Alternative splicing as a modulator of signal transduction


Head: Matthias Platzer
Rolf Backofen (external)
Co-Workers: Ulrike Gausmann, Rileen Sinha
Address: Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Research Group Genome Analysis, Beutenbergstr. 11, 07745 Jena
Phone: +49 (0) 3641 656240
Fax: +49 (0) 3641 656255
Email: mplatzer[at]fli-leibniz.de
URL: Genome Analysis Group at FLI


Project Description

Cells can change their splicing pattern in response to signals. Therefore, alternative splicing contributes to signal protein variability and information flow modulation, besides of posttranslational modification, differential gene expression and others.

Alternative splice variants of FGFR2. All these thirteen transcripts are confirmed by Reference Sequences (S: signal peptide, IG1, 2, 3: immunoglobulin domains, T: transmembrane domains, Boxes: exons, black: coding, grey: non-coding, white: exon­skipping, red: prolonged exon, blue: shortened exon; drawing not to scale).

For this reason, we want to investigate the effect of alternative splicing on multifunctional signalling proteins, and determine regulatory mechanisms. We want to focus both on EST-based as well as on non-EST-based prediction methods for the identification of transcript variants, especially of those which are in the focus of the SFB. We will identify cis-acting elements, which are statistically linked to splicing events. These are, for instance, hexamer distribution patterns, conservation of exons and flanking introns in paralogs and orthologs, the score values of splice sites, as well as secondary structure elements in mRNA molecules. To find conserved secondary structure elements, we will employ and advance algorithms, currently under development. Modern learning techniques such as Bayesian networks, which we have used previously for the identification of transcription factor binding sites, will be applied for the prediction of transcript variants. The predicted splice forms will be validated by RT-PCR and sequencing. To gain more insight into the regulation of alternative splicing of signal proteins, we will cluster biologically related proteins to determine over- and underrepresented sequence or structure elements. In particular, we will focus on the functional effects of an alternative splicing phenomenon at NAGNAG acceptor sites, which was recently described by our group, on genes under investigation within the framework of the SFB. The general project aim is the extraction of splicing rules for classes of proteins, e.g. growth factor receptors, developmentally co-expressed genes or proteins with similar or equal splice pattern variations.
The project was designed and will be carried out in close collaboration with the group of Rolf Backofen (Chair for Bioinformatik, University of Freiburg)

Summary

Elements in pre-mRNA splicing. Five small nuclear ribonucleoproteins (snRNPs) and more than 100 proteins make up the spliceosome. The U1 snRNP binds to the 5'-splice site, and the U2 snRNP binds the branch site through RNA-RNA interactions. Additional enhancer and silencer elements are exon splicing enhancer (ESE) and silencer (ESS) and/or intron splicing enhancer (ISE) and silencer (ISS)). Transacting splicing factors can interact with enhancers and silencers and can accordingly be subdivided into two main groups: members of the serine arginine (SR) family of proteins and of the heterogeneous nuclear ribonucleoprotein particles (hnRNPs).

Multifunctional signalling proteins harbour many protein domains. These can be varied by alternative splicing, a mechanism, how genomic blueprints can be converted into different transcripts. We will predict and analyse new splice variants and apply new machine learning approaches such as Bayesian networks. We want to gain more insight into the processes involved in the regulation of alternative splicing and in the regulation by alternative splicing and will apply this knowledge to selected multifunctional proteins and protein complexes studied within the framework of the SFB.

Zusammenfassung

Multifunktionelle Signalproteine beinhalten viele Proteindomänen, die mittels alternativen Spleissens variiert werden können. Durch diesen Mechanismus können genomische Genbaupläne in verschiedene Transkripte umgesetzt werden. Wir werden neue Spleissvarianten vorhersagen und analysieren und neue Ansätze beim computergestützten Lernen, wie beispielsweise Bayes'sche Netze, anwenden. Ziel ist es, die Prozesse, die bei der Regulation des alternativen Speissens eine Rolle spielen und die durch alternatives Spleissen reguliert werden, besser zu verstehen. Diese Erkenntnisse wollen wir bei ausgewählten multifunktionellen Proteine und Proteinkomplexen, die im Sonderforschungsbereich untersucht werden, anwenden.

