Peresani, Marco, additional, Scheib, Christiana L., additional, Talamo, Sahra, additional, D’Esposito, Maurizio, additional, and Benazzi, Stefano, additional

Published
2020
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26. Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms and the establishment of the Sporothrix Genome DataBase

Author

Giosa, Domenico, Felice, Maria Rosa, Giuffre, Letterio, Cigliano, Riccardo Aiese, Paytuvi-Gallart, Andreu, Passo, Carla Lo, Hoog, G.S. de, Romeo, Orazio, Giosa, Domenico, Felice, Maria Rosa, Giuffre, Letterio, Cigliano, Riccardo Aiese, Paytuvi-Gallart, Andreu, Passo, Carla Lo, Hoog, G.S. de, and Romeo, Orazio

Abstract

Contains fulltext : 226164.pdf (publisher's version ) (Open Access)

Published
2020

28. Maintaining oxidized H3 in heterochromatin is required for the oncogenic capacity of triple-negative breast cancer cells

Author

Serra-Bardenys, Gemma, primary, Tian, Tian, additional, Blanco, Enrique, additional, Querol, Jessica, additional, Pascual-Reguant, Laura, additional, Morancho, Beatriz, additional, Escorihuela, Marta, additional, Segura-Bayona, Sandra, additional, Verde, Gaetano, additional, Cigliano, Riccardo Aiese, additional, Millanes-Romero, Alba, additional, Jerónimo, Celia, additional, Nuciforo, Paolo, additional, Simonetti, Sara, additional, Viaplana, Cristina, additional, Dienstmann, Rodrigo, additional, Saura, Cristina, additional, Peg, Vicente, additional, Stracker, Travis, additional, Arribas, Joaquín, additional, Villanueva, Josep, additional, Di Croce, Luciano, additional, de Herreros, Antonio García, additional, and Peiró, Sandra, additional

Published
2020
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30. Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis

Author

Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, CSIC-USAL - Instituto de Biología Molecular y Celular del Cancer de Salamanca (IBMCC), Junta de Castilla y León, Instituto de Salud Carlos III, European Commission, Asociación Española Contra el Cáncer, Vara, Covadonga, Paytuví-Gallart, Andreu, Cuartero, Yasmina, Le Dily, Francois, García, Francisca, Salvà-Castro, Judit, Gómez Hernández, Laura, Julià, Eva, Moutinho, Catia, Cigliano, Riccardo Aiese, Sanseverino, Walter, Fornas, Oscar, Pendás, Alberto M., Heyn, Holger, Waters, Paul D., Marti-Renom, Marc A., Ruiz-Herrera, Aurora, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, CSIC-USAL - Instituto de Biología Molecular y Celular del Cancer de Salamanca (IBMCC), Junta de Castilla y León, Instituto de Salud Carlos III, European Commission, Asociación Española Contra el Cáncer, Vara, Covadonga, Paytuví-Gallart, Andreu, Cuartero, Yasmina, Le Dily, Francois, García, Francisca, Salvà-Castro, Judit, Gómez Hernández, Laura, Julià, Eva, Moutinho, Catia, Cigliano, Riccardo Aiese, Sanseverino, Walter, Fornas, Oscar, Pendás, Alberto M., Heyn, Holger, Waters, Paul D., Marti-Renom, Marc A., and Ruiz-Herrera, Aurora

Abstract

Mammalian gametogenesis involves dramatic and tightly regulated chromatin remodeling, whose regulatory pathways remain largely unexplored. Here, we generate a comprehensive high-resolution structural and functional atlas of mouse spermatogenesis by combining in situ chromosome conformation capture sequencing (Hi-C), RNA sequencing (RNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) of CCCTC-binding factor (CTCF) and meiotic cohesins, coupled with confocal and super-resolution microscopy. Spermatogonia presents well-defined compartment patterns and topological domains. However, chromosome occupancy and compartmentalization are highly re-arranged during prophase I, with cohesins bound to active promoters in DNA loops out of the chromosomal axes. Compartment patterns re-emerge in round spermatids, where cohesin occupancy correlates with transcriptional activity of key developmental genes. The compact sperm genome contains compartments with actively transcribed genes but no fine-scale topological domains, concomitant with the presence of protamines. Overall, we demonstrate how genome-wide cohesin occupancy and transcriptional activity is associated with three-dimensional (3D) remodeling during spermatogenesis, ultimately reprogramming the genome for the next generation.

