Browsing by Author "Eyras Jiménez, Eduardo"

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  • Epigenetics in alternative splicing : links between chromatin structure, transcription and non-coding RNA mediated regulation
    Agirre Ortiz de Guzmán, Eneritz (Universitat Pompeu Fabra, 2014-01-16)
    Generalment s'ha pensat que la regulació de l'splicing alternatiu està controlada principalment per la interacció entre els factors reguladors de l'splicing i la taxa d'elongació de la ARN polimerasa II (RNAPII). Hi ha un ...
  • Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line
    Wahl, Matthias B.; Caldwell, Randolph B.; Kierzek, Andrzej M.; Arakawa, Hirosi; Eyras Jiménez, Eduardo; Hubner, Nina; Jung, Christian; Soeldenwagner, Manuel; Cervelli, Manuela; Wang, Yan-Dong; Liebscher, Volkmar; Buerstedde, Jean-Marie (BioMed Central, 2004)
    Background: The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures, translated open reading frames ...
  • Exon creation and establishment in human genes
    Corvelo, André; Eyras Jiménez, Eduardo (BioMed Central, 2008)
    BACKGROUND: A large proportion of species-specific exons are alternatively spliced. In primates, Alu elements play a crucial role in the process of exon creation but many new exons have appeared through other mechanisms. ...
  • Exotic branes and non-perturbative seven branes
    Eyras Jiménez, Eduardo; Lozano, Yolanda (Elsevier, 2000)
    We construct the effective action of certain exotic branes in the Type II theories which are not predicted by their space-time supersymmetry algebras. We analyze in detail the case of the NS-7B brane, S-dual to the D7-brane, ...
  • Formation of an invasion-permissive matrix requires TGFβ/SNAIL1-regulated alternative splicing of fibronectin
    Franco Valls, Héctor; Tusquets-Uxó, Elsa; Sala Romanyà, Laura, 1989-; Val Casals, Maria; Peña Arranz, Raúl, 1976-; Iaconcig, Alessandra; Villarino, Álvaro; Jiménez-Arriola, Martín; Massó, Pere; Trincado Alonso, Juan Luis, 1987-; Eyras Jiménez, Eduardo; Muro, Andrés F.; Otero, Jorge; García de Herreros, Antonio; Baulida i Estadella, Josep, 1965- (BioMed Central, 2023)
    Background: As in most solid cancers, the emergence of cells with oncogenic mutations in the mammary epithelium alters the tissue homeostasis. Some soluble factors, such as TGFβ, potently modify the behavior of healthy ...
  • Gene finding in the chicken genome
    Eyras Jiménez, Eduardo; Reymond, Alexandre; Castelo Valdueza, Robert; Bye, Jacqueline M.; Cámara, Francisco; Flicek, Paul; Huckle, Elizabeth J.; Parra Farré, Genís; Shteynberg, David D.; Wyss, Carine; Rogers, Jane; Antonarakis, Stylianos E.; Birney, Ewan; Guigó Serra, Roderic; Brent, Michael R. (BioMed Central, 2005)
    Background: Despite the continuous production of genome sequence for a number of organisms,/nreliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly/ntrue for genomes for which ...
  • Genome-wide association between branch point properties and alternative splicing
    Corvelo, André; Hallegger, Martina; Smith, Christopher, W. J.; Eyras Jiménez, Eduardo (Public Library of Science (PLoS), 2010)
    The branch point (BP) is one of the three obligatory signals required for pre-mRNA splicing. In mammals, the degeneracy of the motif combined with the lack of a large set of experimentally verified BPs complicates the task ...
  • Hepatitis B virus serum RNA transcript isoform composition and proportion in chronic hepatitis B patients by nanopore long-read sequencing
    Vachon, Alicia; Seo, Grace E.; Patel, Nishi H.; Coffin, Carla S.; Marinier, Eric; Eyras Jiménez, Eduardo; Osiowy, Carla (Frontiers, 2023)
    Introduction: Serum hepatitis B virus (HBV) RNA is a promising new biomarker to manage and predict clinical outcomes of chronic hepatitis B (CHB) infection. However, the HBV serum transcriptome within encapsidated particles, ...
  • Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling
    Nadal Ribelles, Mariona, 1984-; Conde Pueyo, Núria, 1983-; Flores, Oscar; González-Vallinas Rostes, Juan, 1983-; Eyras Jiménez, Eduardo; Nadal Clanchet, Eulàlia de; Posas Garriga, Francesc (BioMed Central, 2012)
    Cells are subjected to dramatic changes of gene expression upon environmental changes. Stress/ncauses a general down-regulation of gene expression together with the induction of a set of stress-responsive/ngenes. The ...
  • Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Imanishi, Tadashi; Eyras Jiménez, Eduardo; Sugano, Sumio (Public Library of Science (PLoS), 2004)
    The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. ...
