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NEW NEWS of HUMAN FROM MOUSE and CHIMP

NEW NEWS of HUMAN FROM MOUSE and CHIMP. Nature 420 (6915), 5 Dec 2002 Genome Research 13(3), March 2003. Mouse Genome 1. 2.5 Gb (14% smaller than human): deletion? 21 chromosomes (incl sex) 30,000 genes (1% w no human homologue) 90% syntenic w human at gene level

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NEW NEWS of HUMAN FROM MOUSE and CHIMP

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  1. NEW NEWS of HUMANFROM MOUSE and CHIMP Nature 420 (6915), 5 Dec 2002 Genome Research 13(3), March 2003

  2. Mouse Genome 1 • 2.5 Gb (14% smaller than human): deletion? • 21 chromosomes (incl sex) • 30,000 genes (1% w no human homologue) • 90% syntenic w human at gene level • 40% alignable w human at nucleotide level: deletion? • 2X neutral nucleotide substitutions • 5% under purifying selection • Non-uniform nucleotide changes across mammalian chromosomes

  3. Mouse Genome 2 • Local gene family expansions • Reproduction, immunity, olfaction • Rate of protein evolution high in expanded gene families • 80,000 SNPs • 60,000 mRNAs, 11,000 noncoding, 2500 sense/antisense pairs • Many SNCIRs

  4. Human v. Mouse Junk • SINEs/LINEs: 21%/13% in humans 20%/8% in mouse • 100/3000 active SINEs in modern humans/mouse • Retroposons accumulate orthologously (but independently) in mouse and human.

  5. Why Pan troglodytes? • genetically closest species to human • most recent common ancestor with human among extant species 4.2-6.2 MYA • evidence for development of cognition and language • resistant to some human diseases AIDS, malaria, cancer, Alzheimer’s

  6. Chimp v. Human Genomes • 99.8% identical to human at nucleotide level • HSA2 = fusion of PTR 12 + 13 • Frequent genomic rearrangements • deletions and insertions • often in genic & euchromatic regions • up to 175 kb • Human genome has expanded 30 Mb over past 50 MY, relative to chimp • 90% due to retroposon insertions • Has chimp lost expansion by deletion?

  7. Primates and Vitamin C • Humans, other primates, and guinea pigs cannot synthesize Vitamin C endogenously. • Humans actually have two genetic defects affecting vitamin-C synthesis: one involving "lactonase" and one involving the enzyme utilizing "L-gulonolactone” as substrate The lactonase defect makes humans unable to synthesize C; the gulonolactone defect just makes the synthesis less efficient. Some people don't have the lactonase defect, and are therefore immune to scurvy. These are the people who survived the long European sea voyages in the middle of the millennium. Some other groups, such as desert nomads, have regained vitamin C synthesis ability. • Gene Loci for vitamin C-synthesizing enzymes in primates have accumulated several types of mutation, including Alu element insertion.

  8. Genomic AnalysisThe Basic Strategies

  9. Genomic Analysis • Construction of Genomic Libraries • Mapping Genomic Clones • Nucleotide Sequencing • Compiling the Sequence • Annotating the Sequence • Classifying Genes

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