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

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

  1. You want to estimate how often a distant DNA region is captured near a gene's promoter. Which assay family fits?

    • A chromosome contact assay
    • A chromatin accessibility assay
    • A factor-specific occupancy assay

  2. You want to map DNA regions reachable by an enzyme in the sampled cells. Which assay family fits?

    • A protein occupancy assay
    • A chromosome contact assay
    • An accessibility assay

  3. This binned ATAC-seq excerpt shows depth-normalized signal units. Its highest signal at 600-699 bp proves that this interval regulates the nearest gene.

    500-599 bp2600-699 bp16700-799 bp3

    Circle one:   True   False

  4. A region gains accessibility and enhancer-associated histone modifications as cells change state. What status is justified?

    • A candidate element needing a functional test
    • A confirmed enhancer because accessibility establishes function
    • A confirmed target link because histone marks identify its gene

  5. At one region, comparably processed ChIP-seq signals are 8 for the target antibody and 7 for a non-specific antibody control. What does this comparison support?

    • Strong target specificity because 8 exceeds the control value
    • No target-gene transcription because the signals nearly match
    • Little separation from pull-down background

  6. Which experiment most directly tests whether a candidate element contributes to a proposed target gene's transcription in these cells?

    • Collect another accessibility track without changing the element
    • Change the element and compare target RNA with matched controls
    • Collect another contact map without measuring target-gene RNA

  7. Protein occupancy at an accessible element that contacts a promoter in one cell type proves that the element regulates that gene in every cell type.

    Circle one:   True   False

  8. A lab proposes using an antibody background control in place of quality checks for both ATAC-seq and Hi-C. Which plan better fits their measurements?

    • Use antibody recovery alone to assess both enzyme access and contacts
    • Check assay-specific biases and biological replicate agreement
    • Use raw read totals alone to compare accessibility and contact signals
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Answer key

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

Three questions, three assays W1-mt_W2YKGBADJ--s1

  1. A chromosome contact assay · Contact assays record paired regions captured in proximity. This does not establish permanent contact or regulatory function.
  2. An accessibility assay · Accessibility assays measure enzyme access to DNA. ATAC-seq is one example.
  3. False · The highest signal is 16 at 600-699 bp. It locates accessibility-associated enrichment, not a target gene or a regulatory effect.
  4. A candidate element needing a functional test · These features nominate a candidate. They do not establish its target or show that changing it affects transcription.
  5. Little separation from pull-down background · The signals are close, so this comparison provides weak evidence of enrichment. It does not establish antibody specificity or transcription.
  6. Change the element and compare target RNA with matched controls · A controlled perturbation tests whether changing the element affects target RNA. Further checks address indirect effects.
  7. False · Mapping does not demonstrate a regulatory effect, and observations in one cell type do not establish activity in all other types.
  8. Check assay-specific biases and biological replicate agreement · ATAC-seq and Hi-C need checks suited to enzyme-access and paired-contact measurements. An antibody control cannot replace those checks.
Worksheet · LightMySky