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25 p, 6.3 MB |
Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals
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Álvarez-González, Lucía (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
Arias-Sardá, Cristina (University of Kent. School of Biosciences) ;
Montes-Espuña, Laia (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Marin Gual, Laia (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
Vara González, Covadonga (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Lister, Nicholas C. (University of New South Wales. School of Biotechnology and Biomolecular Sciences) ;
Cuartero, Yasmina (Centre de Regulació Genòmica) ;
García, Francisca (Universitat Autònoma de Barcelona. Servei de Cultius Cel·lulars, Producció d'Anticossos i Citometria) ;
Deakin, Janine (University of Canberra. Institute for Applied Ecology) ;
Renfree, Marilyn B. (The University of Melbourne. School of Biosciences) ;
Robinson, Terence J. (Stellenbosch University. Department of Botany and Zoology) ;
Martí-Renom, Marc A. (Centre de Regulació Genòmica) ;
Waters, Paul D. (University of New South Wales. School of Biotechnology and Biomolecular Sciences) ;
Farré, Marta (University of Kent. School of Biosciences) ;
Ruiz-Herrera Moreno, Aurora (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia)
Studying the similarities and differences in genomic interactions between species provides fertile grounds for determining the evolutionary dynamics underpinning genome function and speciation. Here, we describe the principles of 3D genome folding in vertebrates and show how lineage-specific patterns of genome reshuffling can result in different chromatin configurations. [...]
2022 -  10.1016/j.celrep.2022.111839
Cell reports, Vol. 41, Issue 12 (December 2022) , art. 111839
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17 p, 7.4 MB |
The impact of chromosomal fusions on 3D genome folding and recombination in the germ line
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Vara González, Covadonga (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Paytuví-Gallart, Andreu (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
Cuartero, Yasmina (Centre de Regulació Genòmica) ;
Álvarez-González, Lucía (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Marin Gual, Laia (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
García, Francisca (Universitat Autònoma de Barcelona. Servei de Cultius Cel·lulars, Producció d'Anticossos i Citometria) ;
Florit-Sabater, Beatriu (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Capilla, Laia (Universitat Autònoma de Barcelona. Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia) ;
Sanchéz-Guillén, Rosa Ana (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Sarrate Navas, Zaida (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
Aiese Cigliano, Riccardo (Sequentia Biotech) ;
Sanseverino, Walter (Sequentia Biotech) ;
Searle, Jeremy B. (Cornell University. Department of Ecology and Evolutionary Biology) ;
Ventura Queija, Jacinto (Universitat Autònoma de Barcelona. Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia) ;
Marti-Renom, Marc A. (Institució Catalana de Recerca i Estudis Avançats) ;
Le Dily, François (Centre de Regulació Genòmica) ;
Ruiz-Herrera Moreno, Aurora (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
The spatial folding of chromosomes inside the nucleus has regulatory effects on gene expression, yet the impact of genome reshuffling on this organization remains unclear. Here, we take advantage of chromosome conformation capture in combination with single-nucleotide polymorphism (SNP) genotyping and analysis of crossover events to study how the higher-order chromatin organization and recombination landscapes are affected by chromosomal fusions in the mammalian germ line. [...]
2021 - 10.1038/s41467-021-23270-1
Nature communications, Vol. 12 (May 2021) , art. 2981
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18 p, 6.6 MB |
A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer
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López de Maturana, Evangelina (Centro de Investigación Biomédica en Red de Cáncer) ;
Rodríguez, Juan Antonio (Centre de Regulació Genòmica) ;
Alonso, Lola (Centro de Investigación Biomédica en Red de Cáncer) ;
Lao, Oscar (Centre de Regulació Genòmica) ;
Molina-Montes, Esther (Centro de Investigación Biomédica en Red de Cáncer) ;
Martín-Antoniano, Isabel Adoración (Centro de Investigación Biomédica en Red de Cáncer) ;
Gómez-Rubio, Paulina (Centro de Investigación Biomédica en Red de Cáncer) ;
Lawlor, Rita (University and Hospital Trust of Verona. ARC-Net Centre for Applied Research on Cancer and Department of Pathology and Diagnostics) ;
Carrato, Alfredo (Instituto Ramón y Cajal de Investigación Sanitaria (Madrid)) ;
Hidalgo, Manuel (Weill Cornell Medicine) ;
Iglesias, Mar (Parc de Salut MAR de Barcelona) ;
Molero, Xavier (Universitat Autònoma de Barcelona. Departament de Medicina) ;
Löhr, Matthias (Gastrocentrum, Karolinska Institutet and University Hospital) ;
Michalski, Christopher (Martin-Luther-University Halle-WittenberHalle (Saale). Department of Visceral, Vascular and Endocrine Surgery) ;
Perea, José (Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz) ;
