1. Copyright, ©, 2002, John Wiley & Sons, Inc.,Karp/CELL & MOLECULAR BIOLOGY 3E Footprints and Shadows Looking for Functional Pieces Within Genomes

2. Copyright, ©, 2002, John Wiley & Sons, Inc.,Karp/CELL & MOLECULAR BIOLOGY 3E

3. 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

4. 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

5. Copyright, ©, 2002, John Wiley & Sons, Inc.,Karp/CELL & MOLECULAR BIOLOGY 3E

6. Copyright, ©, 2002, John Wiley & Sons, Inc.,Karp/CELL & MOLECULAR BIOLOGY 3E CETP LXR apoB plas 4 exons and flanking regions

7. Copyright, ©, 2002, John Wiley & Sons, Inc.,Karp/CELL & MOLECULAR BIOLOGY 3E Apo(a) promoter E = exon C = conserved, N = not 9 = TATA, 10 = HNF-alpha

8. Copyright, ©, 2002, John Wiley & Sons, Inc.,Karp/CELL & MOLECULAR BIOLOGY 3E Gel retention (shift) assay

9. Copyright, ©, 2002, John Wiley & Sons, Inc.,Karp/CELL & MOLECULAR BIOLOGY 3E Deletion/Transfection Assay of apo(a)