Research Groups

Molecular Pathology

Research Interests and Description

Group Leader: Francisco E. Baralle, MD, PhD

Group Members

Research Interests

Molecular mechanisms of pre-mRNA processing. Genetic disease caused by defective splicing. RNA-protein interactions.

Description of Research

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 (see Figure). 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.

Recent Publications

Dhir, A., Buratti, E., van Santen, M.A., Lührmann, R., Baralle, F.E. 2010. The intronic splicing code: multiple factors involved in ATM pseudoexon definition. EMBO J. 29, 749-760 [pubmed link]

Haque, A., Buratti, E., Baralle, F.E. 2010. Functional properties and evolutionary splicing constraints on a composite exonic regulatory element of splicing in CFTR exon 12. Nucleic Acids Res. 38(2), 647-659 [pubmed link]

D'Ambrogio, A., Buratti, E., Stuani, C., Guarnaccia, C., Romano, M., Ayala, Y.M., Baralle, F.E. Functional mapping of the interaction between TDP-43 and hnRNP A2 in vivo. 2009. Nucleic Acids Res. 37, 4116-4126 [pubmed link]

Feiguin, F., Godena, V.K., Romano, G., D’Ambrogio, A., Klima, R., Baralle, F.E. Depletion of TDP-43 affects Drosophila motoneurons terminal synapsis and locomotive behavior. 2009. FEBS Lett. 583, 1586-1592 [pubmed link]

Ayala, Y.., Misteli, T., Baralle, F.E. TDP-43 regulates retinoblastoma protein phosphorylation through the repression of cyclin-dependent kinase 6 expression. 2008. Proc. Natl. Acad. Sci. USA 105, 3785-3789 [pubmed link]

Sreedharan, J., Blair, I.P., Tripathi, V.B., Hu, X., Vance, C., Rogelj, B., Ackerley, S., Durnall, J.C., Williams, K.L., Buratti, E., Baralle, F.E., de Belleroche, J., Mitchell, J.D., Leigh, P.N., Al-Chalabi, A., Miller, C.C., Nicholson, G., Shaw, C.E. TDP-43 mutations in familial and sporadic Amyotrophic Lateral Sclerosis. 2008. Science 319, 1668-1672 [pubmed link]

Ayala, Y.M., Zago, P., D'Ambrogio, A., Xu, Y.F., Petrucelli, L., Buratti, E., Baralle, F.E. Structural determinants of the cellular localization and shuttling of TDP-43. 2008. J. Cell Sci. 121, 3778-3785 [pubmed link]