O'Rorke, Michael (The University of Iowa. College of Public Health) ;
Barberà, Victor Manuel (Hospital General Universitario de Elche) ;
Tardón, Adonina (Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública) ;
Farré, Antoni (Institut d'Investigació Biomèdica Sant Pau) ;
Muñoz-Bellvís, Luís (Instituto de Investigación Biomédica de Salamanca) ;
Crnogorac-Jurcevic, Tanja (Queen Mary University of London. Barts Cancer Institute, Centre for Molecular Oncology) ;
Domínguez-Muñoz, Enrique (Complejo Hospitalario Universitario de Santiago de Compostela) ;
Gress, Thomas (University Hospital of Giessen and Marburg (Alemanya)) ;
Greenhalf, William (University of Liverpool. Department of Molecular and Clinical Cancer Medicine) ;
Sharp, Linda (Newcastle University, Institute of Health & Society) ;
Arnes, Luís (Columbia University Medical Center. Department of Systems Biology) ;
Cecchini, Lluís (Parc de Salut MAR de Barcelona) ;
Balsells, Joaquim (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas) ;
Costello, Eithne (University of Liverpool. Department of Molecular and Clinical Cancer Medicine) ;
Ilzarbe, Lucas (Parc de Salut MAR de Barcelona) ;
Kleeff, Jörg (Martin-Luther-University Halle-WittenberHalle (Saale). Department of Visceral, Vascular and Endocrine Surgery) ;
Kong, Bo (Technical University of Munich. Department of Surgery) ;
Márquez, Mirari (Centro de Investigación Biomédica en Red de Cáncer) ;
Mora Brugués, Josefina (Institut d'Investigació Biomèdica Sant Pau) ;
O'Driscoll, Damian (University College Cork. National Cancer Registry Ireland and HRB Clinical Research Facility) ;
Scarpa, Aldo (University and Hospital Trust of Verona. ARC-Net Centre for Applied Research on Cancer and Department of Pathology and Diagnostics) ;
Ye, Weimin (Karolinska Institutet (Estocolm, Suècia). Department of Medical Epidemiology and Biostatistics) ;
Yu, Jingru (Karolinska Institutet (Estocolm, Suècia). Department of Medical Epidemiology and Biostatistics) ;
García-Closas, Montserrat (Centro Nacional de Investigaciones Oncológicas) ;
Kogevinas, M.. (Hospital del Mar (Barcelona, Catalunya)) ;
Rothman, Nathaniel (Centro Nacional de Investigaciones Oncológicas) ;
Silverman, Debra T. (Centro Nacional de Investigaciones Oncológicas) ;
Albanes, Demetrius (Centro Nacional de Investigaciones Oncológicas) ;
Arslan, Alan A. (New York University School of Medicine. Department of Population Health) ;
Beane-Freeman, Laura (Centro Nacional de Investigaciones Oncológicas) ;
Bracci, Paige M. (University of California. Department of Epidemiology and Biostatistics) ;
Brennan, Paul (International Agency for Research on Cancer (IARC)) ;
Bueno-de-Mesquita, Bas (National Institute for Public Health and the Environment (RIVM). Deparment for Determinants of Chronic Diseases (DCD)) ;
Buring, Julie (Brigham and Women's Hospital (Boston, Estats Units d'Amèrica)) ;
Canzian, Federico (German Cancer Research Center (DKFZ. Genomic Epidemiology Group) ;
Du, Margaret (Memorial Sloan Kettering Cancer Center) ;
Gallinger, Steven (Sinai Health System. Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute) ;
Gaziano, J. Michael (Brigham and Women's Hospital (Boston, Estats Units d'Amèrica)) ;
Goodman, Phyllis J. (SWOG Statistical Center, Fred Hutchinson Cancer Research Center) ;
Gunter, Marc (International Agency for Research on Cancer (IARC)) ;
LeMarchand, Loic (University of Hawaii Cancer Center. Cancer Epidemiology Program) ;
Li, Donghui (University of Texas MD Anderson Cancer Center) ;
Neale, Rachael E. (QIMR Berghofer Medical Research Institute (Brisbane, Austràlia). Population Health Department) ;
Peters, Ulrika (Fred Hutchinson Cancer Research Center. Division of Public Health Sciences) ;
Petersen, Gloria M. (Mayo Clinic College of Medicine. Department of Health Sciences Research) ;
Risch, Harvey A. (Yale School of Public Health. Department of Chronic Disease Epidemiology) ;
Sánchez, Maria José (Universidad de Granada) ;
Shu, Xiao-Ou (Vanderbilt University School of Medicine. Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center) ;
Thornquist, Mark D. (Fred Hutchinson Cancer Research Center. Division of Public Health Sciences) ;
Visvanathan, Kala (Mayo Clinic College of Medicine. Department of Health Sciences Research) ;
Zheng, Wei (Vanderbilt University School of Medicine. Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center) ;
Chanock, Stephen (Centro Nacional de Investigaciones Oncológicas) ;
Easton, Douglas F (University of Cambridge. Centre for Cancer Genetic Epidemiology) ;
Wolpin, Brian M. (Dana-Farber Cancer Institute (Boston, Estats Units d'Amèrica)) ;
Stolzenberg-Solomon, Rachael Z. (Centro Nacional de Investigaciones Oncológicas) ;
Klein, Alison P. (Johns Hopkins School of Medicine. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center) ;
Amundadottir, Laufey T. (National Cancer Institute (Bethesda, Estats Units d'Amèrica)) ;
Marti-Renom, Marc A. (Universitat Pompeu Fabra. Centre de Regulació Genòmica (CRG-UPF)) ;
Real, Francisco X (Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut) ;
Malats, Núria (Centro de Investigación Biomédica en Red de Cáncer)
Pancreatic cancer (PC) is a complex disease in which both non-genetic and genetic factors interplay. To date, 40 GWAS hits have been associated with PC risk in individuals of European descent, explaining 4. [...]
