Evaluating evolutionary conservation of TF binding site predictions

Question

[Eisuan]

Hello everyone!

I am trying to validate TF binding site predictions through evolutionary conservation evaluation. Since this moment I was lucky since the potential TF binding sites are encompassed in a few of the very conserved regions of this promoter (human vs mouse). However, I have never taken into consideration a "standard" procedure for doing that.

At the moment I am trying to use "Constrained elements for 90 eutherian mammals EPO-Low-Coverage" track on ENSEMBL. It seems to work fine since I can see all the alignments for each species.

However, I am a little bit concerned about the fact that the information this tool gives is not straightforward: in some cases the region is conserved but the sequence is quite different. This goes to the extent of not being recognized again if you perform a motive scan analysis on that.

So, my question is: which modus operandi would you use in this case?

Answer 1

[Kevin Blighe]

I do not believe there is any standard procedure for this. I have actually been working on something similar, recently, with a focus on enhancer and promoter regions. The program that I am using (never published; I know the developer personally) takes any region as input and then utilises a motif discovery algorithm, SPLASH, to identify transcription regulatory elements (e.g. enhancers and promoters) as being conserved or not across your input sequences. In the process, it utilises PWMs from JASPAR.

So, it is not an alignment-based approach; instead, it uses pattern recognition to create a 'fingerprint' of the sequence of your input region, and then determines the conservation of this in other genomes using the same approach.

I think that if you can simply show conservation and synteny across species for your region, then it's a good indication

Ensembl has some REST utilities that may be of use:

• http://rest.ensembl.org/documentation/info/genomic_alignment_region (courtesy Emily)

You can also look up regions manually in the browser:

• http://www.ensembl.org/Homo_sapiens/Location/Synteny?otherspecies=Homo_sapiens;r=17:63992802-64038237

Kevin