New research from the John Innes Centre on how plants adapt their flowering to climate is also helping to unravel some of the mysteries of how genes are controlled.
Until relatively recently genome sequencing projects, and studies of gene expression have mostly focussed on the messenger RNA transcripts produced from genes that contain the code needed to make proteins. But as well as this coding RNA, it is now becoming apparent that there are extensive amounts of non-coding RNA that has important roles in regulating gene expression.
Despite being widespread amongst many different organisms, our understanding of this non-coding RNA is still very limited. It is thought to play major roles in the differentiation of stem cells, and it has been implicated in cancer development, but we are still a long way from knowing what all of this non-coding RNA is for. Recent studies by Professor Caroline Dean of the John Innes Centre on how plants control flowering in different climates have given indications of how non-coding RNA is processed and how it can affect gene expression, demonstrating the potential use of a plant based model system in unravelling fundamental questions about how genes work.
Prof Dean's research has centred on a gene in Arabidopsis that suppresses flowering, Flowering Locus C (FLC). Turning off this gene triggers the plant's flowering and reproductive phase, and the timing of this is crucial to the plant's reproductive success. Many different signals integrate into FLC to either maintain or release its suppression of flowering. One of these signals is an extended period of cold that is essential for some plants to flower, a process known as vernalization. It ensures that flowering starts in the favourable conditions of spring after the cold of winter has passed.
The studies on FLC are giving us a fuller understanding of the complexities of gene regulation even beyond the plant kingdom. In two papers now published in the journals Nature and Science, Prof Dean and colleagues at the John Innes Centre, an institute of the BBSRC, are providing potential roles for non-coding RNA in silencing the FLC gene.
In response to cold, non-coding anti-sense transcripts covering the entire FLC gene act to silence FLC sense transcription. Once it has been turned off, or silenced, the gene retains the 'memory' of this for the rest of its life and remains silenced even after the cold stimulus has been removed. This epigenetic memory is maintained through changes in chromatin, the DNA plus associated histone proteins.
Prof Dean has also discovered conserved RNA processing factors specifically process the non-coding anti-sense transcripts of FLC. This processing triggers changes in the histone structure of the FLC gene and leads to transcriptional silencing of FLC independently of cold. The conserved nature of the machinery and its functioning in many conditions suggests this antisense processing mechanism may be rather general throughout eukaryotes.
The FLC gene and vernalization have been of interest to researchers because of how changes in our climate could affect plants. Plants grown in colder climates need much longer vernalization periods, and it is variation in the FLC gene and the various pathways that influence it that have allowed plants to adapt to different climates. However, rapidly changing climates may disrupt some plants faster than they can adapt and this could have significant affects for our own food supply, for example if winter wheat doesn't get the prolonged cold periods it needs to vernalise.
Much more needs to be done to get a complete understanding of what all of this mysterious non-coding RNA is for, but Prof Dean's work in Arabidopsis is now giving the research community as a whole an amenable system to study this layer of gene regulation. And by understanding how some plants are able to adapt to different climates, we may also find ways to adapt our food crops to cope with climate change.
- Swiezewski et al. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature, 2009; 462 (7274): 799 DOI: 10.1038/nature08618
- Liu et al. Targeted 3' Processing of Antisense Transcripts Triggers Arabidopsis FLC Chromatin Silencing. Science, December 3, 2009; DOI: 10.1126/science.1180278
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