55-213 Lecture 12 notes.pdf

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Lecture 12 2013-01-10 2:29 PM Human)Genome)Project:$ • See$figure$comparing$the$Human$Genome$Project$to$the$F[35$jets$project$ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ New)scientific)research)prize:$ • “Breakthrough$Prize$in$Life$Sciences”$ • Supposed$to$compete$with$the$Nobel$Prize$ • Can$spend$it$on$anything$ • Each$award$is$3$million$dollars$ • Will$be$5$awards$a$year$ • Primarily$geared$towards$molecular$biology$researchers$ • Idea$of$Zuckerberg$from$Facebook$and$Burin$the$head$of$Google$and$his$wife$who$ founded$23andme.com$ • Decided$to$put$up$these$awards$to$reward$and$to$advertise$the$importance$and$the$ impact$that$these$scientists$have$on$our$lives$ • One$guy$who$got$the$awards$was$Clever,$who$worked$on$the$intestinal$stem$cells$ o He$paid$for$all$his$collaborators$(140)$to$come$from$different$international$ locations$to$his$home$in$Holland$$ • Another$guy$involved$in$the$Human$Genome$Project$got$it$ • Wulderstein$and$Weinburt$got$it;$they$worked$with$cancer$ • The$11$people$who$won$it$the$first$year$get$to$vote$as$judges$next$year$$ $ Important)concepts)for)week)7:$ • What$makes$humans$different$from$each$other$ • How$is$our$DNA$organized$in$our$genome$ o We$know$it’s$on$our$chromosomes,$but$only$some$of$it$codes$for$our$genes.$ Thus,$what$is$the$rest$of$the$DNA$doing?$ • Personalized$medicine:$what$is$it$and$how$will$it$change$your$life$ $ Chapter)5:)Content)of)Genome$ • What$makes$up$our$genome$in$terms$of$DNA$sequences?$ • How$are$our$genomes$related$to$each$other?$ o Egyptian$Pharaohs$ o Who$were$there$ancestors?$ o Swiss$company$IGENEA$world$leader$in$extracting$DNA$from$ancient$ specimens$(e.g.$Neanderthal,$Egyptian$mummies)$ • When$they$did$the$analysis,$got$the$DNA$and$sequenced$it,$they$verified$their$ paternity$and$faced$a$big$surprise:$it$was$long$believed$that$the$Egyptian$Pharaohs$ were$bread$in$the$Egyptian$population$over$many$generations.$However,$it$turns$out$ that$at$some$point,$King$Tut$and$his$father$showed$complete$European$heritage.$ They$don’t$know$how,$but$it’s$certain$that$this$happened$ • IGENEA$is$a$Swiss$company$that$made$its$mark$in$molecular$biology$via$analyzing$ DNA$of$ancient$people$ o They$are$80%$complete$with$the$Neanderthal$genome$ o Who$cares?$Well,$we$all$have$Neanderthal$DNA$in$us.$23andme$even$tests$for$ the$percentage$of$DNA$you$have$from$them$ o They$had$some$unique$features$ o They$are$an$extinct$line$that$was$wiped$out,$but$they$were$around$for$a$very$ long$time.$They$surely$mated$with$Homosapiens$during$migration$through$ Europe$ $ Types)of)Mapping:$ • Genome$mapping:$Physical$arrangement$of$all$the$genes$in$the$genome$on$ chromosomes$ o Human$Project$is$done,$thus$we$know$every$sequence$on$our$chromosomes$ o We$want$to$know$where$every$single$one$of$our$20$000$genes$are$located$ and$which$ones$are$next$to$each$other$ o Physical$structure$of$chromosomes$are$all$identical$among$humans$ • Linkage$map:$genes$are$defined$through$mutations$that$are$known$to$occur$at$ different$sites$on$chromosome$–$determined$through$recombination$frequency$(low$ resolution)$ o In$the$40s$and$50s,$they$knew$genes$sit$on$chromosomes$but$they$didn’t$ know$where$exactly.$They$discovered$that$by$figuring$out$the$recombination$ frequency,$they$could$figure$out$how$far$apart$the$genes$were$on$the$ chromosome$"$linkage$mapping!$ • Restriction$map:$constructed$by$cutting$DNA$with$different$restriction$enzymes$and$ measuring$the$distances$between$sites$of$cleavage$(medium$resolution)$ o You$could$cut$DNA$up$in$little$bits$and$try$to$piece$them$back$again$ o You$could$analyze$how$big$the$fragments$were$$ o It$was$like$a$huge$jigsaw$puzzle$$ o It$was$like$seeing$streets$and$their$names,$but$not$being$able$to$have$Google$ Street$View$ o Thus,$it$still$wasn’t$great$ • DNA$sequence$map:$the$actual$DNA$base$sequence$on$the$chromosome$(high$ resolution)$ o Once$you$have$this$information,$you$could$start$to$look$at$characteristic$flag$ poles$on$the$gene$(i.e.$knowing$if$it’s$a$promoter$for$example)$ o In$2003,$when$the$sequence$was$published,$it$set$off$a$whole$new$age$of$ molecular$biology$which$is$the$genome$map$ o You$could$now$see$a$chromosome$and$know$exactly$where$the$genes$are!