Flowering time control

 How do plants know the time is right to flower? Many respond to environmental cues like temperature and day-length and integrate this information with an endogenous program of development. A crucially important integrator of these different signals is the gene FT, first identified in Arabidopsis, but highly conserved in function in diverse plant species.

We have taken a new approach to identify genes that control flowering time. We have isolated Arabidopsis mutants that flower early in the absence of FT. These mutants therefore identify regulators of flowering time control that work alongside or downstream of FT. The aim of this project is to identify the genes disrupted in these mutants in order to understand how flowering time is controlled. There is much to discover as some of these mutants flower early independently of day-length and some independently of ambient temperature.

Training will be given in molecular genetics and the molecular analysis of gene expression. Our research labs are based at SCRI, giving access to state-of-the-art plant growth facilities and a wider community of researchers focused on plant science.

2. Uncovering Mechanisms of Alternative RNA Polyadenylation in Gene Regulation

Cleavage and the addition of a poly (A) tail at the 3’ end of pre-mRNAs is a fundamental and almost universal feature of eukaryotic mRNA expression. Since the placement of the cleavage site can include or remove RNA sequences that influence transcript stability, transcript localization, protein expression, or protein localisation, cleavage site choice can have profound effects on gene expression. The regulated selection of different cleavage sites is known as alternative polyadenylation (pA) and it is a widespread feature of plant and human gene expression (50% of human genes are alternatively pA). However, the mechanisms underpinning alternative pA are poorly understood.

We have identified two RNA binding proteins from Arabidopsis that control pA site selection and, using genetics, we have shown that they must do this in different ways. Our work is unique, in that we have identified regulators of alternative pA that are not part of the basic splicing or pA machinery. The aim of this project is to make use of this advantage to discover the mechanisms by which alternative pA can be controlled.
The project involves two approaches: First, RNA sequences necessary for alternative polyadenylation will be identified by mutation and testing of reporter genes in plant cells. Second, a mutant screen for factors required to control alternative pA will be performed using a transgene expressing alternative pA sites fused to Green Florescent Protein.

You will join a team currently comprised of 6 researchers studying aspects of alternative pA, with full access to state-of-the-art facilities at the College of Life Sciences and SCRI. Training will be given in molecular biology, genetics, mutant screening and positional cloning.

3. The non-coding Arabidopsis genome

Recent genome-wide studies of gene expression have revealed a more pervasive pattern of transcription than previously appreciated. Much of this comprises non-coding RNAs that previously eluded discovery or confounded genome annotation algorithms. Strikingly, critical roles for these long non-coding RNAs in enhancing or silencing gene expression have been established. We have used so-called third generation direct RNA sequencing technology to reveal regulated patterns of RNA expression during Arabidopsis development. Because this approach avoids spurious artefacts caused by reverse transcriptase, tiling arrays, library construction and amplification, we have great confidence that we have discovered genuinely new RNAs. Working closely with our collaborators in computational biology, the aim of this project will be to validate the discovery of these RNAs using state-of-the-art molecular biology approaches, correcting the annotation of the Arabidopsis genome and associating these RNAs with function. Because Arabidopsis is a path-finding model in plant science, much of the annotation of other plant genomes essential to our future food and energy security depend on knowledge first established in Arabidopsis. Therefore, it is vital that we understand these fundamental features of non-coding RNAs in Arabidopsis in order to translate this knowledge widely. Training in this area with its combination of genome science, plant science, third generation direct RNA sequencing and day-to-day interaction with computational biologists should provide diverse and exciting future opportunities in modern biology.

Arabidopsis transcription factor FLC is a critical regulator of the switch to flower development. FLC expression is controlled by many factors including the autonomous flowering pathway which limits the expression of FLC mRNA. We have recently discovered that two RNA binding components of this pathway called FCA and FPA control alternative 3’ end formation of non-coding antisense RNAs at the FLC locus. Our data suggests that this alternative processing of antisense RNAs controls sense strand transcription. Since it has only recently been recognised that alternative polyadenylation and antisense RNA expression are widespread in eukaryotes, this may represent a generally significant form of gene regulation. The aim of this project will be to take a genetic approach to determine the functional significance of these antisense RNAs and to determine how the interplay between RNA processing and chromatin modifying components of the autonomous pathway mediates this control. State of the art training in working with Arabidopsis, RNA and chromatin will be given.