I am a very beginner in protein-DNA interaction science. Any basic and helpful suggestion will be greatly appreciated.
How do I find promoter regions of a gene for particular proteins such as transcription factors and design primers for that promoter region to perform RT-PCR?
Hello,
Many genes if they are human will already be mapped and a lot have their promoter region amongst other regions identified. So looking on genome databases like the genome project and HapMap will already show the gene sequence.
If you wanted to identify the yourself you could use older techniques from the 70's like positional cloning and linkage analysis.
Hope this helps,
Ben.
Shyam,
With RT-PCR you are going to amplify just the RNA and as you may know the RNA started at the +1 of the transcription and that site is just down stream the promoter.
As ben reported you have to look for the promoter sequence In data bases and make your primers for PCR.
Good a luck
There are several databases like EPD, TRED where you can find the promoter sequences of your target gene. You can use the sequence and try looking for transcription factors using databases like ALGGEN-PROMO, JASPAR. Accordingly you can design primers flanking your desired sequence for ChIP. As mentioned before RT-PCR is for amplificatio of RNA.
EPD,JASPER would help but keep in mind that its always great to go with an integrated database platform
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