$$ o Linkage$maps$and$restriction$maps$were$very$useful$at$the$beginning$of$the$ Human$Genome$project$in$order$to$have$an$orientation$of$where$the$genes$ are$on$the$chromosome$ $ Genome)Variation:$ • Single$nucleotide$polymorphisms$(SNPs):$change$in$a$single$nucleotide$in$an$allele$ o Occurs$1$in$every$100[300$bases$in$humans$ o >$10$million$SNPs$have$been$identified$so$far$ o Only$2$possibilities:$GC$or$AT$base$pair$ o There$are$some$sequences$that$are$identical$in$everyone,$but$there$are$also$ other$sites$that$have$SNPs$(thus$some$people$have$GC$base$pair$and$others$ have$AT$base$pair)$ o This$wasn’t$really$important$until$the$Human$Genome$project$was$done$ o As$the$database$started$getting$bigger,$the$number$became$greater$than$10$ million$ o What$does$this$mean?$Well,$it’s$one$big$answer$to$why$we’re$all$different!$$ o If$everyone$had$the$exact$same$identical$10$million$SNPs,$then$we$would$be$ exactly$the$same$(ex:$identical$twins)$ o Some$SNPs$just$sit$in$the$DNA$somewhere.$They’re$not$in$genes,$they’re$just$ sitting$on$the$chromosome.$There$are$large$stretches$on$the$chromosome$ that$don’t$encode$for$genes,$and$this$is$where$SNPs$are$found$ o They$may$not$serve$any$functional$service$whatsoever$in$terms$of$evolution.$ They$just$change.$The$interesting$thing,$is$that$any$change$in$SNPs$will$ probably$be$inherited$by$the$population.$If$the$change$occurs$in$the$gamete,$ the$change$will$occur$and$be$passed$on$from$generation$to$generation$ o When$you$combine$all$this$SNP$data$and$compare$it$to$different$populations$ around$the$world,$you$could$get$a$very$clear$picture$of$where$everybody$ came$from$originally$ $ SNPs)and)Diseases:$ • Refers$to$when$SNPs$are$actually$on$the$gene$in$the$chromosome$ • Relates$to$disease$ • Apoliprotein$E$(ApoE):$role$in$Alzheimer’s$disease$ o Also$has$a$role$in$heart$disease$ o Three$alleles$on$chromosome$19$at$ApoE$locus$ ! E2:$Cys$at$both$amino$acid$positions$112$and$158$ ! E3:$Cys$at$amino$acid$position$112$and$Arg$at$158$ ! E4:$Arg$at$both$amino$acid$positions$112$and$158$ ! These$are$single$nucleotide$changes$–$it$changes$the$codon$within$the$ open$reading$frame$of$ApoE$ ! The$rest$of$the$gene$is$exactly$the$same,$outside$of$position$112$and$ 158$ o Which$one$is$wild$type$and$which$are$SNPs?$ ! This$is$the$important$question$ ! We$now$have$pretty$good$statistics$on$the$frequency$of$these$alleles$ in$a$population$ ! Thus,$whichever$one$pops$up$the$most$is$usually$wild$type$when$ looking$at$allele$frequencies$ ! E3$is$wild$type:$64%$of$population$$ ! E2:$higher$risk$for$arthrosclerosis$(heart$disease)$ ! E1:$higher$risk$of$Alzheimer’s$disease$(homozygotes$–$where$both$of$ the$alleles$are$E1,$are$20$times$more$likely$to$develop$this$disease$by$ age$75)$ ! Tightest$collaboration$of$any$genetic$disease$we$know$of$ o This$is$one$of$the$tests$23andme.com$does$ • The$statistics$still$don’t$tell$us$exactly$what$is$going$on$here$ • Doctors$always$ask$for$family$history$as$a$result$of$this$$ • 23andme.com$tests$for$around$50$of$these$diseases$ $ Mutations)within)alleles:)RFLPs$ • Mutations$within$alleles$leads$to$different$DNA$sequences$which$causes$different$ restriction$enzyme$sites$ • RFLP$is$an$older$technology,$but$it$was$absolutely$instrumental$in$early$gene$ mapping$experiments$ • RFLP$also$deals$with$SNPs$ • Restriction$Fragment$Length$Polymorphisms$(RFLPs):$ o What$it$means$is$that$when$you$take$any$segment$of$any$of$your$DNA,$and$ you$cut$it$with$specific$restriction$enzyme,$you$get$a$characteristic$patterning$ of$the$bands$of$DNA.$This$is$because$its$all$based$on$the$recognition$ sequence$of$that$restriction$enzyme$ o Difference$in$restriction$maps$between$2$individuals$ o If$a$few$of$us$have$changed$that$sequence$and$mutated$it$in$1$nucleotide,$the$ restriction$enzyme$won’t$work$there$so$your$fragment$will$probably$be$ longer$as$it$won’t$be$cut$at$the$appropriate$place.$That$one$nucleotide$ change$is$probably$an$SNP.$$ o A$single$nucleotide$change$can$affect$the$recognition$sequence$of$a$ restriction$enzyme$ o Differences$are$independent$of$gene$function$–$therefore$RFLPs$are$not$ based$on$phenotypic$differences$ o This$means$that$you$can’t$tell$between$2$people$what$their$RFLPs$are$based$ on$their$appearance$characteristics$ o RFLP$is$an$SNP$that$is$located$within$a$restriction$enzyme$site!$ o You$could$have$a$6$or$8$base$pair$sequence,$and$it$isn’t$a$recognition$ sequence$for$an$enzyme.$However,$by$changing$a