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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