Systems Biology of C. elegans. Stuart Kim Stanford University

Transkript

1 Systems Biology of C. elegans Stuart Kim Stanford University

2 Overview Cell lineage Genome Mutant Phenotypes Protein interaction Gene Expression

3 Early cell divisions

4

5 B A S M E C D 4P C. elegans zygote lineage of 959 cells

6 Overview Cell lineage Genome Mutant Phenotypes Protein interaction Gene Expression

7 100 Mb ~19735 genes 1998

8 94% genes unknown (~1998) 1998

9 94% genes unknown (~1998) interactions for 92% of genes (~2001) 1998

10 Overview Cell lineage Genome Mutant Phenotypes Protein interaction Gene Expression

11 RNA mediated interference (RNAi) ds RNA exogenous cleaved to 22 NT pieces mrna + endogenous causes specific degradation of mrna mrna protein mutant phenotype

12 RNAi in C. elegans Feed worms strains of E. coli expressing ds RNA

13 Download movie of mcm-5(rnai)

14 Mutant cell divisions

15 RNAi screen for 417 fat genes

16 RNAi screens in C. elegans (last two years) No mapping/cloning etc. Order bacterial strain set and do experiments yourself. Examples of screens: ~500 longevity 417 fat genes Genes needed for RNAi Embryonic polarity synaptic function

17 Overview Cell lineage Genome Mutant Phenotypes Protein interaction Gene Expression

18 Global Yeast Two Hybrid Subclone all ORFs into Yeast two hybrid system Systematically describe potential protein-protein interactions

19 Global Yeast Two Hybrid X Y 2898 nodes connected by 5460 edges

20 Protein interaction network et al. Vidal, 2004

21 Overview Cell lineage Genome Mutant Phenotypes Protein interaction Gene Expression

22 Gene expression Networks Eran Segal (Weizmann) Josh Stuart (UCSC)

23 C. elegans gene expression database 553 DNA microarray expts X ~19,000 genes C. elegans expression database (# hybridizations)

24 Cluster of co-expressed genes from DNA microarray experiments 553 DNA microarray experiments Expressed together Which are functionally related? Which are physiologically relevant? ~20,000 genes

25 Evolutionary conservation implies functional interaction Gene A Gene B Gene C A and B are functionally related C is co-expressed, but not functionally related During evolution, all promoter sites are mutated Only enhancers of functionally related genes are preserved Gene A Gene B Gene C

26 Conserved co-expression human Functionally related to YFG? Selective advantage for co-expression YFG Evolutionarily conserved May see co-expression in: 78 Fly 335 YFG Mouse 74 Worm Yeast 1209 YFG YFG

27 worm human gene 1 gene 2 gene 3 gene 1 gene 2 gene 3 Microarray data exp 1 exp 2 exp 3 exp 1 exp 2 exp 3 multi-species topomap Gene correlation matrices gene 1 gene 2 gene 3 gene 1 gene 2 gene 3 gene 1 gene 2 gene gene 1 gene 2 gene gene 1 gene 2 gene 3 gene 1 gene 2 gene 3 Gene rank matrices gene 1 meta-gene 2D scatter plot gene 2 gene gene 1 gene 2 gene meta-gene p-value matrix meg 1 meg 2 meg 3 meg 1 meg 1 meg 2 meg meta-gene network meg 3 meg 2

28 Gene Expression Network

29 Gene Expression Topomap 6886 meta-genes >1000 unknown

30 Ribosomal subunits

31

32 A gene expression microscope Plan A = microarrays Flo Pauli Plan B = GFP reporters Xiao Liu (Fuhui Long, Hanchuan Peng, Gene Myers)

33 Convert image to a data table description Age Age Age Intestines high level in pharynx High level Muscles in body wall muscle Expressed Neurons in some hypodermal cells Gene Gene 1 Gene 2 3 genes 959 cells genes quantitation 959 cells

34 A large number of GFP-reporter transgenic worms 3-D confocal data stack 959 cells Automatic cell lineage analyzer genes Quantitative measurement of GFP expression at the level of single cells

35 Long Term Plan Construct a imaging system to automate cell identification of C. elegans Generate GFP-reporter strains in a large scale Use this GFP analysis system to study aging

36 GFP = BWM (landmarks) RFP = expression DAPI = all nuclei

37 Automatic GFP analyzer Registration = align the image to a standard virtual worm model Segmentation = find the nuclei Recognition = name the nuclei Expression = measure GFP levels in each nucleus

38 Registration = align image to a standard virtual worm model

39 DR DL DR DL VR VL VR VL

40 Segmentation = find the nuclei

41 manual annotation to recognize nuclei cell slice Peak Val Mean Val Size Mass cell name explanation bun_1_1 bwmvl bun_3_1 bwmdr bun_2_1 bwmvr bun_4_1 bwmdl bun_3_22 bwmvr24

42 Gene expression profile at the level of single cells Body Wall Muscle Intestine myo-3 Tissue Specificity

43 Gene expression profile at the level of single cells Body Wall Muscle Intestine myo-3 mir-64 Gradient of gene expression

44 Gene expression profile at the level of single cells Body Wall Muscle Intestine Different levels of transcriptional noise myo-3 mir-64 pha-4

45 Gene expression profile at the level of single cells Body Wall Muscle Intestine myo-3 mir-61 pha-4

46 ~200 GFP-reporter transgenic worms/yr 3-D confocal data stacks ~200 genes 6 conditions ~300 cells 6 developmental time points Automatic cell lineage analyzer Quantitative measurement of GFP expression at the level of single cells

47 Systems Biology + OR

48 Systems Biology of C. elegans Conserved gene expression modules Josh Stuart Eran Segal (Daphne Koller) Automatic GFP lineage analyzer Xiao Liu Fuhui Long Hanchuan Peng Gene Myers