Published
2019

31. Additional file 5: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

Author

Forestan, Cristian, Farinati, Silvia, Cigliano, Riccardo Aiese, Lunardon, Alice, Sanseverino, Walter, and Varotto, Serena

Abstract

Results of abundance filter on transcripts with different coding potential. Abundance filter (based on the Cuffdiff test-status; see Methods) was applied to filter out the not expressed or too lowly expressed transcripts (roughly excluding transcripts with FPKMÂ

Published
2017
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33. Additional file 9: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

Author

Forestan, Cristian, Farinati, Silvia, Cigliano, Riccardo Aiese, Lunardon, Alice, Sanseverino, Walter, and Varotto, Serena

Abstract

b1 gene overexpression in rpd1/rmr6 mutant leaves. The booster1 (b1, GRMZM2G172795) gene, which encodes a basic helix-loop-helix protein, resulted highly up-regulated in all the performed differential expression analyses, represents an hallmark of epigenetic silencing release in rpd1/rmr6 leaves compared with wild type. (DOCX 16Â kb)

Published
2017
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34. Additional file 21: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

Author

Forestan, Cristian, Farinati, Silvia, Cigliano, Riccardo Aiese, Lunardon, Alice, Sanseverino, Walter, and Varotto, Serena

Abstract

Summary of methylation levels at differentially expressed genes flanking regions obtained by permutation analysis. Methylation levels in each context (CG, CHG and CHH) were computed independently for the flanking regions (2 Kb for CG and CHG, 1 Kb for CHH; see Methods) of differentially expressed genes and compared to the average of genes in the genome using regioneR permutation approach [100]. Genes were divided into bins accordingly to fold change expression variation in rpd1/rmr6 mutant compared to wild-type (Additional file 19). For each bin the average methylation value is associated to the p-value obtained by permutation analysis, value that summarizes the statistical significance divergence between bin average methylation level and the average of annotated genes in the genome. Red and blue values indicate statistically higher and lower methylation levels, respectively, compared to the whole gene set. (DOCX 19Â kb)

Published
2017
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35. Additional file 4: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

Author

Forestan, Cristian, Farinati, Silvia, Cigliano, Riccardo Aiese, Lunardon, Alice, Sanseverino, Walter, and Varotto, Serena

Abstract

Results of abundance filter on annotated genes and transcripts. The maize transcriptome annotation used in this study includes 160,488 transcripts at 114,382 loci [40] that were initially filtered based on the Cuffdiff test-status (see Methods) to exclude the not expressed or too lowly expressed genes/transcripts (roughly excluding all those with FPKMÂ

Published
2017
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36. Gene deletion and genome perturbation

Author

Scala, Valeria, Grottoli, Alessandro, Cigliano, Riccardo Aiese, Beccaccioli, Marzia, Fanelli, Corrado, Dall’Asta, Chiara, Battilani, Paola, Reverberi, Massimo, and Sanseverino, Walter

Published
2016

39. Assessment of genomic changes in a CRISPR/Cas9 Phaeodactylum tricornutum mutant through whole genome resequencing.

Author

Russo, Monia Teresa, Cigliano, Riccardo Aiese, Sanseverino, Walter, and Ferrante, Maria Immacolata

Subjects
PHAEODACTYLUM tricornutum, CRISPRS
Abstract

The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, co-opted from a bacterial defense natural mechanism, is the cutting edge technology to carry out genome editing in a revolutionary fashion. It has been shown to work in many different model organisms, from human to microbes, including two diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana. Transforming P. tricornutum by bacterial conjugation, we have performed CRISPR/Cas9-based mutagenesis delivering the nuclease as an episome; this allowed for avoiding unwanted perturbations due to random integration in the genome and for excluding the Cas9 activity when it was no longer required, reducing the probability of obtaining off-target mutations, a major drawback of the technology. Since there are no reports on off-target occurrence at the genome level in microalgae, we performed whole-genome Illumina sequencing and found a number of different unspecific changes in both the wild type and mutant strains, while we did not observe any preferential mutation in the genomic regions in which off-targets were predicted. Our results confirm that the CRISPR/Cas9 technology can be efficiently applied to diatoms, showing that the choice of the conjugation method is advantageous for minimizing unwanted changes in the genome of P. tricornutum. [ABSTRACT FROM AUTHOR]

Published
2018
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40. Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits.

