You discovered two Drosophila mutants that have identical mu

You discovered two Drosophila mutants that have identical mutant embryonic phenotypes and the affected genes have similar patterns of expression. One of the affected genes (gene A) encodes a putative transcription factor and you suspect that the second gene (gene B) may be directly controlled by this transcription factor. You have already tested the 2-kb fragment upstream of the start codon of gene B using a promoter-reporter assay, and this fragment seems to be sufficient to recapitulate the expression pattern of gene B. Which two techniques would be best suited to test whether protein A in fact binds to the promoter of gene B? Briefly explain what reagents you would need in order to perform these techniques.

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Solution

Different methods can be used which include invitro and invivo methods.

Invivo methods include Chromatin Immunoprecipitation (ChIP)Assays. It can be used to monitor transcriptional regulation through histone modeification or transcription factor-DNA binding interactions.It allows to analyse by treating the cells with cross-linking agents such as formaldehyde to stabilize the interactions.

DNA Electrophoretic Mobility Shift Assay can also be used to assess the degree of specifity of the interaction.

In vitro methods may include \"Systematic evolution of ligands by exponential enrichment (SELEX) which is based on incubating transcription factors with a pool of random DNA oligos.It was one of the firstest approaches being used.