Rhythmic growth explained by coincidence between internal and external cues; what gene networks are underlying

1. Rhythmic growth explained by coincidence between internal and external cues; what gene networks are underlying? Kazunari (Kazu) Nozue College of Biological Sciences, University of California Davis May 16, 2007 I am very glad to be invited by Prof. Shimamoto. Today I would like to talk about how clock and light signaling converge. I am very glad to be invited by Prof. Shimamoto. Today I would like to talk about how clock and light signaling converge.

2. Acknowledgements First I would like to express my thanks to these people and special thanks to Julin Maloof, my boss. He started natural variation of light responses in Arabidopsis at Joanne Chorry�s & D*** Weigel lab when he was a postoc. Four years ago, Julin moved to UC Davis and started his lab. I joined his lab three years ago and started new project, which I am going to talk today. This project is a hybrid work with our next door, Stacey Harmer lab. She is working on circadian clock in Arabidopsis. First I would like to express my thanks to these people and special thanks to Julin Maloof, my boss. He started natural variation of light responses in Arabidopsis at Joanne Chorry�s & D*** Weigel lab when he was a postoc. Four years ago, Julin moved to UC Davis and started his lab. I joined his lab three years ago and started new project, which I am going to talk today. This project is a hybrid work with our next door, Stacey Harmer lab. She is working on circadian clock in Arabidopsis.

4. complex network regulates growth As all of you know, endogenous and exogenous factors regulate growth and their signaling pathways interact each other. However, we do not know this network completely. In my talk, I am going to focus how light and clock interact each other. First, I would like to start what is known about clock control of growth because this is not well known compared with other factors. As all of you know, endogenous and exogenous factors regulate growth and their signaling pathways interact each other. However, we do not know this network completely. In my talk, I am going to focus how light and clock interact each other. First, I would like to start what is known about clock control of growth because this is not well known compared with other factors.

6. Molecular mechanisms of circadian clock Andrew Miller�s group showed that under continuous light entrained seedlings showed circadian rhythmic hypocotyl elongation. This graph shows hypocotyl length along time in continuous light. Seedlings are kept 12 hr light/ 12 hr dark cycles for two days before measuring hypocotyl length. Gray area shows subjective night. They found that hypocotyl does not grow constantly, but growth peaks were seen every dusk. Andrew Miller�s group showed that under continuous light entrained seedlings showed circadian rhythmic hypocotyl elongation. This graph shows hypocotyl length along time in continuous light. Seedlings are kept 12 hr light/ 12 hr dark cycles for two days before measuring hypocotyl length. Gray area shows subjective night. They found that hypocotyl does not grow constantly, but growth peaks were seen every dusk.

7. Hypocotyl elongation has circadian rhythm Andrew Miller�s group showed that under continuous light entrained seedlings showed circadian rhythmic hypocotyl elongation. This graph shows hypocotyl length along time in continuous light. Seedlings are kept 12 hr light/ 12 hr dark cycles for two days before measuring hypocotyl length. Gray area shows subjective night. They found that hypocotyl does not grow constantly, but growth peaks were seen every dusk. Andrew Miller�s group showed that under continuous light entrained seedlings showed circadian rhythmic hypocotyl elongation. This graph shows hypocotyl length along time in continuous light. Seedlings are kept 12 hr light/ 12 hr dark cycles for two days before measuring hypocotyl length. Gray area shows subjective night. They found that hypocotyl does not grow constantly, but growth peaks were seen every dusk.

8. circadian clock controls hypocotyl elongation rhythm They proved the circadian clock regulates this rhythmic elongation by showing a clock-deficient mutant has arrhythmic hypocotyl elongation, having continuous elongation. They proved the circadian clock regulates this rhythmic elongation by showing a clock-deficient mutant has arrhythmic hypocotyl elongation, having continuous elongation.

9. Real world is not continuous light�day-night cycles! However, the real world has day and night cycles. However, the real world has day and night cycles.

10. time-lapse photography (Col; short day (SD)) This is my typical movie of plant growth. A practical PROBLEM IS THAT IT IS HARD TO SEE GROWTH IN THE DARK For this purpose, as is shown in here, we monitored hypocotyls under infra-red light background and captured images by web camera every 30 min. This is my typical movie of plant growth. A practical PROBLEM IS THAT IT IS HARD TO SEE GROWTH IN THE DARK For this purpose, as is shown in here, we monitored hypocotyls under infra-red light background and captured images by web camera every 30 min.

11. what molecular mechanisms are underlying? Hypothesis: transcriptional regulation is involved in gating of dark-induced elongation. Method: whole genome microarray analysis Purpose: to find genes which expression patterns are correlated with growth pattern see animationsee animation

12. what is microarray? see animationsee animation

13. TOP 10 of up-regulated genesin growing phase (Dark) vs non-growing phase (Dark) TOP 10 genes of up-regulated genes in all growing phase against all non-growing phase in dark are extracted by a non-parametric method, Rank product method. Among these top 10 genes, two bHLH genes, PIF4 and PIL6, are of most interest because by using another method the two bHLH genes can be also extracted. NB: Dof-type zinc finger domain containing� functions unknown 2. hydrase substrateTOP 10 genes of up-regulated genes in all growing phase against all non-growing phase in dark are extracted by a non-parametric method, Rank product method. Among these top 10 genes, two bHLH genes, PIF4 and PIL6, are of most interest because by using another method the two bHLH genes can be also extracted. NB: Dof-type zinc finger domain containing� functions unknown 2. hydrase substrate

14. Rhythmic growth explained by coincidence between internal and external cues

16. questions what are genes in my lists? Do the genes control growth? If so, how they control growth?

17. what gene networks control plant growth? genotype interaction (cf. Jose�s talk) protein-protein interaction co-expression

18. visualization of network non-overlapping of each gene network Needs to add negative correlationNeeds to add negative correlation

19. visualization of network what are other genes? <plan> GO annotation Gene Ontology (GO) terms (Camon et al., 2004) what GO terms over-represented in these genes? GOHyperG function in R MapMan analysis? skippedskipped

20. how many groups are there? spectral method eigen vector/matrix betweeness (needs to learn more) partitioning of network

21. partitioning of network how many groups are there? spectral gap method ??????? Raissa�s suggestion: use spectral gap method for non-isolated component itselfRaissa�s suggestion: use spectral gap method for non-isolated component itself

23. biological network layered Raissa�s comment: similar to internet network. Q: Is clock independent from others? A: partially yes. External cues can modulate clock parameters.Raissa�s comment: similar to internet network. Q: Is clock independent from others? A: partially yes. External cues can modulate clock parameters.