Transcript Document

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
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Acknowledgements
Stacey Hamer
Maloof lab
Julin Maloof
Andreah Wallace (Andii)
Mike Covington
Cellular networks:
GENOME
protein-gene
interactions
PROTEOME
protein-protein
interactions
METABOLISM
Bio-chemical
reactions
Citrate Cycle
complex network regulates growth
light
GA
Growth
clock
ethylene
Brassino
-steroid
auxin
Molecular mechanisms of circadian clock
negative feedback loop
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Salome (2005)
Hypocotyl elongation has circadian rhythm
Time in continuous light (hrs)
Dowson-Day (1999)
Plant J. 17:63-71
2d 12L/12D entrainment
image recording under continuous dim light
circadian clock controls
hypocotyl elongation rhythm
clock-deficient mutant
wild type
Time in continuous light (hrs)
Dowson-Day (1999)
Plant J. 17:63-71
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 genes
in growing phase (Dark)
vs non-growing phase (Dark)
description
Dof-type zinc finger domain-containing protein
identical to H-protein promoter binding factor-2a
GI:3386546 from [Arabidopsis thaliana]
hydrolase, alpha/beta fold family protein low similarity
to monoglyceride lipase from [Homo sapiens]
GI:14594904
gigantea (GI)
zinc finger (B-box type) family protein / salt-tolerance
protein (STO)
phytochrome-interacting factor 4 (PIF4) / basic helixloop-helix protein 9 (bHLH9)
phytochrome-interacting factor 3 (PIF3)-like 6 (PIL6)
basic helix-loop-helix (bHLH 65) family protein
expressed protein
dentin sialophosphoprotein-related contains weak
similarity to Swiss-Prot:Q9NZW4 dentin
sialophosphoprotein precursor [Homo sapiens]
GH3-3, auxin-responsive GH3 family protein similar to
auxin-responsive GH3 product [Glycine max]
expressed protein
cycling under LL
Yes (CT4-8)
Yes (CT4-8)
Yes (CT8)
Yes (CT4-8)
Yes (CT8)
Yes (CT8)
Yes (CT4)
Yes (CT8)
No
Yes (CT4)
rank-product non-parmetric method(Breitling 2004, FEBS 573:83)
pfp; percentage of false-positives, FC; fold-change
Nozue
(2007) Nature
Rhythmic growth explained by coincidence
between internal and external cues
WT
Nozue (2007) Nature
coincidence between internal & external cues
another 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
PIF4
PIL6
non-overlapping
of each gene network
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UPG; green
UPNG; magenta
visualization of network
what are other genes?
<plan>
a. GO annotation
a.
b.
Gene Ontology (GO) terms (Camon et al., 2004)
what GO terms over-represented in these genes?
a.
b.
GOHyperG function in R
MapMan analysis?
UPG; green
UPNG; magenta
partitioning of network
how many groups are there?
a. spectral method
a.
b.
eigen vector/matrix
betweeness (needs to learn more)
UPG; green
UPNG; magenta
partitioning of network
how many groups are there?
a. spectral gap method

minus in eigen vector 2: blue circle
plus in eigen vector 2; red circle
Most of each component is overlapped with
UPG or UPNG network.
UPG; green
UPNG; magenta
Cellular networks:
GENOME
protein-gene
interactions
PROTEOME
protein-protein
interactions
METABOLISM
Bio-chemical
reactions
Citrate Cycle
biological network layered
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.