Our newest paper is out where we investigate how exogenous RNA triggers innate immune responses, such as PKR activation and stress granule assembly. rnajournal.cshlp.org/content/earl...

We show that 1) treatment of T7 RNA Polymerase-produced transcripts with RNase III, which selectively degrades double-stranded RNA (dsRNA), blocks PKR-dependent phosphorylation of eIF2-alpha, and stress granule assembly by this mRNA.

Although exogenous single-stranded RNA containing uridine analogs do not trigger PKR-dependent phosphorylation of eIF2-alpha, and stress granules, that double-stranded RNA with these analogs do trigger these responses. So uridine analogs DO NOT camouflage RNAs from PKR (as is widely assumed).

Instead, these uridine analogs inhibit double-stranded RNA byproducts that are made at a low level by T7 RNA polymerase! (Note that in these northernblots, antisense transcripts are gone in reactions containing m1-pseudouridine)

As a bonus, we find that if we introduce exogenous RNA at high enough levels, they will trigger stress granule assembly even when these byproducts are removed. These stress granules are however different in that they do not require PKR activation or eIF2-alpha phosphorylation.

These stress granules require G3BP1/2 and support the idea that excess ribosome-free mRNAs can promote stress granule formation, as predicted by the Parker lab. www.pnas.org/doi/10.1073/...