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Josep Vilardell: Molecular mechanisms of pre-mRNA splicing

Lab Presentation

Our goal is to contribute to understanding pre-mRNA splicing and its impact on gene expression. While we follow a reductionist approach with a well-defined working model (yeast), we aim to decipher mechanisms relevant to human and, given the link between splicing and disease, to health. Our research covers the following subjects: (a) sequence elements that act on the core spliceosome, (b) how early spliceosome assembly can be regulated, (c) changes in splicing at cellular level in response to diverse stimuli.

 

Research Lines

 

Exonic and intronic sequences that act on the basal spliceosome
We are developing a working model for the identification of intronic ends by the splicesome. Although the most fundamental requirements have been known for a long time, others and we have shown that there is much left to be understood. Inspecting the genome of yeast, where few genes have introns and alternative splicing is reduced, we have found a splicing thermosensor, a novel intron that requires an unlikely fold to be identified by the spliceosome, and a set of sequences that are not being identified as introns for reasons that escape us. To what extent the sophistication that we observe in the pre-mRNA splicing of metazoan organisms is present in the basal spliceosome (as the yeast one is thought to be) ?
Links between regulated splicing, chromatin, and signal transduction
In the regulatory feed-back loop of the RPL30 transcript, yeast ribosomal protein L30 self-regulates its produc-tion by binding near the 5'ss of its intron and blocking early spliceosome assembly. In more precise terms, L30 binding inhibits a (still unknown) molecular rearrangement required for the association of U2 snRNP with the intron1. We have identified genetic interactions between this repression and some histone mutants, offering an excellent opportunity to study the link between chromatin and regulated splicing. We are developing the reagents needed for a precise screening of all available histone mutants. In addition, we have a set of UV-induced mutants where excess L30 fails to block RPL30 splicing. We have found that this phenotype can be suppressed by an extra copy of the PRP45 gene. Prp45 human homologue, SKIP, is a transcription factor that is phosphorylated. Thus, our working hypothesis is that Prp45 is part of a link between regulated splicing, transcription, and MAPK kinases. As before, there is evidence for such links in metazoans, but with little information on mechanisms. Here we may have a valuable opportunity to investigate this process.
Splicing of gene families and genomes
Using Bioinformatics and RNASeq data we aim to perform meta-analyses to monitor how the yeast spliceosome responds to a number of stresses (including aging and genomic stability). In addition, we explore the transcriptome of the mRNAs encoding ribosomal proteins (RP) in mammalian cells. As in yeast, a growing human cell needs to produce ribosomes and that set of mRNAs will be among the main substrates of the spliceosome. As in yeast as well, there is little alternative splicing in RP pre-mRNAs. Interestingly, most Bioinformatics analyses ignore this abundant set of transcripts mostly because of technical difficulties (i.e. read mapping artifacts). This can be circumvented and we have started exploring splicing and expression of RP RNAs using RNASeq data from tumor cells. These cells are under a strong selection to grow and ribosomes are one of the key elements to achieve this growth. To note are the results from the analysis of data from CLL (Chronic Lymphocytic Leukemia) samples, indicating that while there are no changes in alternative splicing in this set of messages, their expression is diminished in all of them. This was not expected and perhaps it is indicative of chronicity. In addition, given that this dataset is well documented, we could determine that spliceosomal mutations that are present in some CLL patients and are important for tumor prognosis do not cause changes in RP splicing. We intend to expand these preliminary results by looking directly into CLL cells and studying other types of tumors.
Josep Vilardell Trench
  • Josep Vilardell
  • IBMB-CSIC
  • C/ Baldiri Reixac, 10-12
  • 08028 Barcelona, Spain
  • Phone: +34 93 4020549 / +34 93 4020532
  • E-mail: josep.vilardell@ibmb.csic.es

Principal Investigator



Past students

  • Ribosomal proteins as novel players in tumorigenesis. Antonio de Las Heras-Rubio, Laura Perucho, Rosanna Paciucci, Josep Vilardell, and Matilde Lleonart. Cancer and Metastasis Reviews [Epub ahead of print] (2013) Abstract
     
  • Intronic features that determine the selection of the 3' splice site. Jorge Pérez-Valle and Josep Vilardell. Wiley Interdiscip Rev RNA. Sep-Oct;3(5): 707-717 (2012) Abstract
     
  • RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae. Mireya Plass, Carles Codony-Servat, Pedro Gabriel Ferreira, Josep Vilardell, and Eduardo Eyras. RNA Jun;18(6):1103-15 (2012) Abstract
     
  • Regulated pre-mRNA Splicing: The Ghostwriter of the Eukaryotic Genome. Tracy L. Johnson and Josep Vilardell. Biochim. Biophys. Acta 1819: 538–545 (2012) Abstract
     
  • Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing. Markus Meyer, Mireya Plass*, Jorge Pérez-Valle*, Eduardo Eyras, and Josep Vilardell. (*Equal contribution). Molecular Cell 43: 1033-1039 (2011) Abstract, (Science Editor's Choice 30 Sept)
     
  • SUS1 introns are required for efficient mRNA nuclear export in yeast. Bernardo Cuenca-Bono&, Varinia García-Molinero&, Pau Pascual-García, Hernan Dopazo, Ana Llopis1, Josep Vilardell*, and Susana Rodríguez-Navarro*. (&: Equal contribution *: corresponding author). Nucleic Acids Research  Oct 1;39(19): 8599-611 (2011) Abstract
     
  • RPL30 regulation of splicing reveals distinct roles for Cbp80 in U1 and U2 snRNP cotranscriptional recruitmentMireia Bragulat, Markus Meyer, Sara Macías, Maria Camats, Mireia Labrador, and Josep VilardellRNA Oct;16(10): 2033-2041 (2010) AbstractSupplemental Material
     
  • The quest for a message: budding yeast, a model organism to study the control of pre-mRNA splicing. Markus Meyer and Josep VilardellBriefings in Functional Genomics & Proteomics 8(1):60-7 (2009)Abstract
     
  • L30 binds the nascent RPL30 transcript to repress U2 snRNP recruitmentMacías S, Bragulat M, Tardiff DF, Vilardell JMolecular Cell 30(6):732-42  (2008). Abstract
     
  • Powering a two-stroke RNA engineJuan Valcárcel, Josep VilardellNature Structural & Molecular Biology 14(7):574-6 (2007)PubMed
     
  • Repositioning of the reaction intermediate within the catalytic center of the spliceosomeKonarska MM, Vilardell J, Query CC. Molecular Cell 21:543-553 (2006). Abstract

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We are currently seeking highly motivated PhD students and postdocs. Candidates are expected to successfully apply to any suitable fellowship (most Spanish fellowships are competitive and selection is based on the candidate's CV).

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