Author

Tranchida-Lombardo, Valentina, Cigliano, Riccardo Aiese, Anzar, Irantzu, Landi, Simone, Palombieri, Samuela, Colantuono, Chiara, Bostan, Hamed, Termolino, Pasquale, Aversano, Riccardo, Batelli, Giorgia, Cammareri, Maria, Carputo, Domenico, Chiusano, Maria Luisa, Conicella, Clara, Consiglio, Federica, D'Agostino, Nunzio, De Palma, Monica, Di Matteo, Antonio, Grandillo, Silvana, and Sanseverino, Walter

Abstract

Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65.8M and 56.4M of 30-150 bp paired-end reads, respectively. New contigs including reads that could not be mapped to the tomato reference genome were assembled, and a total of 43, 054 and 44, 579 gene loci were annotated in COR and LUC. Both genomes showed novel regions with similarity to Solanum pimpinellifolium and Solanum pennellii. In addition to small deletions and insertions, 2, 000 and 1, 700 single nucleotide polymorphisms (SNPs) could exert potentially disruptive effects on 1, 371 and 1, 201 genes in COR and LUC, respectively. A detailed survey of the SNPs occurring in fruit quality, shelf life and stress tolerance related-genes identified several candidates of potential relevance. Variations in ethylene response components may concur in determining peculiar phenotypes of COR and LUC. [ABSTRACT FROM AUTHOR]

Published
2018
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44. Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription.

Author

Forestan, Cristian, Farinati, Silvia, Cigliano, Riccardo Aiese, Lunardon, Alice, Sanseverino, Walter, and Varotto, Serena

Subjects
RNA, DNA methylation, POLYMERASE chain reaction, TRANSPOSONS, CYTOSINE
Abstract

Background: RNA-directed DNA methylation (RdDM) is a plant-specific epigenetic process that relies on the RNA polymerase IV (Pol IV) for the production of 24 nucleotide small interfering RNAs (siRNA) that guide the cytosine methylation and silencing of genes and transposons. Zea mays RPD1/RMR6 gene encodes the largest subunit of Pol IV and is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs) and transcriptional regulation of specific alleles. Results: In this study we applied a total RNA-Seq approach to compare the B73 and rpd1/rmr6 leaf transcriptomes. Although previous studies indicated that loss of siRNAs production in RdDM mutants provokes a strong loss of CHH DNA methylation but not massive gene or TEs transcriptional activation in both Arabidopsis and maize, our total RNA-Seq analysis of rpd1/rmr6 transcriptome reveals that loss of Pol IV activity causes a global increase in the transcribed fraction of the maize genome. Our results point to the genes with nearby TE insertions as being the most strongly affected by Pol IV-mediated gene silencing. TEs modulation of nearby gene expression is linked to alternative methylation profiles on gene flanking regions, and these profiles are strictly dependent on specific characteristics of the TE member inserted. Although Pol IV is essential for the biogenesis of siRNAs, the genes with associated siRNA loci are less affected by the pol IV mutation. Conclusions: This deep and integrated analysis of gene expression, TEs distribution, smallRNA targeting and DNA methylation levels, reveals that loss of Pol IV activity globally affects genome regulation, pointing at TEs as modulator of nearby gene expression and indicating the existence of multiple level epigenetic silencing mechanisms. Our results also suggest a predominant role of the Pol IV-mediated RdDM pathway in genome dominance regulation, and subgenome stability and evolution in maize. [ABSTRACT FROM AUTHOR]

Published
2017
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46. Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP.

