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   https://doi.org/10.1093/molbev/msp112  

   Stadler, P. F.; Chen, J. J.-L.; Hackermuller, J.; Hoffmann, S.; Horn, F.; Khaitovich, P.; Kretzschmar, A. K.; Mosig, A.; Prohaska, S. J.; Qi, X.; et al (August 2009, Molecular Biology and Evolution)
2. Translation of circular RNAs

   https://doi.org/10.1093/nar/gkae1167  

   Margvelani, Giorgi; Maquera, Karol Andrea Arizaca; Welden, Justin Ralph; Rodgers, David W.; Stamm, Stefan (December 2024, Nucleic Acids Research)

   Abstract Circular RNAs (circRNAs) are covalently closed RNAs that are present in all eukaryotes tested. Recent RNA sequencing (RNA-seq) analyses indicate that although generally less abundant than messenger RNAs (mRNAs), over 1.8 million circRNA isoforms exist in humans, much more than the number of currently known mRNA isoforms. Most circRNAs are generated through backsplicing that depends on pre-mRNA structures, which are influenced by intronic elements, for example, primate-specific Alu elements, leading to species-specific circRNAs. CircRNAs are mostly cytosolic, stable and some were shown to influence cells by sequestering miRNAs and RNA-binding proteins. We review the increasing evidence that circRNAs are translated into proteins using several cap-independent translational mechanisms, that include internal ribosomal entry sites, N6-methyladenosine RNA modification, adenosine to inosine RNA editing and interaction with the eIF4A3 component of the exon junction complex. CircRNAs are translated under conditions that favor cap-independent translation, notably in cancer and generate proteins that are shorter than mRNA-encoded proteins, which can acquire new functions relevant in diseases. 

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3. Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs

   https://doi.org/10.1073/pnas.2409090121  

   Borniego, M_Lucía; Singla-Rastogi, Meenu; Baldrich, Patricia; Sampangi-Ramaiah, Megha_Hastantram; Zand_Karimi, Hana; McGregor, Madison; Meyers, Blake_C; Innes, Roger_W (January 2025, Proceedings of the National Academy of Sciences)

   Transgenic expression of a double-stranded RNA in plants can induce silencing of homologous mRNAs in fungal pathogens. Although such host-induced gene silencing is well documented, the molecular mechanisms by which RNAs can move from the cytoplasm of plant cells across the plasma membrane of both the host cell and fungal cell are poorly understood. Indirect evidence suggests that this RNA transfer may occur at a very early stage of the infection process, prior to breach of the host cell wall, suggesting that silencing RNAs might be secreted onto leaf surfaces. To assess whether Arabidopsis plants possess a mechanism for secreting RNA onto leaf surfaces, we developed a protocol for isolating leaf surface RNA separately from intercellular (apoplastic) RNA. This protocol yielded abundant leaf surface RNA that displayed an RNA banding pattern distinct from apoplastic RNA, suggesting that it may be secreted directly onto the leaf surface rather than exuded through stomata or hydathodes. Notably, this RNA was not associated with either extracellular vesicles or protein complexes; however, RNA species longer than 100 nucleotides could be pelleted by ultracentrifugation. Furthermore, pelleting was inhibited by the divalent cation chelator EGTA, suggesting that these RNAs may form condensates on the leaf surface. These leaf surface RNAs are derived almost exclusively from Arabidopsis, but come from diverse genomic sources, including rRNA, tRNA, mRNA, intergenic RNA, microRNAs, and small interfering RNAs, with tRNAs especially enriched. We speculate that endogenous leaf surface RNA plays an important role in the assembly of distinct microbial communities on leaf surfaces. 

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4. Epitranscriptomic modifications in plant RNAs

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5. Cas9 deactivation with photocleavable guide RNAs

   https://doi.org/10.1016/j.molcel.2021.02.007  

   Zou, Roger S.; Liu, Yang; Wu, Bin; Ha, Taekjip (April 2021, Molecular Cell)

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