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Function of Splicing factor Tra2-beta1 in Alternative Splicing and Translation

Authors: Tang, Yesheng;

Function of Splicing factor Tra2-beta1 in Alternative Splicing and Translation

Abstract

In this work, I performed a genome wide analysis and systematical collection of alternative exons. It resulted in the improvement of a database of alternatively spliced exons collected from literature (AEdb) for ASD (Alternative Splicing Database). Based on this data, a custom splice array covering around 300 splicing factors was constructed. This created a platform for further research on alternative splicing and splicing factors. An increasing number of diseases are associated with alternative splicing. These diseases can be caused by mutation in regulatory sequences of the pre-mRNA or by changes in the concentration of trans-acting factors. Among them, we concentrated on the Alzheimer’s Disease (AD) and breast cancer. We found that the regulation of the CD44 gene by tra2-beta1 was associated with tumor progression and metastasis in breast cancer. In sporadic AD patients, the amount of mRNAs of tau isoforms including exon 10, the htra2-beta1 isoform and an inactive form of clk2 are significantly increased. This suggests that a mis-regulation of alternative splicing contributes to sporadic AD. Previous research shows that TRA2-BETA1, an important SR-like splicing factor, accumulates in the cytosol under cellular stress conditions. Yeast two hybrid studies showed that TRA2-BETA1 directly binds to RPL3, a protein of the large ribosomal subunit that plays a role in peptidyltransferase center formation. To identify the regulation of translation by tra2-beta1, we confirmed the interaction between TRA2-BETA1 and RPL3 using in vitro pull down assays with recombinant proteins. Using sucrose gradient fractionation, TRA2-BETA1 was found to co-sediments with ribosomes and polysome fractions. Furthermore, CLIP (RNA Cross-Linking and ImmunoPrecipitation) of TRA2-BETA1 shows that most of the tra2-beta1 targets from cytoslic RNA is ribosomal RNA. The CLIP targets were localized mainly on the large subunit of the ribosome, near the RPL3 binding sites in the 28S rRNA that is closed to RPL3 binding site. In functional assay, TRA2-BETA1 with an inserted nuclear export signal strongly activates luciferase reporter constructs that contain a TRA2-BETA1 binding motif. This stimulation is regulated by the dephosphorylation in its PP1 (Protein Phosphatase 1) binding site which is localized between RRM (RNA Recognition Motif) and the second RS domain. In summary, we demonstrated that tra2-beta1 has a novel role in translation regulation in addition to its general function in splicing. In dieser Arbeit wurden in einer genomweiten Analyse Daten zu alternativem Spleißen und Spleißfaktoren systematisch gesammelt und annotiert. Das Ergebnis war die Verbesserung einer Datenbank alternativ gespleißter Exons, die aus der Literatur gesammelt wurden (AEdb) in der Datenbank ASD („alternative splicing database). Basierend auf diesen Daten wurde ein kommerzieller Splice Array konstruiert, der rund 300 Spleißfaktoren umfasst. Dieser Array bildet eine Plattform zur weiteren Untersuchung von alternativem Spleißen und Spleißfaktoren. Eine zunehmende Anzahl von Krankheiten steht im Zusammenhang mit alternativem Spleißen. Diese Krankheiten können durch Mutationen in regulatorischen Sequenzen der prä-mRNA oder durch Veränderungen in der Konzentration von Proteinfaktoren verursacht werden. Unter diesen haben wir uns auf Morbus Alzheimer und Brustkrebs konzentriert. Wir haben herausgefunden, dass die Regulation des CD44 Genes durch Tra2-beta1 in Zusammenhang mit Tumorprogression und Metastasenbildung in Brustkrebs steht. In Patienten mit sporadischer Alzheimer-Krankheit ist die Menge der mRNAs der tau isoform mit Exon 10, der htra2-beta1 Isoform und einer inaktiven Form von clk2 signifikant erhöht. Dies deutete darauf hin, dass eine Fehlregulation von alternativem Spleißen zur sporadisch auftretenden Alzheimerschen Erkrankung beiträgt. Bisherige Versuche zeigen, dass Tra2-beta1, ein wichtiger SR-ähnlicher Spleißfaktor, sich unter zellulären Stressbedingungen im Cytosol ansammelt. Untersuchungen in Hefe haben demonstriert, dass Tra2-beta1 direkt an RPL3 bindet, ein Protein der großen Ribosomenuntereinheit, das eine Rolle in der Bildung des Peptidyl-Transferase Zentrums spielt. Um die Regulation der Translation durch Tra2-beta1 zu untersuchen, wurde die Interaktion zwischen Tra2-beta1 und RPL3 in vitro mit rekombinanten Proteinen bestätigt. In Saccharose Gradienten co-sedimentiert Tra2-beta1 mit den Ribosomen und Polysomen Fraktionen. Zudem zeigen CLIP (UV Cross-Linking und Immunopräzipitation) Daten von Tra2-beta1, dass die meisten Tra2-beta1 Zielgene in cytosolischer RNA ribosomale RNA sind. Die CLIP Zielgene wurden hauptsächlich an der großen Ribosomenuntereinheit, in der Nähe der RPL3 Bindestelle in 28S rRNA gefunden. In Funktionsanalysen wird gezeigt, dass Tra2-beta1 mit einem Nukleus-Export-Signal Luciferase Reporter Konstrukte mit einem Tra2-beta1 Bindemotiv stark aktiviert. Diese Stimulierung wird durch Dephosphorylierung von Tra2-beta1 an der PP1 (Protein Phosphatase 1) Bindestelle zwischen RRM (RNA Erkennungsmotiv) und der zweiten RS Domäne reguliert. Zusammen zeigen diese Untersuchungen eine neuartige Rolle für Tra2-beta1 in der Regulation der Translation neben seiner generellen Funktion im Spleißen.

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Keywords

Translation, Naturwissenschaftliche Fakultät -ohne weitere Spezifikation-, RNS, ddc: ddc:570

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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