Detection of bidirectionnal promoter.

Question

[alexis.delabriere78]

Hello,

I m a Student in Bioinformatics and for a project I need to find a way to detect bidirectional promoters regions in human genome (for example, it can be another mammals). Here are the methods that we thought about, and the reason why they didn't work.

Method 1 :

• Creating a list of all putative bidirectional promoters by making a selection on intergenic region based on a distance of approximately 1000 between the start of two genes in opposite strands. (DONE)
• Finding a list of curated,or confirmed bidirectionnal promoters in Homo Sapiens on one chromosomes or more. That's where it didn't work, we didn't find it, we found a lot of study about putative bidirectionals promoters and study about their characteristics, but none of them curated a meaningful amount of bidirectional promoters.
• Trying to find sequence differences, between the true promoters and the other candidate, using some kind of Markovian model on the position of traditional promoters elements, such as TATA box. Or any other model based on sequence.

Method 2:

• The same first step as Method 1.
• Searching if there is a correlation of expression in the microarray database (Stanford Micro Array Database, NCBI and EBI)(IN PROGRESS). Main issue is that it's for a few genes it's working but for the majority of the other, there 0 or only a few micro array where they are together, so we can't really conclude anything, on the majority of their promoters.

Did anyone have a clue about how to solve our issue in method 1 and 2, a list of curated bidirectional promoter that we missed, or another idea to solve our problem ?

Thanks!

Answer 1

[PoGibas]

Hi Alexis, try adding evolutionary component to your strategy.

1. Filter your putative bi-promoter list: select only those intergenic regions that have approximately same length in human and mouse.
2. I haven`t heard and really doubt that annotated bi-promoter database exists (I even doubt that "normal" promoter database exists).
3. I doubt that there will be any sequence differences between two promoter types. On the other hand, try searching for epigenetic differences (methylation and histones).
4. Use not only protein coding genes, but lncRNAs from Gencode.

Good luck with your project!

[alexis.delabriere78]

thx you for your answer ! i will try to add your idea.