Help identifying TATA boxes

Question

[kajaenilsen]

Hi!

Im doing a bioinformatics exercise, but Im new to this and now I need help.. I have a list of 5 genes that Im going to analyze with different bioinformatic tools. They are all transcription factors, and I want to "prove" that they are part of the immediate early response process. As a part of doing that, I want to identify TATA boxes in their promoter regions, but the problem is I dont know how to do this. Is there any way to find TATA boxes with some of the following tools; Meme Suite, UCSC genome browser, Ensembl, Jaspar, Transfac, or Genomic Hyperbrowser? And how do I find them (if it is possible)?

Thanks in advance!

[Bogdan]

You can use http://homer.salk.edu/homer/motif/ or http://homer.salk.edu/homer/motif/fasta.html THE TATA box position-weight matrix can be found in the JASPAR database and you can use it for scanning the sequences.

Answer 1

[Michael]

As you mention the Genomic Hyperbrowser (Hyperbrowser is a Elixir.no project and I guess you are in Norway, if you need more help we can contact the developers directly):

Edit: There are tools that do search for TATA patterns directly, and there is a tool called Transcription factor analysis that gives you known TF's for genes of interest. There are the Motif Tools providing FIMO (need to scroll a little).

Other options:

• Motiv finder IGV: https://www.broadinstitute.org/igv/motif_finder
• In MEME suit, there is FIMO: http://meme-suite.org/tools/fimo
• there ar possibly dozens of other motif finders, most will need a PWM of the TATA box.

Another possibly better way of evidence of transcription by RNA-pol II is to check for the presence of an RNA-pol II signal in Encode data (if that is available). Note that the TATA box in the promoter is not specific to TFs, in fact most RNA-pol II transcribed mRNA has that.

[kajaenilsen]

Ok, thank you very much!