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Combinatorial control of cell fates Signal 1Signal 2Selector ASelector B Target Gene XTarget Gene Y Target Gene Z Cell fate Cell fate Cell fate A relatively small “toolkit” of signals and selector genes can specify a wide range of cell fates by a combinatorial mechanism
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Control of gene expression by selector genes and signaling pathways Different signal/selector combinations define different cell fates and gene expression domains
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Visceral mesoderm induction
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Dpp tin twi eve Wg bap slp cardiac mesoderm visceral mesoderm mesoderm DV axis AP axis Visceral mesoderm induction Enhancers: tin: Mad/Med + Tin eve: Mad/Med + Tin + dTCF bap: Mad/Med + Tin + Slp Dpp and Wg act cooperatively on eve, but antagonistically on bap
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Dissecting the regulatory region of bagpipe
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DNaseI protection ("footprinting") assay
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Comparative analysis of bap enhancer ("phylogenetic footprinting")
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Testing the in vivo functions of TF binding sites identified in vitro
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Genome-wide profiling of gene expression
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Arbeitman, M. N. et al. Development 2004;131:2007-2021 Somatic portion of the sex determination hierarchy
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Wild-type males and females (8 timepoints) Males and females lacking germline (progeny of tudor females) Sex-transformed females (XX; tra / tra) Pseudomales (XX; dsxD / dsx) Female intersexes (XX; dsx / dsx) Male intersexes (XY; dsx / dsx) Fruitless mutant males (XY; fru / fru) Genotypes
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Sex-specific gene expression? Comparison of wild-type males and females, 7 timepoints ANOVA: Level = Global mean + sex + timepoint + residual H 0 : sex1 = sex2; P=??? 1576 out of 4040 genes differ at P<0.001 ( 897 females > males, 679 males > females ) Adjust significance threshold for multiple comparisons
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Sex-specific gene expression? 1.Is gene expression sexually dimorphic in the soma? (tudor males versus tudor females, P < 0.05) 2.Is it regulated by the canonical sex determination pathway? (wild type females versus XX; tra / tra, P < 0.05) 147 genes out of 1576 3.Is the gene expressed mainly in the soma? (wild type females versus tudor females, P > 0.2; wild type males versus tudor males, P > 0.2) 73 genes out of 147 (37 females > males; 36 males > females) 10 cDNAs turned out to be chimaeric
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Arbeitman, M. N. et al. Development 2004;131:2007-2021 good not so good not good at all Re-testing candidate genes by Northern blots control
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Re-testing candidate genes by Northern blots Overall 20 out of 32 re-tested candidate genes were confirmed
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Is the gene regulated by dsx or fru ? Forced-choice statistical model (strain-specific variation is a problem) Expression level = X ij, where i = genotype, j = replicate If controlled by dsx, expression should not differ between wild-type males and fru males If controlled by fru, expression should not differ between tudor females and dsxD / dsx pseudomales
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Is the gene regulated by dsx or fru ?
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Arbeitman, M. N. et al. Development 2004;13:2007-2021 Gene expression in male internal genitalia Accessory glands Anterior ejaculatory duct Ejaculatory bulb Testes
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Arbeitman, M. N. et al. Development 2004;131:2007-2021 Gene expression in female internal genitalia Spermathecae & parovaria Nurse and follicle cells, oviducts Male-enriched genes
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What are the functions of dsxM and dsxF ?
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~ Half of the fly genome is deployed sex-specifically (Arbeitman et al 2002, Parisi et al 2003, Ranz et al 2003, …) Less than 2% of the genome is expressed sex-specifically in the soma ?? Why are they all in the internal genitalia? Considerations: - Size of the tissue? - Transcript abundance? - Extent of sexual dimorphism? - Tissue + sex specificity?
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Overview of early myogenesis twist snail Mesoderm fate Dpp Wg myoblast competence RTKs (EGF & FGF) eve equivalence group Notch (Mad+dTCF+Pnt) Fusion - competent cells (lame duck) Founder cells (dumbfounded) Founder cell FCMs myotube muscle
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Combining genetic analysis with FACS
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FACS works Identified 335 genes with higher expression in GFP-positive cells Tested 207 by RNA in situ hybridization True positive rate 95.3%
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Compare gene expression profiles in wild-type and mutant mesodermal cells 12 mutant genotype Use the behavior of each gene across genotypes to infer the cell type in which it is expressed Example: If a gene is upregulated by Wg, Dpp, and RTK/Ras pathways, upregulated by loss of Dl, downregulated by Notch, downregulated by loss of wg - then it is likely to be expressed in FCs.
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Deriving the statistical metric to detect FC/FCM specificity
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Clustering of gene expression changes by genotype
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Empirical validation of predicted FC and FCM genes
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Functional assay for myoblast development Co-injection of dsRNA and myosin-tau.GFP RNAi for mbc and blow reproduces their mutant phenotypes
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FC gene Loss of fusion competence FCM gene Myotubes replaced by multi-nucleate spheres
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