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11.
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17 p, 2.5 MB |
Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction
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Català-Moll, Francesc (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ferreté-Bonastre, Anna G. (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Li, Tianlu (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Weichenhan, Dieter (German Cancer Research Center (DKFZ)) ;
Lutsik, Pavlo (German Cancer Research Center (DKFZ)) ;
Ciudad, Laura (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Álvarez-Prado, Ángel F. (Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares) ;
Rodríguez-Ubreva, Javier (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Klemann, Christian (University of Freiburg) ;
Speckmann, Carsten (University of Freiburg) ;
Vilas-Zornoza, Amaya (Universidad de Navarra) ;
Abolhassani, Hassan (Karolinska University) ;
Martínez Gallo, Mónica (Hospital Universitari Vall d'Hebron) ;
Dieli-Crimi, Romina (Hospital Universitari Vall d'Hebron) ;
Rivière, Jacques G.. (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Martín-Nalda, Andrea (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Colobrán Oriol, Roger (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
Soler-Palacín, Pere (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Kracker, Sven (Universite de Paris) ;
Hammarström, Lennart (Karolinska University) ;
Prosper, Felipe (Universidad de Navarra) ;
Durandy, Anne (Universite de Paris) ;
Grimbacher, Bodo (University of Freiburg) ;
Plass, Christoph (German Cancer Research Center (DKFZ)) ;
Ballestar, Esteban (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras)
Activation-induced deaminase (AID) initiates antibody diversification in germinal center B cells by deaminating cytosines, leading to somatic hypermutation and class-switch recombination. Loss-of-function mutations in AID lead to hyper-IgM syndrome type 2 (HIGM2), a rare human primary antibody deficiency. [...]
2021 -  10.1093/nar/gkab322
Nucleic acids research, Vol. 49, Issue 9 (May 2021) , p. 5057-5073
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12.
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20 p, 10.5 MB |
Binding site profiles and N-terminal minor groove interactions of the master quorum-sensing regulator LuxR enable flexible control of gene activation and repression
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Zhang, Jun (East China University of Science and Technology. State Key Laboratory of Bioreactor Engineering (China)) ;
Liu, Bing (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Gu, Dan (Yangzhou University. Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses (China)) ;
Hao, Yuan (East China University of Science and Technology. State Key Laboratory of Bioreactor Engineering (China)) ;
Chen, Mo (East China University of Science and Technology. State Key Laboratory of Bioreactor Engineering (China)) ;
Ma, Yue (East China University of Science and Technology. State Key Laboratory of Bioreactor Engineering (China)) ;
Zhou, Xiaohui (University of Connecticut. Department of Pathobiology and Veterinary Science (USA)) ;
Reverter i Cendrós, David (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Zhang, Yuanxing (Southern Marine Science and Engineering Guangdong Laboratory (China)) ;
Wang, Qiyao (East China University of Science and Technology. State Key Laboratory of Bioreactor Engineering (China)) ;
Universitat Autònoma de Barcelona.
Departament de Bioquímica i de Biologia Molecular
LuxR is a TetR family master quorum sensing (QS) regulator activating or repressing expression of hundreds of genes that control collective behaviors in Vibrios with underlying mechanism unknown. To illuminate how this regulator controls expression of various target genes, we applied ChIP-seq and DNase I-seq technologies. [...]
2021 - 10.1093/nar/gkab150
Nucleic acids research, Vol. 49, Issue 6 (April 2021) , p. 3274-3293
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13.
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7 p, 1.9 MB |
DualSeqDB : the host-pathogen dual RNA sequencing database for infection processes
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Macho Rendón, Javier (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Lang, Benjamin (Centre de Regulació Genòmica.) ;
Ramos Llorens, Marc (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Tartaglia, Gian Gaetano (Centre de Regulació Genòmica.) ;
Torrent Burgas, Marc (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Despite antibiotic resistance being a matter of growing concern worldwide, the bacterial mechanisms of pathogenesis remain underexplored, restraining our ability to develop new antimicrobials. The rise of high-throughput sequencing technology has made available a massive amount of transcriptomic data that could help elucidate the mechanisms underlying bacterial infection. [...]
2020 - 10.1093/nar/gkaa890
Nucleic acids research, Vol. 49, Issue D1 (October 2020) , p. D687-D693
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14.
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14 p, 2.4 MB |
Structural analysis of SARS-CoV-2 genome and predictions of the human interactome
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Vandelli, Andrea (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Monti, Michele (Universitat Pompeu Fabra) ;
Milanetti, Edoardo (Sapienza Università di Roma) ;
Armaos, Alexandros (Universitat Pompeu Fabra) ;
Rupert, Jakob (Istituto Italiano di Tecnologia) ;
Zacco, Elsa (Istituto Italiano di Tecnologia) ;
Bechara, Elias (Universitat Pompeu Fabra) ;
Delli Ponti, Riccardo (Nanyang Technological University) ;
Tartaglia, Gian Gaetano (Universitat Pompeu Fabra)
Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2000 coronaviruses and computed >100 000 human protein interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). [...]
