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Genes Eukaryotic Protein-Coding Gene Structure coding non-coding Regulatory Region Size: 50 > 10,000 bp Contains multiple small DNA sequence elements (5 – 20 bp) > bind regulatory proteins Regulatory elements can be negative or positive acting Regulatory regions found in 5’ flanking region, introns, and 3’ flanking regions – most common in 5’ flanking regions and large introns 5’-Untranslated Region Contained in mRNA Spans from start of transcription to start of translation Multiple functions – translational efficiency Size varies greatly - average > 300 nt (human) coding non-coding Coding Sequence Begins with initiator methionine (AUG codon) Sometimes multiple initiator methionines are used Stops with termination codon (UAA, UAG, and UGA) Sizes varies: average = 1340 nt (human); encodes ~450 aa protein coding non-coding 3’ Untranslated Region Spans translational termination codon > end of mRNA Multiple functions: mRNA stability and localization AAUAAA sequence signals where poly(A) is to be added (10-35 nt upstream from cleavage/poly(A) site) Size varies: average - 700 nt (human) coding non-coding Poly(A) Added posttranscriptionally (not encoded in gene) Size varies (10-200 nt) depending on organism Functions: mRNA stability and translational efficiency Size of tract shortens with time All mammalian mRNAs have poly(A) except histone mRNAs Poly(A) Exons Genes have a modular design Evolutionarily assembled in pieces Functional unit > exons # exons can vary from 1 > 178 Average # exons/gene – different organisms Yeast ~1 Drosophila 4 Human 9 Human genes (mean sizes) Exon size 145 bp coding non-coding Introns Introns vary greatly in size Most ~ 50 bp but can be > 15 kb Large genes – large introns Small genes – small introns Size differs between species C. elegans 267 bp Drosophila 487 bp Human 3,365 bp Human introns > exons in size Intron 1 Intron 2 Genetics Mutants Wild-type – “normal” fully-active gene Null – absence of any activity (e.g. deletion) Hypomorph – reduced function Hypermorph – enhanced activity Neomorph – expressed in cells normally not expressed (transgenic approach) Phenotypic analysis – development, morphology, behavior, fertility, etc. Gene regulation Examine how mutation in Gene A influences expression of other genes Genetic and Molecular Genic Relationships Organism Genes Lethal loci (%total genes) Yeast 5,800 1,800 (30%) Nematode 18,400 3,500 (20%) Drosophila 13,600 3,600 (25%) Mouse – similar % based on gene knockout studies Lethal loci – loss of function mutant that results in death Result: Only ~20-30% genes can be mutated to lethality Genetic and Molecular Genic Relationships Why are there genes with no apparent function? Gene may not be doing anything Other genes may compensate for defect (redundancy) Double mutant analysis often provides evidence for this explanation Common for highly-related genes to be (at least partially) redundant Defect may be too subtle to detect Proper assay not used Need proper ecological setting and evolutionarilyrelevant time span to detect May be conditional CNS Midline Cell Development and Transcription Requires Single-minded Function Wild-type Cell division Cell morphology Gene expression sim Ubiquitously-Expressed Sim Transforms Entire CNS into CNS Midline Cells Heat shock-sim Rhomboid-lacZ Uninduced Induced a-LacZ Gene Regulation Regulatory proteins > DNA cis-control elements Positive and negative regulation Combinatorial regulation > highly specific patterns of spatial, temporal and quantitative expression Murine transthyretin gene Sim:Tgo Binding Sites (CNS Midline Elements - CMEs) are Required for Midline Transcription 0.95 kb Toll-lacZ 1 2 3 4 X X X X CME > ACGTG a-LacZ Array Analysis of Gene Expression: Drosophila Understand complete array of gene regulatory events that underlie: Development Tissue and cell identity Aging Behavior Circadian rhythms Learning and memory Example: Single-minded (Sim): Master Regulator of CNS Midline Cell Development and Transcription Sim protein (green) > CNS midline cells Vnd protein (red) > lateral CNS Array Analysis of Gene Expression Midline gene expression program > identify all genes expressed in midline cells Study: function and regulation Approaches: Purify midline cells (GFP) > compare to other cell types and developmental time intervals Mutant (sim) vs. wild-type Misexpression of sim vs. wild-type Transgenes – express in entire CNS Genetics – snail mutant > express in entire mesoderm Midline and Lateral CNS GFP Lines sim-GFP vnd-GFP Dissociate embryonic cells > FACS Compare expression at different stages and to other cell types Results: midline-specific transcripts high in midline cells when compared to levels in other tissues Fluorescence Activated Cell Sorter (FACS) Allows isolation of fluorescently-labeled (GFP+) cells Array Analysis of Gene Expression Midline gene expression program > identify all genes expressed in midline cells Study: function and regulation Approaches: Purify midline cells (GFP) > compare to other cell types and developmental time intervals Mutant (sim) vs. wild-type Misexpression of sim vs. wild-type Transgenes – express in entire CNS Genetics – snail mutant > express in entire mesoderm Comparison of Wild-type to sim Mutant Embryos Wild-type sim Results: Expect to see midline gene expression reduced in sim mutant Array Analysis of Gene Expression Midline gene expression program > identify all genes expressed in midline cells Study: function and regulation Approaches: Purify midline cells (GFP) > compare to other cell types and developmental time intervals Mutant (sim) vs. wild-type Misexpression of sim vs. wild-type Transgenes – express in entire CNS Genetics – snail mutant > express in entire mesoderm Analysis of Midline Transcription by Ectopic Sim Expression: Transgenic Approaches Wild-type sca-Gal4 X UAS-sim-GFP a-Wrapper GFP a-Wrapper Result: Expect to see midline gene expression increased in sca-Gal4 X UAS-sim-GFP Analysis of Midline Transcription by Ectopic Sim Expression: Genetic Approaches Wild-type sim RNA localization snail Result: Expect to see midline gene expression increased in snail mutant Cluster Analysis of Combined Data Sets Compare different data sets Midline genes Test by in situ hybridization for midline expression Array Analysis of Mesoderm Gene Expression Mesoderm Somatic muscles Visceral muscles Fat body, hemocytes twist gene Encodes transcription factor required for mesodermal gene expression twist mutant – no mesoderm or mesodermal gene expression twist overexpression (Toll10B mutation) – excess mesoderm and mesodermal gene expression Twist Mutant and Overexpression Phenotypes Mutant Embryo Purification twist is embryonic lethal mutation twi / + X twi / + only 25% embryos are mutant (twi / twi) Use GFP-CyO chromosome and sort mutant embryos GFP-CyO / twi GFP-CyO / GFP-Cyo twi / twi Mutant Sorting GFP-labeled organisms Hand sort with fluorescence microscope Machine sort Array Analysis: Clustering Confirm expected expression pattern by in situ hybridization