Mapping Regulatory Elements: Accessibility, Occupancy and Contact · seed 1 · A4, ink-friendly. The answer key prints on its own page for grown-ups.

Three questions, three assays

Science · Genetics & Evolution · ages 22-24
Name ______________________   Date ____________

  1. You want to know whether an enhancer loops to touch its promoter. Which assay fits?

    • A contact assay
    • An accessibility assay
    • Sequencing the enhancer letters alone

  2. You want to know which DNA stretches sit open and reachable. Which assay fits?

    • An occupancy assay
    • A contact assay
    • An accessibility assay

  3. A tall browser peak by itself proves the spot controls a nearby gene.

    Circle one:   True   False

  4. A region opens exactly as cells change state, with enhancer-like tags. What is its status?

    • A candidate needing binding or contact proof
    • A proven driver of the state change
    • Junk DNA to ignore forever

  5. An occupancy peak for your factor sits barely above the non-specific antibody line. What should you conclude?

    • Strong proof of binding
    • Proof the gene is off
    • Doubt: the signal may be accidental sticking

  6. Which evidence stack best supports that an element drives its target gene?

    • One accessibility track alone
    • Openness plus factor binding plus promoter contact
    • The DNA letters of the element alone

  7. Finding a factor bound at an open element that touches a promoter settles that the element drives that gene in all cell types.

    Circle one:   True   False

  8. A paper claims a new enhancer from one tall peak with no controls and no second assay. What is the central flaw?

    • Tall peaks are always meaningless
    • The peak shows signal only; function needs controls plus another assay
    • Enhancers can never sit far from genes
LightMySky · lightmysky.comW1-mt_W2YKGBADJ--s1

Answer key

For grown-ups. Fold this page away before handing over the rest.

Three questions, three assays W1-mt_W2YKGBADJ--s1

  1. A contact assay · Touching in space is the contact question.
  2. An accessibility assay · Openness is the accessibility question.
  3. False · Peaks show signal, and function needs a follow-up test.
  4. A candidate needing binding or contact proof · Tags suggest, but only binding or contact earns a function label.
  5. Doubt: the signal may be accidental sticking · The control sets the background that true peaks must clearly beat.
  6. Openness plus factor binding plus promoter contact · Honest claims stack at least two assays covering open, bound, and touching.
  7. False · Marks and loops differ between cell types, so the claim cannot travel for free.
  8. The peak shows signal only; function needs controls plus another assay · Signal without background checks or follow-up cannot carry a function claim.
Worksheet · LightMySky