DMS-MaPseq of Germ Granule mRNAs from Purified Drosophila Germ Granules

Drosophila germ granules are enriched with mRNAs essential for development. Within these granules, mRNAs cluster through intermolecular interactions, which may involve base pairing. However, the type and prevalence of intermolecular base pairing in these RNA clusters remain poorly understood. Here, we used DMS-MaPseq to probe the base accessibility of the 3 prime untranslated regions of germ granule mRNAs, including nos, pgc, and gcl, from isolated Drosophila germ granules. We compared DMS profiles of mRNAs inside and outside of granules and found that mRNAs exhibit a similar degree of foldedness in both contexts. These results suggest that extensive unfolding of RNA secondary structures is unlikely to occur within germ granule environment.