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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 QuickTimeý Dz MPEG-4 Video êLí£ÉvÉçÉOÉâÉÄ Ç™Ç±ÇÃÉsÉNÉ`ÉÉǾå©ÇÈÇž ǽDžÇÕïKóvÇ Ç• ÅB QuickTi meý Dz MPEG-4 Video êLí£ÉvÉçÉOÉâÉÄ Ç™Ç±ÇÃÉsÉNÉ`ÉÉ Ç¾å©ÇÈǞǽDžÇÕïKóvÇÇ• ÅB 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 QuickTime™ and a TIFF (LZW) decompressor are needed to see this picture. 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)) QuickTi meý Dz MPEG-4 Video êLí£ÉvÉçÉOÉâÉÄ Ç™Ç±ÇÃÉsÉNÉ`ÉÉ Ç¾å©ÇÈǞǽDžÇÕïKóvÇÇ• ÅB 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 QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. 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.