Chapter9BGenomes and Proteomes10-1
Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display 10-1 Genomes and Proteomes Genomes and Proteomes Chapter 9B
Sections to study1Large-scale genome mapping and analysis2 Major insights from the human and model organism genomesequences3Global analysis of genes and theirmRNAs4Globalanalysisofproteomes5 Repercussions of the human genome project and highthroughputtechnology10-2
Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display 10-2 Sections to study Sections to study 1 Large 1 Large-scale genome mapping and analysis scale genome mapping and analysis 2 Major insights from the human and model organism genome 2 Major insights from the human and model organism genome sequences sequences 3 Global analysis of genes and their mRNAs 3 Global analysis of genes and their mRNAs 4 Global analysis of proteomes 4 Global analysis of proteomes 5 Repercussions of the human genome project and high 5 Repercussions of the human genome project and highthroughput technology throughput technology
The major advances that have transformed geneticsRecombinantHumanDNADNAGenomeMendel'stechnologystructureProjectdiscoveries186619531970s1990Genetics10-3
Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display 10-3 The major advances that have transformed genetics The major advances that have transformed genetics 1866 Mendel’s discoveries 1953 DNA structure 1990 Human Genome Project Genetics 1970s Recombinant DNA technology
1 Large-scale genome mapping and analysisGenome: The entire geneticChromosomeromatidChromatidchNuclnuinformation in a particularTolomerecell or organism.Genomics:The study of wholegenomes. It dedicated to theCelldevelopmentand applicationofmore effectivemappingsequencing,andcomputational toolsNA/doubi
Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display 10-4 1 Large-scale genome mapping and analysis Genome: The entire genetic information in a particular cell or organism. Genomics: The study of whole genomes. It dedicated to the development and application of more effective mapping, sequencing, and computational tools
Techniques forgenome mapping and sequencingCloningLibraryofDNAfragments500-1,000,000bpInsertintoone vectorHybridization Location of aparticular DNAsequencewithina library offragmentsPCRamplification DirectamplificationofaparticularregionofDNArangingfrom1oobpto>2okbDNA sequencingAutomated DNA sequencer using Sangermethod determines sequenceslooo bpat a time.Computational toolsPrograms for identifying matches between a particular sequence and a largepopulation of previously sequenced fragmentsPrograms foridentifying overlaps ofDNA fragmentsPrograms for estimating errorratesPrograms foridentifyinggenes in chromosomal sequences10-5
Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display 10-5 Techniques for genome mapping and sequencing Techniques for genome mapping and sequencing Cloning Cloning Library of DNA fragments 500 Library of DNA fragments 500 – 1,000,000 1,000,000 bp Insert into one vector Insert into one vector Hybridization Hybridization Location of a particular DNA se Location of a particular DNA sequence within a library of fragme quence within a library of fragments PCR amplification PCR amplification Direct amplification of a particul Direct amplification of a particular region of DNA ranging from ar region of DNA ranging from 100 bp to > 20kb to > 20kb DNA sequencing DNA sequencing Automated DNA sequencer using Sang Automated DNA sequencer using Sanger method determines sequences er method determines sequences 1000 bp at a time. at a time. Computational tools Computational tools Programs for identifying matches Programs for identifying matches between a particular sequence a between a particular sequence and a large nd a large population of previously sequenced fragments population of previously sequenced fragments Programs for identifying overlaps of DNA fragments Programs for identifying overlaps of DNA fragments Programs for estimating error rates Programs for estimating error rates Programs for identifying ge Programs for identifying genes in chromosomal sequences nes in chromosomal sequences
Vectors used for cloning large inserts for physical mappingYACs(yeastartificialchromosomes)Insertsize250-2,000kbBACs(bacterialartificialchromosomes)Insertsize100-300kbMore stableand easier to purifyfromhostDNA than YACs10-6
Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display 10-6 Vectors used for cloning large inserts for physical mapping Vectors used for cloning large inserts for physical mapping YACs (yeast artificial chromosomes) (yeast artificial chromosomes) Insert size 250 Insert size 250-2,000 kb 2,000 kb BACs (bacterial artificial chromosomes) (bacterial artificial chromosomes) Insert size 100 Insert size 100 – 300 kb More stable and easier to purify from host DNA than More stable and easier to purify from host DNA than YACs
EcoRIcloning siteCEN4SUP4ARS1TRP1PYACURA3vectorAmporiTELTELTargetDNABamHIBamHlBamHl and EcoRl digestPartial EcoRl digestTELTRPARSCENTEL福URALigateURATELTELTRPARSCENVZ10-7
Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display 10-7
Large-scale linkage maps serve as guides to whole genomesAFLP281AFLP201AFLP010AFLP003AFLP331 DNA Markerstrait ALinkedtoAAFLP057AFLP099AFLP291AFLP020AFLP458AFLP222DNAMarkerstraitBLLinkedtoBAFLP142AFLP033AFLP19910-8
Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display 10-8 Large-scale linkage maps linkage maps serve as guides to whole genomes serve as guides to whole genomes
Long-range physical mapsPhysical maps: a constellation of overlapping DNA fragments thatare ordered and oriented and span each of the chromosomes in agenome.STS (Sequence tagged sites):ShortDNA sequences that are alreadylocatedandamplifiedbyapairofPCRprimers.EachSTSrepresentsauniqueDNA sequenceinthegenome.STS1STS2BAC1BAC2STS3BAC3STS4BAC4STS5BAC5STS6BAC6STS7BAC7BAC810-9
Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display 10-9 Long-range physical maps physical maps Physical maps: a constellation of overlapping DNA fragments that are ordered and oriented and span each of the chromosomes in a genome. STS (Sequence tagged sites): Short DNA sequences that are already (Sequence tagged sites): Short DNA sequences that are already located and amplified by a pair located and amplified by a pair of PCR primers. Each STS represe of PCR primers. Each STS represents a unique DNA sequence in the genome. unique DNA sequence in the genome
Locating cloned genes or markers on the chromosomeof a karyotype》BY11Complete set ofa3humanchromosomes川11%1格路216stained with9.2-7104Giemsa dye shows16RR14品品4bands.1316174Ddab)Ideograms（染色体308866.42G带图）showxChnidealized bandingpattern.888102innxxxxxxxnFig. 10.2 a, b22
Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display 10-10 Locating cloned genes or markers on the chromosome Locating cloned genes or markers on the chromosome of a karyotype karyotype a) Complete set of Complete set of human chromosomes chromosomes stained with stained with Giemsa dye shows bands. b) Ideograms ( Ideograms (染色体 G带图) show idealized banding idealized banding pattern. pattern. Fig. 10.2 a, b