Why do Alu repeats form secondary structures?

Question

I've been doing a lot of research on Alu repeats and how they mediate the gene expression. I read the following article "Useful junk: Alu RNAs in the human transcriptome".

And it says that alu repeats embedded in 5'UTR makes stable secondary structure that prevents the assembly of ribosomal subunits, thus blocking the process of translation. I've been reading various articles to find out why Alu repeats form this secondary structure and why only in the 5'UTR and not in the 3'UTR. But haven't been able to find an answer.

Answer 1

Single-stranded RNA can easily form secondary structures, a very important example of this are tRNAs.

From a quick look at the article you read it seems that these Alu repeats work similar to riboswitches in the 5'-UTR. They can form secondary structures that block translation initiation, riboswitches commonly do this by hiding the Shine-Dalgarno sequence in a stable helix.

This kind of regulation of translation can obviously only work in the 5'-UTR as that is the place where the translation starts. The 3'-UTR can't affect translation in this way as the translation starts at the other end of the mRNA.

The Alu repeats still can form secondary structures in the 3'-UTR, and the article suggests that those might have an effect on mRNA stability.