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Footprints and Shadows. Looking for Functional Pieces Within Genomes. 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 - PowerPoint PPT Presentation
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Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
Footprints and Shadows
Looking for Functional Pieces
Within Genomes
Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
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
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
Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
CETP
LXR
apoB
plas
4 exons and flanking regions
Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
Apo(a) promoter
E = exonC = conserved, N = not9 = TATA, 10 = HNF-alpha
Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
Gel retention (shift) assay
Copyright, ©, 2002, John Wiley & Sons, Inc., Karp/CELL & MOLECULAR BIOLOGY 3E
Deletion/Transfection Assay of apo(a)
