Fig. 7: GC-rich complementary sequences are embedded within the RNA structure in germ granule mRNAs. | Nature Communications

Fig. 7: GC-rich complementary sequences are embedded within the RNA structure in germ granule mRNAs.

From: Controlling intermolecular base pairing in Drosophila germ granules by mRNA folding and its implications in fly development

Fig. 7

a Types of CSs that enable intermolecular and intramolecular base pairing between mRNAs. b Alignment and abundance of total (magenta boxes) and GC-rich CSs, which had a minimal length of 6 nts in nos, pgc, and gcl 3′UTRs. c Predicted secondary structures of nos 3′UTR with mapped total CSs (magenta, left) or GC-rich CSs with a minimum of 6 nucleotides (magenta, right) outside of the germ granules. The RNA structures were generated based on two DMS-MaPseq replicates. The green sequences (“CGGCCG” and “CUCGAG”) and lines were nos CSs used in nos-nos experiments. A zoom-in image of “CUCGAG” demonstrating that this sequence is partially embedded within the RNA structure. d Predicted secondary structures of pgc 3′UTR with mapped total CSs (magenta, left) or GC-rich CSs with a minimum of 6 nucleotides (magenta, right) outside of the germ granules. The RNA structures were generated based on two DMS-MaPseq replicates. e Predicted secondary structures of gcl 3′UTR with mapped total CSs (magenta, left) or GC-rich CSs with a minimum of 6 nucleotides (magenta, right) outside of the germ granules (i). An example of IR in which half of the sequence was base-paired intramolecularly (ii). The RNA structures were generated based on two DMS-MaPseq replicates. f Proposed model depicting that mRNAs remain folded within mRNA clusters in germ granules (panel 1). The interactions among germ granule mRNAs in clusters are controlled by RNA folding. These interactions are mainly driven by regions with low complementarity and exhibit low probability for sustained interactions (panel 2). Flies expressing germ granule mRNAs with stem loop structures (blue) exhibit major defects in embryogenesis and the maintenance of female germline stem cells (panel 3). Notably, those with exposed GC-rich CSs (red) within the stem loops display exacerbated phenotypes and enhanced intermolecular interactions among the mRNAs (panel 4). See also Supplementary Data S5–S7.

Back to article page