2021 - 10.1186/s13073-020-00816-4
Genome Medicine, Vol. 13 (february 2021)
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4.
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26 p, 7.4 MB |
Three-dimensional genomic structure and cohesin occupancy correlate with transcriptional activity during spermatogenesis
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Vara González, Covadonga (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Paytuví-Gallart, Andreu (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Cuartero, Yasmina (Centre de Regulació Genòmica) ;
Le Dily, François (Centre de Regulació Genòmica) ;
García, Francisca (Universitat Autònoma de Barcelona. Servei de Cultius Cel·lulars, Producció d'Anticossos i Citometria) ;
Salvà Castro, Judith (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Gomez Hernández, Laura (Centro de Investigación del Cáncer) ;
Julià, Eva (Institut Hospital del Mar d'Investigacions Mèdiques) ;
Moutinho, Catia (Centre de Regulació Genòmica) ;
Aiese Cigliano, Riccardo (Sequentia Biotech) ;
Sanseverino, Walter (Sequentia Biotech) ;
Fornas, Òscar (Centre de Regulació Genòmica) ;
Martín Pendas, Alberto (Centro de Investigación del Cáncer) ;
Heyn, Holger (Centre de Regulació Genòmica) ;
Waters, Paul D. (University of New South Wales. School of Biotechnology and Biomolecular Sciences) ;
Martí Renom, Marc A. (Centre de Regulació Genòmica) ;
Ruiz-Herrera Moreno, Aurora (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia)
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. [...]
2019 - 10.1016/j.celrep.2019.06.037
Cell reports, Vol. 28, issue 2 (Jul. 2019) , p. 352-367
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42 p, 12.6 MB |
"Manga-fying" la Commedia : dialogismo testuale e visivo in Dante Shinkyoku di Go Nagai
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Ciannella, Raul Ivan (Universitat Autònoma de Barcelona) ;
Martí Escayol, Maria Antònia (Universitat Autònoma de Barcelona. Departament d'Història Moderna i Contemporània)
L'articolo analizza Dante Shinkyoku, ダンテ神曲 (La Divina Commedia di Dante, 1994) un adattamento manga del poema dantesco realizzato da Go Nagai. Attraverso lo studio degli elementi strutturali, impiegati da Nagai per sostenere l'adattamento, e dei meccanismi di significazione e rappresentazione del linguaggio proprio del manga, sveleremo la molteplicità di livelli (storici, estetici, narrativi, discorsivi, ecc. [...]
In this article we will examine Dante Shinkyoku, ダンテ神曲 (The Divine Comedy of Dante, 1994), Go Nagai's manga adaptation of the Italian poem. Through the study of both the structural elements upon which the adaptation is sustained and manga's language inherent signifying and representational mechanisms, we will unveil the multiplicity of levels (historical, aesthetic, narrative, discursive, etc. [...]
2018 - 10.5565/rev/dea.101
Dante e l'Arte, Vol. 5 (2018) , p. 135-176 (Dossier monografico)
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8 p, 958.4 KB |
Prediction of enzyme function by combining sequence similarity and protein interactions
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Espadaler Mazo, Jordi (Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut) ;
Eswar, Narayanan (University of California. Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry) ;
Querol Murillo, Enrique (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Avilés, Francesc X. (Francesc Xavier) (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Sali, Andrej (University of California. Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry) ;
Martí Renom, Marc A. (Centro de Investigación Príncipe Felipe (València)) ;
Oliva Miguel, Baldomero (Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut)
Background: A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protein sequences are more likely to perform the same function if they share similar interacting partners. [...]
2008 - 10.1186/1471-2105-9-249
BMC bioinformatics, Vol. 9, N. 249 (May 2008), p. 1-8
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