Research Group Wachter

Dr. Andreas Wachter

ZMBP, Allgemeine Genetik
Universität Tübingen
Auf der Morgenstelle 32
D-72076 Tübingen
Germany

Tel. +49-7071 / 29 76 1 49
Fax. +49-7071 / 29 50 42
e-mail: awachter(at)zmbp.uni-tuebingen.de

 

Research Topic

Alternative Splicing in Plants

Figure 1: Regulation and functional implications of alternative splicing.



Alternative splicing (AS) describes the formation of two or more transcript variants from one type of precursor mRNA (pre-mRNA) by removal of different intron sequences. AS has been demonstrated to be widespread in higher eukaryotes and can both increase proteome diversity and contribute to gene regulation via formation of instable mRNAs (Figure 1). Despite its wide distribution, many questions, especially concerning the functional implications and regulation of AS events, remain to be addressed.


In our work, we are interested to gain deeper insight into the biological implications and regulation of AS in plants. The following sections will provide short descriptions of the ongoing research projects in our group.





1. Functional Characterization of Novel Splicing Regulatory Proteins from Plants

Pre-mRNA splicing is accomplished by a complex ribonucleoprotein machinery, which is characterized by its highly dynamic and flexible composition. A plethora of splicing factors has been described and their interaction with cis elements and additional trans factors can alter AS decisions.

One class of splicing factors is constituted by the Polypyrimidine Tract Binding Proteins (PTBs), which have been shown to regulate AS during developmental processes in animals. In our recent work, we functionally characterized three PTB homologues from Arabidopsis and provided insight into their auto- and cross-regulation via AS (Stauffer et al., 2010). Furthermore, we could demonstrate that Arabidopsis PTBs also localize to processing bodies pointing at functions downstream of splicing such as translational control or mRNA storage. In our future work, we are interested to understand the mechanisms of PTB actions in more detail and to identify novel PTB regulation targets, thereby gaining insight into their biological implications.

2. Coupled AS and nonsense-mediated decay in plant gene control

Based on our previous studies, coupling of AS and nonsense-mediated decay (NMD) plays an important role as a means of gene regulation in plants. Interestingly, NMD target features such as long 3’ untranslated regions (UTRs) or introns within 3’ UTRs can be found for a large number of Arabidopsis transcripts raising the question how widespread NMD-mediated gene control might be. We are addressing this question on a transcriptome-wide level applying both bioinformatical and experimental approaches such as next generation sequencing. With this work, we would like to identify novel natural NMD targets and reveal their functional significance in gene regulation.

3. Coordinated Splicing Programs in Plant Development

AS holds an enormous potential for altering expression of large numbers of genes in a coordinated manner as it is required in many plant adaptation and developmental processes. However, currently it is not known if this potential is actually used in plants. We are employing both biased approaches starting from certain splicing regulatory proteins and unbiased strategies focused on defined developmental programs to investigate a possible role of coordinated splicing programs in plants.

4. Regulation of AS by Structured mRNA Motifs

Our previous studies revealed an important role of mRNA structures in the control of splicing decisions. For example, metabolite-sensing mRNA motifs, so-called riboswitches, can bind cellular metabolites with high specificity and exploit alternate RNA folds for controlling AS events (Wachter, 2010). Furthermore, a structural mimic of 5S rRNA, positioned within the pre-mRNA of transcription factor IIIA, was found to control AS in cis and thereby coordinate synthesis of two ribosomal components (Hammond et al., 2009). It can be anticipated that the structural capacity of RNA is used in many more instances to regulate various steps of gene expression. We are interested to discover novel mRNA motifs and to elucidate their functions in plants.