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Footprints and Shadows

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

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Footprints and Shadows

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  1. Footprints and Shadows Looking for Functional Pieces Within Genomes Karp/CELL & MOLECULAR BIOLOGY 3E

  2. Karp/CELL & MOLECULAR BIOLOGY 3E

  3. 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 Karp/CELL & MOLECULAR BIOLOGY 3E

  4. 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 Karp/CELL & MOLECULAR BIOLOGY 3E

  5. Karp/CELL & MOLECULAR BIOLOGY 3E

  6. 4 exons and flanking regions apoB CETP LXR plas Karp/CELL & MOLECULAR BIOLOGY 3E

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

  8. Gel retention (shift) assay Karp/CELL & MOLECULAR BIOLOGY 3E

  9. Deletion/Transfection Assay of apo(a) Karp/CELL & MOLECULAR BIOLOGY 3E

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