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This chapter explain how linkage mapping, physical mapping, and DNA sequencing each contributed to the Human Genome Project, define the fields of proteomics and genomics, describe the surprising findings of the Human Genome Project with respect to the size of the human genome, distinguish between transposons and retrotransposons.
Genomes and Their Evolution Bioinformatics Use of computers, software, and math models to process and integrate data from sequencing projects Human Genome Project Purpose: to sequence the entire human genome Completed in 2003 Genomes sequenced thus far*: 58,000 prokaryotes, 2700 eukaryotes, 5300 viruses * Data as of 1/27/16 Human DNA • billion base pairs • ~20,000 genes • Only 1.5% codes for proteins (or RNA) • Mostly Repetitive DNA: DNA sequences present in multiple copies Transposable Elements Make up 75% of repetitive DNA Stretches of DNA that can be moved from one location to another in genome Discovered by Barbara McClintock – corn breeding experiments Types: Transposons Retrotransposons Transposons Moves within genome via DNA intermediate “cut & paste” or “copy & paste” mechanisms Requires enzyme transposase Retrotransposons Move by means of RNA intermediate Leaves copy at original site Involves enzyme reverse transcriptase Genome Evolution Insertion effects of transposons: Can interrupt or alter gene function Multiple copies of genes Duplication genes with related functions Genes diverge by accumulating mutations Some become nonfunctional pseudogenes Eventually, new genes with new functions can occur Multigene Families Collections of or more identical or very similar genes Eg hemoglobin: α-globin and β-globin gene families Transposable elements contribute to evolution Promote recombination, disrupt genes or control elements, & carry genes to new locations May be harmful or lethal, but can also have small beneficial effects Provides raw material for natural selection Illustrative Example: Antifreeze Gene in Fish Antifreeze proteins (AFP): produced by vertebrates, plants, fungi, bacteria to aid survival in sub-zero environments Function: bind to ice crystals and prevent growth Antarctic fish: fish old protein gene transformed into a new gene with new structure/function Gene mutates duplicated divergent evolution Evolutionary Development (Evo-devo) • Compares developmental processes to understand how changes can lead to evolution of organisms Homeotic genes: genes master regulatory genes • Control placement and spatial organization of body parts Homeobox: Homeobox widely conserved 180-nucleotide sequence within homeotic (Hox) genes • Found in many groups (fungi, animals, plants) • Hints at relatedness between all life forms Conservation of homeotic genes ... Gene mutates duplicated divergent evolution Evolutionary Development (Evo-devo) • Compares developmental processes to understand how changes can lead to evolution of organisms Homeotic genes:... of or more identical or very similar genes Eg hemoglobin: α-globin and β-globin gene families Transposable elements contribute to evolution Promote recombination, disrupt genes or control... computers, software, and math models to process and integrate data from sequencing projects Human Genome Project Purpose: to sequence the entire human genome Completed in 2003 Genomes sequenced