BIOL 142 Chapter Notes - Chapter 20.6: Functional Genomics, Dna Microarray, Proteome
30 Apr 2018
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!20.6!Functional!Genomics,!Proteomics,!and!Systems!
Biology!
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Functional*genomics:!the!study!of!how,!when,!and!where!specific!genes!are!expressed!within!the!
genome!and!how!their!products!interact!to!produce!a!functional!organism!
• Whole-genome!sequencing!supplies!the!list!of!parts!
• Functional!genomics!answers!questions!about:!!
o What!particular!genes!do!
o How!they're!expressed!
o How!genes!work!together!to!produce!a!phenotype!
• Focus!on!large-scale!analysis!of!gene!expression!
o Inspired!by!knowledge!that!many!RNAs!and!proteins!act!together!to!response!to!
environmental!challenges!(extreme!heat,!drought)!
o Similarly,!large!groups!of!genes!must!be!transcribed!together!to!allow!an!organism!to!grow!
and!develop!
• DNA*microarray:!a!set!of!single-stranded!DNA!fragments,!representing!thousands!of!different!
genes!that!are!permanently!fixed!to!a!surface!such!as!a!glass!slide;!can!be!used!to!determine!
which!genes!are!expressed!in!different!cell!types,!under!different!conditions,!or!at!different!
developmental!stages!
o Let!researchers!study!the!expression!of!thousands!of!genes!at!a!time!
o Can!identify!which!set!of!genes!are!expressed!together!under!specific!conditions!
• Which!genes!are!transcribed!in!different!organs,!tissues,!cancers!
• Deep*sequencing:!a!method!to!learn!the!types!of!mRNAs!or!DNA!sequences!present!in!cells!and!
their!relative!amounts;!involves!preparing!and!extensively!sequencing!cDNAs!prepared!from!the!
cell!or!tissue!under!investigation!
o Large-scale!approach!to!assessing!gene!expression!by!directly!sequencing!cDNAs!using!next-
generation!sequencing!technologies!
o Relative!amounts!of!each!cDNA!(and!corresponding!mRNA)!are!determined!by!extensively!
sequencing!a!population!of!cDNAs!from!a!particular!cell!type!or!tissue!
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Proteomics:!the!systematic!study!of!the!full!set!of!proteins!(the!proteome)!in!a!cell,!tissue,!or!organism,!
including!their!interactions,!localization,!functions,!regulations,!and!other!features!
• Transcriptome:!the!complete!set!of!gene!transcripts!in!a!particular!cell!
• Proteome:!the!complete!set!of!proteins!produced!by!a!particular!cell!type!
• Like!genomic,!proteomics!begins!by!establishing!a!parts!list!of!all!the!proteins!present!in!a!cell,!
tissue,!or!organism!
• Technique:!use!mass$spectroscopy!and!computational!methods!to!learn!the!precise!side!and!
amino!acid!sequence!of!each!protein!in!a!sample!
o Techniques!for!protein!identification!are!different!from!those!with!DNA!
o After!the!proteins!are!identified,!researchers!study!how!they!change!through!time,!interact,!
and!vary!between!cells!
o Studies*all*the*proteins*that*are*present!
• Instead!of!studying!individual!proteins!or!how!a!pair!of!proteins!interact!
