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Francisco E. Baralle

Research Focus

The group studies the basic mechanisms involved in the pathogenesis of human diseases and their possible prevention and treatment through recombinant DNA procedures. Clinical, animal and in vitro models are used to investigate, at the molecular level, genotype-phenotype correlations in pre-mRNA splicing defects.

This approach allows us to reach two main objectives. First, to identify pathogenic mutations in human disease and second, to take advantage of the pointers provided by human pathology, to explore novel molecular mechanisms involved in the splicing process.

The systems under study cover diverse topics within the splicing field. The 5’ and 3’ splice site definition is being studied in gene systems such as the breast cancer gene BRCA1, the potassium channel KCHN2 (responsible for some forms of long QT syndrome), Cystic Fibrosis (CFTR gene), Neurofibromatosis type 1 (NF-1 gene), Thrombopoietin (TPO) and Cystathionine Beta Synthase (CBS). Several intronic and exonic cis-acting splicing regulatory elements have been characterised, many of them are involved in RNA-protein interactions with well known splicing factors such as hnRNPs and SR proteins. Genomic variations in their RNA target sequences are associated with inherited diseases.

Furthermore, follow-up studies on TDP43 have shown that this protein has an essential biological function. In fact after depletion of TDP43 the cell’s nuclei lose their round smooth shape and trigger apoptosis. Current research is looking into the biochemical mechanisms involved and the possible link to the recently reported role of TDP43 in several neurodegenerative diseases.

The analysis of the effect of extended, complex genomic regions on the splicing is also studied. In fact, gene expression develops in a dynamic fashion with transcription and RNA processing occurring simultaneously. The group has carried out studies on the role that the transcription machinery may play on modulating pre mRNA splicing, demonstrating a close link between RNA polymerase processivity and splicing decisions. The spliceosome composition/conformation and, as a consequence, its function is conditioned by the upstream sequences that were previously transcribed and processed as shown by studies on the NF1, TPO and Fibronectin genes.

Finally, the laboratory has a longstanding interest in the influence of RNA secondary structure on the splicing processes. On the Fibronectin EDA alternative splicing model we have shown that secondary structure changes may be responsible for the loss of affinity of the RNA molecule for specific splicing factors and hence improper exon definition. This process may be extremely important in situations where new genomic variations cause the inclusion of cryptic or pseudo exons in the mature mRNA.

We are presently assessing the importance of RNA secondary structure on pseudoexon inclusion in several disease linked gene systems such as Ataxia Telangectasia (ATM), CFTR and Duchenne Muscular Dystrophy (DMD). Our studies have uncovered factors such as TDP-43, YB1 and DAZAP that were not originally identified as RNA processing factors but that it has shown to play surprising roles on splicing modulation.