2020 - 10.1093/nar/gkaa864
Nucleic acids research, Vol. 48, Issue 20 (November 2020) , p. 11270-11283
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15.
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16 p, 2.3 MB |
SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina
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Vazquez Prat, Berta Nieves (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Thackray, J. K. (Department of Genetics. Human Genetics Institute of New Jersey. Rutgers University) ;
Simonet, N. G. (Institut d'Investigació Biomèdica de Bellvitge) ;
Chahar, S. (Montpellier Institute of Molecular Genetics (IGMM). CNRS. University of Montpellier) ;
Kane-Goldsmith, N. (Department of Genetics. Human Genetics Institute of New Jersey. Rutgers University) ;
Newkirk, S. J. (Department of Pharmaceutical Sciences. College of Pharmacy and Allied Health Professions. South Dakota State University) ;
Lee, S. (Department of Pharmaceutical Sciences. College of Pharmacy and Allied Health Professions. South Dakota State University) ;
Xing, J. (Department of Genetics. Human Genetics Institute of New Jersey. Rutgers University) ;
Verzi, M. P. (Department of Genetics. Human Genetics Institute of New Jersey. Rutgers University) ;
An, W. (Department of Pharmaceutical Sciences. College of Pharmacy and Allied Health Professions. South Dakota State University) ;
Vaquero, Alejandro (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Tischfield, J. A. (Department of Genetics. Human Genetics Institute of New Jersey. Rutgers University) ;
Serrano, L. (Department of Genetics. Human Genetics Institute of New Jersey. Rutgers University) ;
Universitat Autònoma de Barcelona
Long interspersed elements-1 (LINE-1, L1) are retrotransposons that hold the capacity of self-propagation in the genome with potential mutagenic outcomes. How somatic cells restrict L1 activity and how this process becomes dysfunctional during aging and in cancer cells is poorly understood. [...]
2019 - 10.1093/nar/gkz519
Nucleic acids research, Vol. 47 Núm. 15 (january 2019) , p. 7870-7885
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16.
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22 p, 5.2 MB |
Chromatin regulation by Histone H4 acetylation at Lysine 16 during cell death and differentiation in the myeloid compartment
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Urdinguio, Rocío G. (Instituto de Oncología de Asturias-IUOPA) ;
López, Virginia (Centro de Investigación en Nanociencia y Nanotecnología (Oviedo, Astúries)) ;
Fernández Bayón, Gustavo (Instituto de Oncología de Asturias-IUOPA) ;
Díaz de la Guardia, Rafael (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Sierra, Marta I. (Instituto de Oncología de Asturias-IUOPA) ;
García-Toraño, Estela (Instituto de Oncología de Asturias-IUOPA) ;
Pérez, Raúl F. (Instituto de Oncología de Asturias-IUOPA) ;
García, María G. (Instituto de Oncología de Asturias-IUOPA) ;
Carella, Antonella (Instituto de Oncología de Asturias-IUOPA) ;
Pruneda, Patricia C. (Instituto de Oncología de Asturias-IUOPA) ;
Prieto, Cristina (Instituto de Oncología de Asturias-IUOPA) ;
Dmitrijeva, Marija (Instituto de Oncología de Asturias-IUOPA) ;
Santamarina-Ojeda, Pablo (Instituto de Oncología de Asturias-IUOPA) ;
Belmonte, Thalia (Instituto de Oncología de Asturias-IUOPA) ;
Mangas, Cristina (Instituto de Oncología de Asturias-IUOPA) ;
Diaconu, Elena (Instituto de Oncología de Asturias-IUOPA) ;
Ferrero, Cecilia (Instituto de Oncología de Asturias-IUOPA) ;
Tejedor, Juan Ramón (Instituto de Oncología de Asturias-IUOPA) ;
Fernandez-Morera, Juan Luis (Instituto de Oncología de Asturias-IUOPA) ;
Bravo, Cristina (Instituto de Oncología de Asturias-IUOPA) ;
Bueno, Clara (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Sanjuan-Pla, Alejandra (Instituto de Investigación Sanitaria La Fe) ;
Rodríguez López, Ramón María (Hospital Universitario Central de Asturias) ;
Suárez-Álvarez, Beatriz (Hospital Universitario Central de Asturias) ;
López-Larrea, Carlos (Hospital Universitario Central de Asturias) ;
Bernal, Teresa (Hospital Universitario Central de Asturias) ;
Colado, Enrique (Hospital Universitario Central de Asturias) ;
Balbín, Milagros (Hospital Universitario Central de Asturias) ;
García-Suarez, Olivia (Universidad de Oviedo. Departamento de Morfología y Biología Celular) ;
Chiara, María Dolores (Hospital Universitario Central de Asturias) ;
Sáenz De Santa María, Inés (Hospital Universitario Central de Asturias) ;
Rodríguez, Francisco (Universidad de Oviedo. Departamento de Bioquímica y Biología Molecular) ;
Pando-Sandoval, Ana (Hospital Universitario Central de Asturias) ;
Rodrigo-Sáez, Luis (Hospital Universitario Central de Asturias) ;
Santos, Laura. (Instituto de Investigación Sanitaria del Principado de Asturias) ;
Salas, Ana (Universidad de Oviedo. Servicio de Citometría) ;
Vallejo-Díaz, Jesús (Centro Nacional de Biotecnología (CNB-CSIC)) ;
Carrera, Ana C. (Centro Nacional de Biotecnología (CNB-CSIC)) ;
Rico, Daniel (Newcastle University. Institute of Cellular Medicine) ;
Hernández-López, Inmaculada (Newcastle University. Institute of Cellular Medicine) ;
Vayá, Amparo (Hospital Universitari i Politècnic La Fe (València)) ;
