calculating cis / trans regulatory elements

[sphil]

hi guys,

i know there is a lot of literature out there but somehow i don't get it right know.
I got several RNA-seq runs and I want to try to calculate cis / trans effects out of it. Is there any tool or a nice review on that topic?

Thanks in advance,

phil

[dpryan]

Err, as written that doesn't actually make any biological sense (you need more information than is available from an RNAseq experiment to look at cis- and trans- regulatory effects). If you describe more about what your actual experiment is, then you'll get more worthwhile advice.

[sphil]

So i got two closely related strains of a fungi which, under certain conditions, show different phenotypes. After a few wet lab designs i got 3 (biological) replicates for both strains which were sequenced using RNA-seq (HiSeq2500). Now, I calculated allel specific expression for all six datasets which indicate that the different phenotypes may be caused by a shift in allelic expression. Now I wanted to know if those changes are coming from differnt regulation. So my first shot at it was to look for a differnt amount of cis and trans regulatory elements, with respect to their amount of RNA present in the sequencing results, in different conditions. My problem now is that i don't know how to calculate or indicate whether there is a shift. Say in condition A there is more cis regulation than in condition B. But how can i calculate this?

Hope that helps!

Thank you!

[a_mt]

Hi,

There is this paper where they have measured effect of cis and trans regulatory elements on gene expression between two closely related Drosophila species, by mRNA -seq. Methodology they have used is simple.

They even have written scripts to measure allele specific gene expression which I think is available upon request. Besides that I dont think there is any direct way to do so.

Hope it helps.

[sphil]

Thank you!

[dpryan]

So i got two closely related strains of a fungi which, under certain conditions, show different phenotypes. After a few wet lab designs i got 3 (biological) replicates for both strains which were sequenced using RNA-seq (HiSeq2500). Now, I calculated allel specific expression for all six datasets which indicate that the different phenotypes may be caused by a shift in allelic expression. Now I wanted to know if those changes are coming from differnt regulation. So my first shot at it was to look for a differnt amount of cis and trans regulatory elements, with respect to their amount of RNA present in the sequencing results, in different conditions. My problem now is that i don't know how to calculate or indicate whether there is a shift. Say in condition A there is more cis regulation than in condition B. But how can i calculate this?

Hope that helps!

Thank you!

You don't actually need a change in RNA level of a trans element for it to be the cause of a modulation, that's why I said that RNAseq alone won't answer your question. In the paper linked to by a_mt, they just use the RNAseq to determine allelic expression. It's their crosses and knowledge of the genomic sequence in the area around the genes that allows them to start addressing how the regulation occurs. I should note that even that isn't really sufficient to do more than suggest a vague mechanism. To truly show it, you need to do individual molecular biology experiments.