BIOL 483 Lecture Notes - Lecture 86: Deoxyribonuclease, K562 Cells, Restriction Digest

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Heat map to show strength of interactions -> can see all the places in the genome that the gene interacts with. Strengths: find novel interactions, can measure long range interaction in cis and trans. Disadvantages: needs lots of seuqencing for promoter/enhancer interactions - not good for finding things close to each other, signal strength too low at < 50kb, need to use 4 or 6 bp cutters -> low resolution. Steps: crosslink dna (bind 2 pieces of dna with protein, restriction digest - make the ends smaller so it"s just x held tgt by protein. 3: reverse crosslink - remove protein holding things tgt so it"s just straight line, hybridise to oligos that overlap cut sites. Strengths: can compare strength of different interactions, find closer range interactions, good at finding enhancer promoter interactions. Disadvantages: low resolution - not all ends are matched to oligos but oligos can turn up in pcr, limited byn umber of oligos used.

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