Publications

2008

Hiller M. and M. Platzer (2008) Widespread and subtle: alternative splicing at short-distance tandem sites. Trends Genet 24: 246-55. PubMed

Hiller M., K. Szafranski, K. Huse, R. Backofen and M. Platzer (2008) Selection against tandem splice sites affecting structured protein regions. BMC Evol Biol 8: 89. PubMed

Hiller M., K. Szafranski, R. Sinha, K. Huse, S. Nikolajewa, P. Rosenstiel, S. Schreiber, R. Backofen, and M. Platzer (2008) Assessing the fraction of short-distance tandem splice sites under purifying selection. RNA 14: 616-29. PubMed

Schindler S., K. Szafranski, M. Hiller, G. S. Ali, S. G. Palusa, R. Backofen, M. Platzer and A. S. Reddy (2008) Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes. BMC Genomics 9: 159. PubMed

2007

Hiller M., S. Nikolajewa, K. Huse, K. Szafranski, P. Rosenstiel, S. Schuster, R. Backofen, and M. Platzer (2007) TassDB: a database of alternative tandem splice sites. Nucleic Acids Res 35: 188-192. PubMed

Nikolajewa S., R. Pudimat, M. Hiller, M. Platzer, and R. Backofen (2007) BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data. Nucleic Acids Res 35: 688-693. PubMed

Szafranski K., S. Schindler, S. Taudien, M. Hiller, K. Huse, N. Jahn, S. Schreiber, R. Backofen, and M. Platzer (2007) Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns. Genome Biol 8: R154. PubMed

2006

Hiller M., K. Huse, K. Szafranski , N. Jahn, J. Hampe, S. Schreiber, R. Backofen, and M. Platzer (2006) Single-nucleotide polymorphisms in NAGNAG acceptors are highly predictive for variations of alternative splicing. Am J Hum Genet 78: 291-302. PubMed

Hiller M., K. Huse K, K. Szafranski, P. Rosenstiel, S. Schreiber, R. Backofen, and M. Platzer (2006) Phylogenetically widespread alternative splicing at unusual GYNGYN donors. Genome Biol 7: R65. PubMed

Hiller M., K. Szafranski, R. Backofen, and M. Platzer (2006) Alternative Splicing at NAGNAG Acceptors: Simply Noise or Noise and More? PLoS Genet 2: 207-208. PubMed

Platzer M., M. Hiller, K. Szafranski K, N. Jahn, J. Hampe, S. Schreiber, R. Backofen, and K. Huse (2006) Sequencing errors or SNPs at splice-acceptor guanines in dbSNP? Nat Biotechnol 24: 1068-70. PubMed

2005

Hiller M., K. Huse, M. Platzer, and R. Backofen (2005) Non-EST based prediction of exon skipping and intron retention events using Pfam information. Nucleic Acids Res 33: 5611-5621. PubMed

Hiller M., K. Huse, M. Platzer, and R. Backofen (2005) Creation and disruption of protein features by alternative splicing -- a novel mechanism to modulate function. Genome Biol 6: R58. PubMed

Platzer M., K. Huse, and M. Hiller (2005) Alternatives Spleissen an NAGNAG-Motiven: kleine Ursache - grosse Protein-Vielfalt. Biol Unserer Zeit 35: 80-82. Link

Valentonyte R., J. Hampe, K. Huse, P. Rosenstiel, M. Albrecht, A. Stenzel, M. Nagy, K. I. Gaede, A. Franke, R. Haesler, A. Koch, T. Lengauer, D. Seegert, N. Reiling, S. Ehlers, E. Schwinger, M. Platzer, M. Krawczak, J. Muller-Quernheim, M. Schurmann, and S. Schreiber (2005) Sarcoidosis is associated with a truncating splice site mutation in BTNL2. Nat Genet 37: 357-64. PubMed

Wen G., J. Ramser, S. Taudien , U. Gausmann, K. Blechschmidt, A. Frankish, J. Ashurst, A. Meindl, and M. Platzer (2005) Validation of mRNA/EST-based gene predictions in human Xp11.4 revealed differences to the organization of the orthologous mouse locus. Mamm Genome 16: 934-41. PubMed

2004

Hiller M., R. Backofen, S. Heymann, A. Busch, T. M. Glaesser, and J. C. Freytag (2004) Efficient prediction of alternative splice forms using protein domain homology. In Silico Biol 4: 195-208. PubMed

Hiller M., K. Huse, K. Szafranski, N. Jahn, J. Hampe, S. Schreiber, R. Backofen, and M. Platzer (2004) Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity. Nat Genet 36: 1255-7. PubMed


Impressum