Transcription Factor Question

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mxnick262
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Transcription Factor Question

Post by mxnick262 » Wed Apr 04, 2012 6:59 pm

You have isolated a novel transcription factor. How will you determine the genes regulated by transcription factor in the whole genome?

How will you determine the transcription factor binding sites in the whole genome?

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JackBean
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Post by JackBean » Thu Apr 05, 2012 2:11 pm

No idea? Really not at all?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

mxnick262
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Re: Transcription Factor Question

Post by mxnick262 » Tue Apr 17, 2012 1:19 am

ChIP coupled with ChIP-seq. Please do not mock me. I have obviously looked into it but, am looking for second opinions.

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Post by JackBean » Tue Apr 17, 2012 6:57 am

Obviously you have done nothing. If you did, you would provide some answers, although they might be wrong or incomplete.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

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Post by mxnick262 » Tue Apr 17, 2012 1:30 pm

Is chromatin immunoprecipitation wrong?

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JackBean
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Post by JackBean » Tue Apr 17, 2012 1:34 pm

For which part?
http://www.biolib.cz/en/main/

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Post by mxnick262 » Tue Apr 17, 2012 3:47 pm

For how to determine the transcription factor binding sites in the whole genome, I'd use ChIP with ChIP sequencing. I'm more than 100% positive that's the way my professor expects us to do it since he just talked about Monday.

As for the for the first question, I guess use a DNAse1 Foot-Printing Assay? A classmate of mine mentioned knockout mutations but, it's not asking what the gene does. So I don't see how that would be correct.

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Post by JackBean » Wed Apr 18, 2012 6:32 am

Actually you are wrong and your friend is right. The DNase foot-printing is good to recognize the particular binding place. I.e. answer to question 2. But to recognise, which genes are controled by this TF (without being interested in actual binding site), you need to change it's expression and see, what changes in transcription of other genes you get ;)
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

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