Mapping Regulatory Elements: Accessibility, Occupancy and Contact
Three assay families answer three different questions about a piece of DNA: which regions are open, which protein sits there, and which distant regions touch it. This stop matches the question to the assay and to the controls its claim needs.
What a learner can do afterwards
- Choose between an accessibility, an occupancy and a contact assay for a stated claim about an element
- State the control that keeps each assay honest, including input and non-specific antibody controls
- Read a genome browser track and say what it shows and what it does not show about function
1 · Read
Three assay families answer three different questions about a piece of DNA. Accessibility asks which regions sit open and reachable, where regulators could bind. Occupancy asks which protein actually sits there, found by fishing one factor out with whatever DNA it held. Contact asks which distant pieces touch in the nucleus, such as an enhancer looping to its promoter. Enhancers and silencers can sit far away yet dial a gene through such loops.
Suppose you claim one factor drives a gene through a distant element. First show the element sits open in the right cells. Then pull that factor down and show it binds the element above background. Then show the element touches the gene's promoter in space. No single assay answers everything, so honest claims stack at least two of them, and chemical tags marking open neighborhoods only suggest candidates until binding or contact confirms them.
Every assay needs the control that keeps it honest. For occupancy work the key control is the non-specific antibody pull down: it measures DNA that sticks around by accident and sets the background line that true peaks must beat. Peaks barely above that line deserve doubt, not headlines. Input controls play the same role elsewhere, catching bias before it becomes a claim.
To read a genome browser track, remember what a peak is: many fragments piled at one spot, not proof the spot controls a gene. A tall peak says signal came from there. The jump from peak to function always needs a second experiment. Say what the track shows and what it does not show, and never let one beautiful peak carry a function claim alone.
Open, bound, and touching are three separate facts, each needing its own assay plus controls.
2 · Watch
Take it off screen
Where it sits
8 questions wait behind this lesson, each with its answer explained. Every answer feeds the sky: stars light as they are learned, and dim when it is time to come back.