Ricart, José María (Quirón Clinic. Dermatology Service) ;
Seto, Edward (George Washington University Cancer Center) ;
Sima, Núria (Institut d'Investigació Biomèdica de Bellvitge) ;
Vaquero, Alejandro (Institut d'Investigació Biomèdica de Bellvitge) ;
Valledor, Luís (Universidad de Oviedo. Facultad de Biología) ;
Cañal Villanueva, María Jesús Fátima (Universidad de Oviedo. Facultad de Biología) ;
Pisano, David (Centro Nacional de Investigaciones Oncológicas) ;
Graña-Castro, Osvaldo (Centro Nacional de Investigaciones Oncológicas) ;
Thomas, Tim (University of Melbourne. Department of Medical Biology (Austràlia)) ;
Voss, Anne Kathrin (University of Melbourne. Department of Medical Biology (Austràlia)) ;
Menéndez Bujan, Pablo (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Villar-Garea, Ana (University of Regensburg) ;
Deutzmann, Rainer (University of Regensburg) ;
Fernández, Agustín F (Instituto de Oncología de Asturias-IUOPA) ;
Fraga, Mario F. (Centro de Investigación en Nanociencia y Nanotecnología (Oviedo, Astúries)) ;
Universitat Autònoma de Barcelona
Histone H4 acetylation at Lysine 16 (H4K16ac) is a key epigenetic mark involved in gene regulation, DNA repair and chromatin remodeling, and though it is known to be essential for embryonic development, its role during adult life is still poorly understood. [...]
2019 - 10.1093/nar/gkz195
Nucleic acids research, Vol. 47 Núm. 10 (april 2019) , p. 5016-5037
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17.
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18 p, 4.0 MB |
Targeting OGG1 arrests cancer cell proliferation by inducing replication stress
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Visnes, T. (Sintef Industry. Department of Biotechnology and Nanomedicine) ;
Benítez-Buelga, Carlos (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Cázares-Körner, A. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Sanjiv, K. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Hanna, Bishoy (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Mortusewicz, O. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Rajagopal, Veera M (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Albers, J. J. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Hagey, D. W. (Karolinska Institutet (Estocolm, Suècia). Department of Laboratory Medicine) ;
Bekkhus, T. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Eshtad, S. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Baquero, Juan Miguel (Centro Nacional de Investigaciones Oncológicas) ;
Masuyer, G. (University of Bath. Department of Pharmacy and Pharmacology) ;
Wallner, O. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Müller, S. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Pham, T. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Göktürk, C. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Rasti, A. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Suman, S. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Torres, Raul (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Sarno, A. (Sintef Ocean. Department of Environment and New Resources) ;
Wiita, E. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Homan, E. J. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Karsten, S. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Marimuthu, K. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Michel, M. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Koolmeister, T. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Scobie, M. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Loseva, O. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Almlöf, I. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Unterlass, J. E. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Pettke, A. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Boström, J. (Karolinska Institutet (Estocolm, Suècia). Department of Laboratory Medicine) ;
Pandey, M. (University of Sheffield. Weston Park Cancer Centre) ;
Gad, H. (University of Sheffield. Weston Park Cancer Centre) ;
Herr, P. (University of Sheffield. Weston Park Cancer Centre) ;
Jemth, A. S. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
El Andaloussi, S. (Karolinska Institutet (Estocolm, Suècia). Department of Laboratory Medicine) ;
Kalderén, C. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Rodriguez-Perales, Sandra (Centro Nacional de Investigaciones Oncológicas) ;
Benítez, J. (Centro de Investigación Biomédica en Red de Enfermedades Raras) ;
Krokan, H. E. (Research and Innovation in Central Norway) ;
Altun, M. (Karolinska Institutet (Estocolm, Suècia). Department of Laboratory Medicine) ;
Stenmark, P. (Lund University. Department of Experimental Medical Science.) ;
Berglund, U. W. (Karolinska Institutet (Estocolm, Suècia). Department of Oncology and Pathology) ;
Helleday, Thomas (University of Sheffield.Weston Park Cancer Centre) ;
Universitat Autònoma de Barcelona
Altered oncogene expression in cancer cells causes loss of redox homeostasis resulting in oxidative DNA damage, e. g. 8-oxoguanine (8-oxoG), repaired by base excision repair (BER). PARP1 coordinates BER and relies on the upstream 8-oxoguanine-DNA glycosylase (OGG1) to recognise and excise 8-oxoG. [...]
