Identifying pairwise RNA-RNA interactions is key to understanding how RNAs fold and interact with other RNAs inside the cell. We present a high-throughput approach, sequencing of psoralen crosslinked, ligated, and selected hybrids (SPLASH), that maps pairwise RNA interactions in vivo with high sensitivity and specificity, genome-wide. Applying SPLASH to human and yeast transcriptomes revealed the diversity and dynamics of thousands of long-range intra- and intermolecular RNA-RNA interactions. Our analysis highlighted key structural features of RNA classes, including the modular organization of mRNAs, its impact on translation and decay, and the enrichment of long-range interactions in noncoding RNAs. Additionally, intermolecular mRNA interactions were organized into network clusters and were remodeled during cellular differentiation. We also identified hundreds of known and new snoRNA-rRNA binding sites, expanding our knowledge of rRNA biogenesis. These results highlight the underexplored complexity of RNA interactomes and pave the way to better understanding how RNA organization impacts biology.

RNAs are well-suited to act as cellular sensors that detect and respond to metabolite changes in the environment, due to their ability to fold into complex structures. Here, we introduce a genome-wide strategy called PARCEL that experimentally identifies RNA aptamers in vitro, in a high-throughput manner. By applying PARCEL to a collection of prokaryotic and eukaryotic organisms, we have revealed 58 new RNA aptamers to three key metabolites, greatly expanding the list of natural RNA aptamers. The newly identified RNA aptamers exhibit significant sequence conservation, are highly structured and show an unexpected prevalence in coding regions. We identified a prokaryotic precursor tmRNA that binds vitamin B2 (FMN) to facilitate its maturation, as well as eukaryotic mRNAs that bind and respond to FMN, suggesting FMN as the second RNA-binding ligand to affect eukaryotic expression. PARCEL results show that RNA-based sensing and gene regulation is more widespread than previously appreciated in different organisms.

Treatment for dental avulsion cases is early or late replantation of the traumatized teeth. Prognosis of the replanted tooth depends on the level of periodontal injury. Adipose tissue stem cells (ATSCs) were reported to improve periodontal ligament tissue (PDL) regeneration. Fibrin sealant (FS) contains thrombin and fibrinogen to form an adhesive fibrin clot routinely used in surgical procedures. Here, we aimed to investigate the effects of ATSCs + FS treatment on healing of PDL after tooth replantation in a rat model. After 60 min of extraction, maxillary central incisor teeth were replanted with ATSCs + FS. Two months later, the rats were sacrificed and hemimaxilla blocks were dissected out for histological analysis. The results showed that there was a significant improvement in histological findings of ATSCs + FS treated group compared to only FS treated and non-treated groups corresponding to reduced inflammatory resorption and increased new PDL formation. Furthermore, the ankylosis levels were lowered after ATSCs + FS treatment. Singular use of FS improved PDL healing moderately. Our results indicated that ATSCs + FS treatment improves PDL healing after tooth replantation suggesting a new therapeutic potential in the treatment of dental avulsion cases.

No abstract