  • Integrative single-cell expression and functional studies unravels a sensitization to cytarabine-based chemotherapy through HIF pathway inhibition in AML leukemia stem cells
    Velasco Hernandez, Talia; Beneyto Calabuig, Sergi; Velten, Lars; Lorden, Patricia; Eyras Jiménez, Eduardo; Heyn, Holger; Menéndez, Pablo (Wiley, 2024)
    Relapse remains a major challenge in the clinical management of acute myeloid leukemia (AML) and is driven by rare therapy-resistant leukemia stem cells (LSCs) that reside in specific bone marrow niches. Hypoxia signaling ...
  • IRFinder: assessing the impact of intron retention on mammalian gene expression
    Middleton, Robert; Gao, Dadi; Thomas, Aubin; Singh, Babita, 1986-; Au, Amy; Wong, Justin J.-L.; Bomane, Alexandra; Cosson, Bertrand; Eyras Jiménez, Eduardo; Rasko, John E.J.; Ritchie, William (BioMed Central, 2017)
    Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis ...
  • Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21
    Lyle, Robert; Prandini, Paola; Osoegawa, Kazutoyo; Ten Hallers, Boudewijn; Humphray, Sean; Zhu, Baoli; Eyras Jiménez, Eduardo; Castelo Valdueza, Robert; Bird, Christine P.; Gagos, Sarantos; Scott, Carol; Cox, Antony; Deutsch, Samuel; Ucla, Catherine; Cruts, Marc; Dahoun, Sophie; She, Xinwei; Bena, Frederique; Wang, Sheng-Yue; Broeckhoven, Christine van; Eichler, Evan E.; Guigó Serra, Roderic; Rogers, Jane; De Jong, Pieter J.; Reymond, Alexandre; Antonarakis, Stylianos E. (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)
    The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p), estimated to be 10% of 21p. ...
  • ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer
    Trincado Alonso, Juan Luis, 1987-; Reixachs i Solé, Marina; Pérez-Granado, Judith; Fugmann, Tim; Sanz, Ferran; Yokota, Jun; Eyras Jiménez, Eduardo (Public Library of Science (PLoS), 2021)
    Immunotherapies provide effective treatments for previously untreatable tumors and identifying tumor-specific epitopes can help elucidate the molecular determinants of therapy response. Here, we describe a pipeline, ISOTOPE ...
  • Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks
    Sebestyén, Endre; Singh, Babita, 1986-; Miñana Gómez, Belén; Pagès Pinós, Amadís; Mateo, Francesc; Pujana, Miguel Angel; Valcárcel, J. (Juan); Eyras Jiménez, Eduardo (Cold Spring Harbor Laboratory Press (CSHL Press), 2016)
    Alternative splicing is regulated by multiple RNA-binding proteins and influences the expression of most eukaryotic genes. However, the role of this process in human disease, and particularly in cancer, is only starting ...
  • Large-scale study of RNA processing alterations in multiple cancers
    Singh, Babita (Universitat Pompeu Fabra, 2018-06-07)
    RNA processing and their alterations are determinant to understand normal and disease cell phenotypes. In particular, specific alterations in the RNA processing of genes has been linked to widely accepted cancer hallmarks. ...
  • Leveraging transcript quantification for fast computation of alternative splicing profiles
    Alamancos, Gael P.; Pagès Pinós, Amadís; Trincado Alonso, Juan Luis, 1987-; Bellora Pereyra, Nicolás; Eyras Jiménez, Eduardo (Cambridge University Press, 2015)
    Alternative splicing plays an essential role in many cellular processes and bears major relevance in the understanding of multiple diseases, including cancer. High-throughput RNA sequencing allows genome-wide analyses of ...
  • Lineage-specific roles of the cytoplasmic polyadenylation factor CPEB4 in the regulation of melanoma drivers
    Pérez-Guijarro, Eva; Bellora Pereyra, Nicolás; Eyras Jiménez, Eduardo; Soengas, María S. (Nature Publishing Group, 2016)
    Nuclear 3’-end-polyadenylation is essential for the transport, stability and translation of virtually all eukaryotic mRNAs. Poly(A) tail extension can also occur in the cytoplasm, but the transcripts involved are incompletely ...
  • Mechanisms of evolutionary innovation in mammalian genes
    Toll i Riera, Macarena (Universitat Pompeu Fabra, 2012-11-06)
    Actualment, degut a la disponibilitat d’un gran nombre de genomes seqüenciats, el camp de la genòmica comparativa està experimentant grans avenços. Ara són possibles una àmplia gama d’estudis que fins fa poc eren inimaginables. ...
  • Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB
    Coelho, Miguel B.; Attig, Jan; Bellora Pereyra, Nicolás; König, Julian; Hallegger, Martina; Kayikci, Melis; Eyras Jiménez, Eduardo; Ule, Jernej; Smith, Christopher, W. J. (EMBO Press, 2015)
    Matrin3 is an RNA- and DNA-binding nuclear matrix protein found to be associated with neural and muscular degenerative diseases. A number of possible functions of Matrin3 have been suggested, but no widespread role in RNA ...

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