2021 - 10.1093/nar/gkaa1048
Nucleic acids research, Vol. 48 Núm. 21 (february 2021) , p. 12234-12251
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18.
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14 p, 5.6 MB |
The role of ZFP57 and additional KRAB-zinc finger proteins in the maintenance of human imprinted methylation and multi-locus imprinting disturbances
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Monteagudo-Sánchez, A. (Institut d'Investigació Biomèdica de Bellvitge) ;
Hernandez Mora, J. R. (Institut d'Investigació Biomèdica de Bellvitge) ;
Simon, C. (Department of Obstetrics and Gynecology. BIDMC. Harvard University) ;
Burton, A. (Institute of Epigenetics and Stem Cells. Helmholtz Zentrum München) ;
Tenorio, Jair (Centro de Investigación Biomédica en Red de Enfermedades Raras) ;
Lapunzina, Pablo (ITHACA. European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability) ;
Clark, S. (Epigenetics Programme. The Babraham Institute) ;
Esteller, M. (Centro de Investigación Biomédica en Red de Cáncer) ;
Kelsey, G. (University of Cambridge. Centre for Trophoblast Research) ;
López-Siguero, J. P. (Hospital Regional Universitario Carlos Haya (Málaga)) ;
De Nanclares, G. P. (Instituto de Investigación Sanitaria Bioaraba (Vitoria, País Basc)) ;
Torres-Padilla, M. E. (Institute of Epigenetics and Stem Cells. Helmholtz Zentrum München) ;
Monk, D. (University of East Anglia. Biomedical Research Centre) ;
Universitat Autònoma de Barcelona
Genomic imprinting is an epigenetic process regulated by germline-derived DNA methylation that is resistant to embryonic reprogramming, resulting in parental origin-specific monoallelic gene expression. [...]
2020 - 10.1093/nar/gkaa837
Nucleic acids research, Vol. 48 Núm. 20 (18 2020) , p. 11394-11407
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19.
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17 p, 3.2 MB |
SIRT1/2 orchestrate acquisition of DNA methylation and loss of histone H3 activating marks to prevent premature activation of inflammatory genes in macrophages
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Li, Tianlu (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Garcia-Gomez, Antonio (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Morante-Palacios, Octavio (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ciudad, Laura (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Özkaramehmet, S. (Institut d'Investigació Biomèdica de Bellvitge) ;
Van Dijck, E. (Institut d'Investigació Biomèdica de Bellvitge) ;
Rodríguez-Ubreva, Javier (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Vaquero, Alejandro (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ballestar, Esteban (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Universitat Autònoma de Barcelona
Sirtuins 1 and 2 (SIRT1/2) are two NAD-dependent deacetylases with major roles in inflammation. In addition to deacetylating histones and other proteins, SIRT1/2-mediated regulation is coupled with other epigenetic enzymes. [...]
2020 - 10.1093/nar/gkz1127
Nucleic acids research, Vol. 48 Núm. 2 (24 2020) , p. 665-681
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20.
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14 p, 3.1 MB |
RNA-binding and prion domains : the Yin and Yang of phase separation
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Gotor, Nieves Lorenzo (Centre de Regulació Genòmica) ;
Armaos, Alexandros (Centre de Regulació Genòmica) ;
Calloni, Giulia (Goethe University Frankfurt) ;
Torrent Burgas, Marc (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Vabulas, R. Martin (Goethe University Frankfurt) ;
Sánchez de Groot, Natalia (Centre de Regulació Genòmica) ;
Tartaglia, Gian Gaetano (Centre de Regulació Genòmica)
Proteins and RNAs assemble in membrane-less organelles that organize intracellular spaces and regulate biochemical reactions. The ability of proteins and RNAs to form condensates is encoded in their sequences, yet it is unknown which domains drive the phase separation (PS) process and what are their specific roles. [...]
2020 - 10.1093/nar/gkaa681
Nucleic acids research, Vol. 48, Issue 17 (September 2020) , p. 9491-9504
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