Kazunari (Kazu) Nozue College of Biological Sciences, University of California Davis May 16, 2007
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Transcript of Kazunari (Kazu) Nozue College of Biological Sciences, University of California Davis May 16, 2007
Rhythmic growth explained by coincidence between internal and
external cues; what gene networks are underlying?
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Kazunari (Kazu) NozueCollege of Biological Sciences, University of California Davis
May 16, 2007
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Acknowledgements
Julin Maloof
Stacey Hamer
Mike Covington
Andreah Wallace (Andii)
Maloof lab
protein-gene interactions
protein-protein interactions
PROTEOME
GENOME
METABOLISM
Bio-chemical reactions
Citrate Cycle
Cellular networks:
complex network regulates growth
Brassino-steroid
light
ethylene auxin
clock
GA
Growth
Nozue & Maloof (2006)
Molecular mechanisms of circadian clock
Salome (2005)
negative feedback loop
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Hypocotyl elongation has circadian rhythm
Dowson-Day (1999) Plant J. 17:63-71
2d 12L/12D entrainmentimage recording under continuous dim light
Time in continuous light (hrs)
circadian clock controls hypocotyl elongation rhythm
Dowson-Day (1999) Plant J. 17:63-71
Time in continuous light (hrs)
clock-deficient mutant
wild type
Real world is not continuous light…day-night cycles!
time-lapse photography (Col; short day (SD))
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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
what is microarray?
TOP 10 of up-regulated genesin growing phase (Dark)
vs non-growing phase (Dark)
rank-product non-parmetric method(Breitling 2004, FEBS 573:83) pfp; percentage of false-positives, FC; fold-change
description cycling under LL Dof-type zinc finger domain-containing protein identical to H-protein promoter binding factor-2a GI:3386546 from [Arabidopsis thaliana] Yes (CT4-8) hydrolase, alpha/beta fold family protein low similarity to monoglyceride lipase from [Homo sapiens] GI:14594904 Yes (CT4-8) gigantea (GI) Yes (CT8) zinc finger (B-box type) family protein / salt-tolerance protein (STO) Yes (CT4-8) phytochrome-interacting factor 4 (PIF4) / basic helix-loop-helix protein 9 (bHLH9) Yes (CT8)phytochrome-interacting factor 3 (PIF3)-like 6 (PIL6) basic helix-loop-helix (bHLH 65) family protein Yes (CT8) expressed protein Yes (CT4) dentin sialophosphoprotein-related contains weak similarity to Swiss-Prot:Q9NZW4 dentin sialophosphoprotein precursor [Homo sapiens] Yes (CT8)GH3-3, auxin-responsive GH3 family protein similar to auxin-responsive GH3 product [Glycine max] No expressed protein Yes (CT4)
Nozue (2007) Nature
Rhythmic growth explained by coincidence between internal and
external cues
WTNozue (2007) Nature
coincidence between internal & external cuesanother example: flowering time
Imaizumi (2006)
questions
• what are genes in my lists?
• Do the genes control growth?
If so,
• how they control growth?
what gene networks control plant growth?
• genotype interaction (cf. Jose’s talk)
• protein-protein interaction
• co-expression
visualization of network
PIL6PIF4
UPG; green
UPNG; magenta
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non-overlapping
of each gene network
visualization of network
what are other genes?
<plan>
a. GO annotationa. Gene Ontology (GO) terms (Camon et al., 2004)
b. what GO terms over-represented in these genes?a. GOHyperG function in R
b. MapMan analysis?
UPG; green
UPNG; magenta
how many groups are there?
a. spectral methoda. eigen vector/matrix
b. betweeness (needs to learn more)
partitioning of network
UPG; green
UPNG; magenta
partitioning of network
minus in eigen vector 2: blue circleplus in eigen vector 2; red circle
Most of each component is overlapped withUPG or UPNG network.
how many groups are there?
a. spectral gap method
UPG; green
UPNG; magenta
protein-gene interactions
protein-protein interactions
PROTEOME
GENOME
METABOLISM
Bio-chemical reactions
Citrate Cycle
Cellular networks:
biological network layered
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are needed to see this picture.