Poster (download)
428Antonina Kiseleva1, Maria Bragina2, Elena Salina3
1ICG SB RAS, Novosibirsk, Russia, antkiseleva@bionet.nsc.ru
2ICG SB RAS, Novosibirsk, Russia, koltunova@bionet.nsc.ru
3ICG SB RAS, Novosibirsk, Russia, salina@bionet.nsc.ru
The study of daily oscillations of the wheat transcriptome, the identification of both the core circadian genes and the genes of metabolic pathways under the influence of daily rhythms is the main topic of this work.
Interesting work! I have several questions:
1) On your slide 5 which annotation is presented? for all 2704 genes with significant cyrcadian pattern? Have you analyzed functionally 7 modules? Are there any differences?
2) Have you tried to trace the known cyrcadian rhythm regulators in your data (like CCA1 and LHY)?
And one suggestion: if the promoters of wheat genes can be traced, we suggest you to use our tool metaRE (Novikova et al., Genes, 2020) to search for k-mers associated with the expression patterns. It might be that you could define the binding sites for the main regulators (they are usually conservative among species, they can give you a hint, which TFs are involved).
Dear Dr Mironova,
Thank you for your interest to our study and for your suggestion! We will certainly use the proposed tool for the analysis.
The responses are as follows:
1) The slide 5 presents annotation of all genes with circadian expression. We have also analyzed functional enrichment of all the modules separately and revealed specific GO terms to every module. For example, module M3 is enriched by genes expressing in response to different stresses and involved in immune system processes. M1 is enriched by genes that are specifically involved in metabolism of nitrogen compounds. M2 is enriched by genes related to organelle organization and photosystem II repair.
2) Yes, we have traced the known circadian genes (LHY, TOC, GI, LUX, PRR73…) and compared their expression patterns with patterns of homologue genes in Arabidopsis thaliana. Their expression patterns coincided. So, we may conclude that the core circadian rhythms work in the same way in model plant and in common wheat.
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