“the identity of plant thermometers remains one of the great mysteries in the plant sciences” CR McClung @Dartmouth
We are Plant Science researchers – one group from the University of Glasgow, the other from The James Hutton Institute in Dundee – who have come together to collaborate on a research project funded by the British Biotechnology & Biosciences Research Council (BBSRC). We hope that this informal blog will chart our research journey. Please click on the ‘Research Scientists‘ link to meet some of us, and also on the ‘Research Benefits‘ link to find out how our research will benefit society. We have called this blog ‘It’s About Time’ because it’s about a ubiquitous molecular timing mechanism that almost all living systems, including plants, possess – circadian clocks. Maybe it’s about time we told you some more….
We are aiming to use our combined expertise to contribute to the understanding of the molecular processes that buffer the plant circadian clock from temperature changes. This is important as maintaining clock function is essential for optimal photosynthesis, growth, and the timing of reproduction – factors that influence seed abundance (a yield output for crop plants). When genes are expressed the DNA sequence is first copied into RNA (transcription), the RNA is processed and then it directs synthesis of the corresponding protein (translation) – this flow of genetic information is sometimes referred to as the Central Dogma of Molecular Biology. In recent years there has been an explosion in RNA research, and in particular there is now a growing realisation of the importance of the multitude of processes operating at the post-transcriptional level – that is – the point in the central dogma between transcription and translation of a gene. One example of a post-transcriptional mechanism involved in regulating how genes are expressed is called “alternative splicing” – often abbreviated as “AS”
We have already made significant progress in deciphering the role of AS in temperature-dependent clock function in the model plant Arabidopsis. AS generates different transcripts from the same gene and thereby can modulate transcript and protein levels and functions. We have shown that AS is important in controlling clock gene expression. We are now looking at AS in genes closely associated with the clock, and how AS of these genes are affected at low temperature and how this might influence expression and/or AS of the central, or ‘core’ clock genes.
Plants experience continued and variable temperature changes throughout the normal day/night cycle. We are interested in deciphering the degree and timing of temperature change which is able to elicit a temperature-dependent AS response. Light also has a major influence on the clock and we are aiming to identify which AS events respond to light intensity changes and whether they are different from temperature-dependent events.
A major question that we are addressing is how the different types of AS in different clock genes are regulated and how this mechanism contributes to temperature buffering of the circadian clockwork. Here, we will use RNA sequencing – or RNA-seq – to assess AS events during cooling. Co-expression and co-splicing network analysis will identify genes whose expression/splicing profiles correlate with those of the core clock and clock-associated genes to identify putative regulatory genes. We will also examine the natural genetic variation in this process and how this might aid our understanding.
The role of AS in regulation of clock gene expression is highly relevant to crop plants and yield. To utilise the knowledge and approaches from our Arabidopsis research, we have started to examine AS control in potato and barley to begin the translation toward application. We anticipate that this work will provide new insights into what controls phenotypes such as earliness in barley and endodormancy in potato and ultimately lead to strategies for the generation of new genotypes that have increased robustness to temperature and other stresses that can affect plants.