Transcription factor - (Nov/11/2009 )
Suppose I have (what I hypothesize) is a transcription factor. I want to find out if this binds to a sequence specific DNA, and if so what the sequence is. Next I want to find the genes that are turned on by it. Can you help me about how to go with it. A plan?
Bioinformatics can give you homologs, which may have identified binding specificity, which would give a place to start. You can raise an antibody to your TF, bind it to your DNA, crosslink with formaldehyde, shear for small fragments, precipitate with your antibody, release the crosslink, and either bind the released DNA to an array (old school) or use new high throughput sequencing to sequence all of the released fragments. Read articles and protocols for CHIP, but when they talk about arrays, think 454 or Illumina sequencing.