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Visualitza Articles (Departament de Ciències Experimentals i de la Salut) per matèria "RNA"

Visualitza Articles (Departament de Ciències Experimentals i de la Salut) per matèria "RNA"

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  • Guigó Serra, Roderic; Sammeth, Michael; Foissac, Sylvain (Public Library of Science (PLoS), 2008)
    Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells is/none of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) ...
  • Jungfleisch, Jennifer, 1986-; Nedialkova, Danny D.; Dotu, Ivan; Sloan, Katherine E.; Martínez Bosch, Neus; Brüning, Lukas; Raineri, Emanuele; Navarro Medrano, Pilar; Bohnsack, Markus T.; Leidel, Sebastian; Díez Antón, Juana, 1962- (Cold Spring Harbor Laboratory Press (CSHL Press), 2017)
    The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here, we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences ...
  • Kremsky, Isaac Jacob, 1983-; Bellora Pereyra, Nicolás; Eyras Jiménez, Eduardo (Public Library of Science (PLoS), 2015)
    High-throughput sequencing, and genome-based datasets in general, are often represented as profiles centered at reference points to study the association of protein binding and other signals to particular regulatory ...
  • Takeuchi, Akiko; Schmitt, David; Chapple, Charles E.; Babaylova, Elena; Karpova, Galina; Guigó Serra, Roderic; Krol, Alain; Allmang, Christine (Oxford University Press, 2009)
    Selenoproteins contain the amino acid selenocysteine which is encoded by a UGA Sec codon. Recoding UGA Sec requires a complex mechanism, comprising the cis-acting SECIS RNA hairpin in the 3′UTR of selenoprotein mRNAs, and ...
  • Marchese, Domenica, 1986-; Sanchez de Groot, Natalia; Lorenzo Gotor, Maria de las Nieves; Livi, Carmen Maria; Tartaglia, Gian Gaetano (Wiley, 2016)
    From transcription, to transport, storage, and translation, RNA depends on association with different RNA-binding proteins (RBPs). Methods based on next-generation sequencing and protein mass-spectrometry have started to ...
  • Lloréns Rico, Verónica, 1989-; Serrano Pubull, Luis, 1982-; Lluch-Senar, Maria 1982- (BioMed Central, 2014)
    Background: RNA sequencing methods have already altered our view of the extent and complexity of bacterial and eukaryotic transcriptomes, revealing rare transcript isoforms (circular RNAs, RNA chimeras) that could play an ...
  • Zhang, Runxuan; Calixto, Cristiane P. G.; Tzioutziou, Nikoleta A.; James, Allan B.; Simpson, Craig G.; Guo, Wenbin; Marquez, Yamile; Kalyna, Maria; Patro, Rob; Eyras Jiménez, Eduardo; Barta, Andrea; Nimmo, Hugh G.; Brown, John W. S. (Wiley, 2015)
    RNA-sequencing (RNA-seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of transcript variants generated by alternative splicing (AS) remains a challenge. We have developed ...
  • Lloréns Rico, Verónica, 1989-; Cano, Jaime; Kamminga, Tjerko; Gil, Rosario; Latorre, Amparo; Chen, Wei-Hua; Bork, Peer; Glass, John I.; Serrano Pubull, Luis, 1982-; Lluch-Senar, Maria 1982- (American Association for the Advancement of Science (AAAS), 2016)
    cis-Encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of most of these RNAs remains unknown, and there is an ongoing discussion as to what extent these transcripts are the ...
  • Agostini, Federico, 1985-; Zanzoni, Andreas; Klus, Petr; Marchese, Domenica, 1986-; Cirillo, Davide; Tartaglia, Gian Gaetano (Oxford University Press, 2013)
    SUMMARY: Here we introduce catRAPID omics, a server for large-scale calculations of protein-RNA interactions. Our web server allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences ...
  • Livi, Carmen Maria; Klus, Petr; Delli Ponti, Riccardo; Tartaglia, Gian Gaetano (Oxford University Press, 2016)
    MOTIVATION: Recent technological advances revealed that an unexpected large number of proteins interact with transcripts even if the RNA-binding domains are not annotated. We introduce catRAPID signature to identify ...
