chIP and Q-PCR

Pragnya Das via (by drpragnyadas from
Wed Jan 20 10:24:11 EST 2010

Hi everybody

I'm new to this field and I want to study whether my transcription factor
(gene A) binds to the promoter of (gene B). To start with, here's is what I
plan to do after doing a literature survey:

(1) Isolate chromatin from my tissue, sonicate, and IP it with an antibody
that recognize my gene A
(2) Design primers spanning the promoter region, enhancer region AND EXON 1
 of (gene B)
(3) Do a Q-PCR with chIP'd DNA as the template and primers for gene B

Now my ques is;

(1) How do I know whether my gene A binds to gene B. What should I expect to
see when I run it on an agarose gel or do a real time Q-PCR?

(2) What should be my positive and negative controls for the above expt?

I would highly appreciate feedback from all the experts out there in the



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