Author

Ruggieri, Valentino, Anzar, Irantzu, Paytuvi, Andreu, Calafiore, Roberta, Cigliano, Riccardo Aiese, Sanseverino, Walter, and Barone, Amalia

Abstract

The recent development of Sequence Capture methodology represents a powerful strategy for enhancing data generation to assess genetic variation of targeted genomic regions. Here, we present SUPER-CAP, a bioinformatics web tool aimed at handling Sequence Capture data, fine calculating the allele frequency of variations and building genotype-specific sequence of captured genes. The dataset used to develop this in silico strategy consists of 378 loci and related regulative regions in a collection of 44 tomato landraces. About 14,000 high-quality variants were identified. The high depth (>40x) of coverage and adopting the correct filtering criteria allowed identification of about 4,000 rare variants and 10 genes with a different copy number variation. We also show that the tool is capable to reconstruct genotype-specific sequences for each genotype by using the detected variants. This allows evaluating the combined effect of multiple variants in the same protein. The architecture and functionality of SUPER-CAP makes the software appropriate for a broad set of analyses including SNP discovery and mining. Its functionality, together with the capability to process large data sets and efficient detection of sequence variation, makes SUPER-CAP a valuable bioinformatics tool for genomics and breeding purposes. [ABSTRACT FROM AUTHOR]

Published
2017
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47. Flowering and trichome development share hormonal and transcription factor regulation.

Author

Luis Matías-Hernández, Aguilar-Jaramillo, Andrea E., Cigliano, Riccardo Aiese, Sanseverino, Walter, and Pelaz, Soraya

Subjects
FLOWERING of plants, CYTOKINES, TRICHOMES, GIBBERELLINS, PLANT hormones
Abstract

Gibberellins (GAs) and cytokinins (CKs) are plant hormones that act either synergistically or antagonistically during the regulation of different developmental processes. In Arabidopsis thaliana, GAs and CKs overlap in the positive regulation of processes such as the transition from the vegetative to the reproductive phase and the development of epidermal adaxial trichomes. Despite the fact that both developmental processes originate in the rosette leaves, they occur separately in time and space. Here we review how, as genetic and molecular mechanisms are being unraveled, both processes might be closely related. Additionally, this shared genetic network is not only dependent on GA and CK hormone signaling but is also strictly controlled by specific clades of transcription factor families. Some key flowering genes also control other rosette leaf developmental processes such as adaxial trichome formation. Conversely, most of the trichome activator genes, which belong to the MYB, bHLH and C2H2 families, were found to positively control the floral transition. Furthermore, three MADS floral organ identity genes, which are able to convert leaves into floral structures, are also able to induce trichome proliferation in the flower. These data lead us to propose that the spatio-temporal regulation and integration of diverse signals control different developmental processes, such as floral induction and trichome formation, which are intimately connected through similar genetic pathways. [ABSTRACT FROM AUTHOR]

Published
2016
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49. Effects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling.

Author

Vacca, Marcella, Tripathi, Kumar Parijat, Speranza, Luisa, Cigliano, Riccardo Aiese, Scalabrì, Francesco, Marracino, Federico, Madonna, Michele, Sanseverino, Walter, Perrone-Capano, Carla, Guarracino, Mario Rosario, and D'Esposito, Maurizio

Subjects
RETT syndrome, BIOINFORMATICS, NEUROLOGICAL disorders, CEREBRAL cortex abnormalities, MORPHOMETRICS, ANIMAL disease models
Abstract

Background: Mecp2 null mice model Rett syndrome (RTT) a human neurological disorder affecting females after apparent normal pre- and peri-natal developmental periods. Neuroanatomical studies in cerebral cortex of RTT mouse models revealed delayed maturation of neuronal morphology and autonomous as well as non-cell autonomous reduction in dendritic complexity of postnatal cortical neurons. However, both morphometric parameters and high-resolution expression profile of cortical neurons at embryonic developmental stage have not yet been studied. Here we address these topics by using embryonic neuronal primary cultures from Mecp2 loss of function mouse model. Results: We show that embryonic primary cortical neurons of Mecp2 null mice display reduced neurite complexity possibly reflecting transcriptional changes. We used RNA-sequencing coupled with a bioinformatics comparative approach to identify and remove the contribution of variable and hard to quantify non-neuronal brain cells present in our in vitro cell cultures. Conclusions: Our results support the need to investigate both Mecp2 morphological as well as molecular effect in neurons since prenatal developmental stage, long time before onset of Rett symptoms. [ABSTRACT FROM AUTHOR]

Published
2016
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