  • Iglesias-Platas, Isabel; Martin-Trujillo, Alex; Cirillo, Davide; Court, Franck; Guillaumet-Adkins, Amy; Camprubí, Cristina; Bourc'his, Deborah; Hata, Kenichiro; Feil, Robert; Tartaglia, Gian Gaetano; Arnaud, Philippe; Monk, David (Public Library of Science (PLoS), 2012)
    Genomic imprinting is a complex epigenetic mechanism of transcriptional control that utilizes DNA methylation and histone modifications to bring about parent-of-origin specific monoallelic expression in mammals. Genes ...
  • Agirre Ortiz de Guzmán, Eneritz, 1983-; Eyras Jiménez, Eduardo (BioMed Central, 2011)
    Recent advances in high-throughput sequencing have facilitated the genome-wide studies of small non-coding RNAs (sRNAs). Numerous studies have highlighted the role of various classes of sRNAs at different levels of gene ...
  • Payer, Bernhard, 1975- (Elsevier, 2016)
    With the emergence of sex-determination by sex chromosomes, which differ in composition and number between males and females, appeared the need to equalize X-chromosomal gene dosage between the sexes. Mammals have devised ...
  • Shen, Manli; Eyras Jiménez, Eduardo; Wu, Jie; Josiah, Serene; Rederstorff, Mathieu; Zhang, Michael Q; Stamm, Stefan (Oxford University Press, 2011)
    We describe a new method that allows cloning of double-stranded RNAs (dsRNAs) that are generated in RNase protection experiments. We demonstrate that the mouse C/D box snoRNA MBII-85 (SNORD116) is processed into at least ...
  • Djebali, Sarah; Lagarde, Julien; Lacroix, Vincent; Foissac, Sylvain; Ribeca, Paolo; Martin, David; Guigó Serra, Roderic; Gingeras, Thomas R. (Public Library of Science (PLoS), 2012)
    The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast ...
  • Gallego, Alicia; Melé Messeguer, Marta, 1982-; Balcells, Ingrid; García Ramallo, Eva; Torruella Loran, Ignasi; Fernández Bellon, Hugo; Abelló, Teresa; Kondova, Ivanela; Bontrop, Ronald E.; Hvilsom, Christina; Navarro i Cuartiellas, Arcadi, 1969-; Marquès i Bonet, Tomàs, 1975-; Espinosa Parrilla, Yolanda (Public Library of Science, 2016)
    microRNAs are crucial post-transcriptional regulators of gene expression involved in a wide range of biological processes. Although microRNAs are highly conserved among species, the functional implications of existing ...
  • Faherty, Sheena L.; Villanueva Cañas, José Luis, 1984-; Klopfer, Peter H.; Albà Soler, Mar; Yoder, Anne D. (Oxford University Press, 2016)
    Hibernation is a complex physiological response that some mammalian species employ to evade energetic demands. Previous work in mammalian hibernators suggests that hibernation is activated not by a set of genes unique to ...
  • Monlong, Jean; Calvo, Miquel; Ferreira, Pedro G.; Guigó Serra, Roderic (Nature Publishing Group, 2014)
    Identification of genetic variants affecting splicing in RNA sequencing population studies is still in its infancy. Splicing phenotype is more complex than gene expression and ought to be treated as a multivariate phenotype ...
  • Bussotti, Giovanni, 1983-; Leonardi, Tommaso; Clark, Michael B.; Mercer, Tim R.; Crawford, Joanna; Malquori, Lorenzo; Notredame, Cedric; Dinger, Marcel E.; Mattick, John S.; Enright, Anton J. (Cold Spring Harbor Laboratory Press (CSHL Press), 2016)
    Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied ...
  • Andreu Martínez, David; Freire, Joao Miguel; Veiga, Anna; Conceiçao, Thaís M.; Kowalczyk, Wioleta; Mohana-Borges, Ronaldo; Santos, Nuno C.; Da Poian, Andrea T.; Castanho, Miguel A.R.B. (Public Library of Science (PLoS), 2014)
    Supercharged proteins are a recently identified class of proteins that have the ability to efficiently deliver functional macromolecules into mammalian cells. They were first developed as bioengineering products, but were ...