Publications

  1. Valacca, C., Bonomi, S., Buratti, E., Pedrotti, S., Baralle, F.E., Sette, C., Ghigna, C., Biamonti, G. (2010). Sam68 regulates EMT through alternative splicing-activated NMD of the SF2/ASF proto-oncogene. Journal of Cell Biology 191(1), 87-99.
  2. Haque, A., Buratti, E., Baralle, F.E. (2009). Functional properties and evolutionary splicing constraints on a composite exonic regulatory element of splicing in CFTR exon 12. Nucleic Acids Research 38(2), 647-59. (doi:10.1093/nar/gkp1040)
  3. Dhir, A., Buratti, E., van Santen, M.A., Lührmann, R., Baralle, F.E. (2009). The intronic splicing code: multiple factors involved in ATM pseudoexon definition. EMBO Journal 29, 749-760. (doi:10.1038/emboj.2009.397)
  4. Buratti, E., Baralle, F.E. (2009). The molecular links between TDP-43 dysfunction and neurodegeneration. Advances in Genetics 66, 1-34. (doi: 10.1016/S0065-2660(09)66001-6)
  5. D'Ambrogio, A., Buratti, E., Stuani, C., Guarnaccia, C., Romano, M., Ayala, Y.M., Baralle, F.E. (2009). Functional mapping of the interaction between TDP-43 and hnRNP A2 in vivo. Nucleic Acids Research37(12), 4116-4126. (doi:10.1093/nar/gkp342).
  6. Feiguin, F., Godena, V.K., Romano, G., D'Ambrogio, A., Klima, R., Baralle, F.E. (2009). Depletion of TDP-43 affects Drosophila motoneurons terminal synapsis and locomotive behavior. FEBS Letters 583, 1586-1592.
  7. Raponi, M., Buratti, E., Dassie, E., Upadhyaya, M., Baralle, D. (2009). Low U1 snRNP dependence at the NF1 exon 29 donor splice site. FEBS Journal 276(7), 2060-73.
  8. Zago, P., Baralle, M., Ayala, Y.M., Skoko, N., Zacchigna, S., Buratti, E., Tisminetzky, S. (2009). Improving human beta interferon production in mammalian cell lines by insertion of an intronic sequence within its naturally uninterrupted gene. Biotechnology and Applied Biochemistry 52(3), 191-198.
  9. Marcucci, R., Romano, M., Feiguin, F., O'Connell, M., Baralle, F.E. (2009). Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR. Nucleic Acids Research 37(5), 1663-1671.
  10. Raponi, M., Buratti, E., Llorian, M., Stuani, C., Smith, C.W., Baralle, D. (2008). Polypyrimidine tract binding protein regulates alternative splicing of an aberrant pseudoexon in NF1. FEBS Journal 275 (24), 6101-6108. (doi: 10.1111 /j.1742-4658.2008.06734.x)
  11. Ayala, Y.M., Zago, P., D'Ambrogio, A., Xu, Y.F., Petrucelli, L., Buratti, E., Baralle, F.E. (2008). Structural determinants of the cellular localization and shuttling of TDP-43. Journal of Cell Science 121, 3778-3785. (doi: 10.1242/jcs.038950).
  12. Hasegawa, M., Arai, T., Nonaka, T., Kametani, F., Yoshida, M., Hashizume, Y., Beach, T.G., Buratti, E., Baralle, F., Morita, M., Nakano, I., Oda, T., Tsuchiya, K., Akiyama, H. (2008) Phosphorylated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Annals of Neurology 64(1), 60-70.
  13. Raponi, M., Baralle, D. (2008). Can donor splice site recognition occur without the involvement of U1 snRNP? Biochemical Society Transactions 36(3).
  14. Romano, M., Bacalini, M.G., Verschoor, E.J., Crovella, S., Baralle, F.E. (2008). Origin and evolution of the c.844_845ins68/c.833T>C mutations within the cystathionine beta-synthase gene in great apes. FEBS Letters 582(3), 423-426.
  15. Ayala, Y.M., Misteli, T., Baralle, F.E. (2008). TDP-43 regulates retinoblastoma protein phosphorylation through the repression of cyclin-dependent kinase 6 expression. Proceedings of the National Academy of Sciences USA 105(10), 3785-3789.
  16. Buratti, E. and Baralle, F.E. (2008). Multiple roles of TDP-43 in gene expression, splicing regulation, and human disease. Frontiers in Bioscience 13, 867-878.
  17. Buratti, E., Dhir, A., Lewandowska, M.A. and Baralle, F.E. (2007). RNA structure is a key regulatory element in pathological ATM and CFTR pseudoexon inclusion events. Nucleic Acids Research 35, 4369-4383.
  18. Buratti, E., Stuani, C., De Prato, G. and Baralle, F.E. (2007). SR protein-mediated inhibition of CFTR exon 9 inclusion: molecular characterization of the Intronic Splicing Silencer. Nucleic Acids Research 35, 4359-4368.
  19. Marcucci, R., Baralle, F.E. and Romano, M. (2007). Complex splicing control of the human Thrombopoietin gene by intronic G runs. Nucleic Acids Research 35, 132-142.
  20. Buratti, E., Baralle, M., and Baralle, F.E. (2006). Defective splicing, disease, and therapy: searching for master checkpoints in exon definition. Nucleic Acids Research 34, 3494-3510.
  21. Buratti, E., Muro, A.F., Giombi, M., Gherbassi, D., Iaconcig, A., and Baralle, F.E. (2004). RNA folding affects the recruitment of SR proteins by mouse and human polypurinic enhancer elements in the fibronectin EDA exon. Molecular and Cellular Biology 24, 1387-1400.
  22. Pagani, F., Buratti, E., Stuani, C., Benedix, R., Dörk, T., and Baralle, F.E. (2002). A new type of genetic mutation causing a splicing defect in ATM. Nature Genetics 30, 426-429.

Key lab techniques: In vivo splicing analyses using minigenes; RNA secondary structure probing; RNA protein interactions; Mouse models with modified fibronectin splicing.

Key lab reagents: siRNAs, Anti hnRNP, SR antibodies, Expression of splicing factors in mammalian and eukaryotic systems.

Lab contact: Nerina Brandolin: brandon@icgeb.org

Lab website: http://www.icgeb.org/francisco-baralle.html