Footprints and Shadows
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Transcript of Footprints and Shadows
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Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
Footprints and Shadows
Looking for Functional Pieces
Within Genomes
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Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
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Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
Footprints vs. Shadows
• Footprints
– sequences conserved in “distant” organisms
– works less well than you might think
– many alignments not functional (about 40%)
– typical comparison: mouse and man
• limited to mammalian conserved sequence
• primate conserved sequence would be missed
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Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
Footprints vs. Shadows
• Shadows
– sequences conserved in “similar” organisms
– not very effective when comparing two organisms
– high fraction of pairwise similarity
– multiple simultaneous comparisons better
• 10-20 primates
• MORE evolutionary distance than mouse/man
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Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
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Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
CETP
LXR
apoB
plas
4 exons and flanking regions
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Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
Apo(a) promoter
E = exonC = conserved, N = not9 = TATA, 10 = HNF-alpha
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Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
Gel retention (shift) assay
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Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
Deletion/Transfection Assay of apo(a)