Identify trans-regulatory regions

Question

[carlosalfonsogonzalez6]

Hello everyone

I was wondering, Which are the current methods to identify trans-regulatory modules? I have seen in recent articles, the use of hybrids where the expression of the parental lines is compared with the heterozygotes of F1 through RNA-seq, although this method is able to identify the genes that are differentially regulated, does not say much about the regulatory regions that contribute to the differential expression, What methods would you suggest to find these regulatory modules that occur in trans?

Answer 1

[Hussain Ather]

Clustering and linkage analysis has been used https://www.nature.com/articles/ng1222

Answer 2

[jared.andrews07]

Trans regulation is a difficult thing to pin down, though one of the more high throughput methods is to utilize Hi-C to find interchromosomal/long-distance DNA interactions. Of course, this doesn't help pin down more convoluted trans regulation (ie. by your differentially expressed lncRNAs or transcription factors), but it's one of the more straightforward genome-wide analyses you can do if you're not trying to determine the regulation of specific loci.

Answer 3

[carlosalfonsogonzalez6]

i didnt see this method as a solution, i think they take too many asumptions, clustering gene expresión seems like an easy path, What do you think?

[jared.andrews07]

Welcome to biostars! This isn't an answer - if you want to comment on somebody's answer, add a comment to it (as I'm doing now). This helps keep the question organized and makes discussions easier to follow.