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This work is partially supported by the Scottish Government's Rural and Environment Science and Analytical Services (RESAS) Division ; Potato mop-top pomovirus (PMTV) is one of a few viruses that can move systemically in plants in the absence of the capsid protein (CP). Pomoviruses encode the triple gene block genetic module of movement proteins (TGB 1, 2, and 3) and recent research suggests that PMTV RNA is transported either as ribonucleoprotein (RNP) complexes containing TGB1 or encapsidated in virions containing TGB1. Furthermore, there are different requirements for local or systemic (long-distance) movement. Research suggests that nucleolar passage of TGB1 may be important for the long-distance movement of both RNP and virions. Moreover, and uniquely, the long-distance movement of the CP-encoding RNA requires expression of both major and minor CP subunits and is inhibited when only the major CP sub unit is expressed. This paper reviews pomovirus research and presents a current model for RNA movement. ; Publisher PDF ; Peer reviewed

From transcription, to transport, storage, and translation, RNA depends on association with different RNA-binding proteins (RBPs). Methods based on next-generation sequencing and protein mass-spectrometry have started to unveil genome-wide interactions of RBPs but many aspects still remain out of sight. How many of the binding sites identified in high-throughput screenings are functional? A number of computational methods have been developed to analyze experimental data and to obtain insights into the specificity of protein–RNA interactions. How can theoretical models be exploited to identify RBPs? In addition to oligomeric complexes, protein and RNA molecules can associate into granular assemblies whose physical properties are still poorly understood. What protein features promote granule formation and what effects do these assemblies have on cell function? Here, we describe the newest in silico, in vitro, and in vivo advances in the field of protein–RNA interactions. We also present the challenges that experimental and computational approaches will have to face in future studies. WIREs RNA 2016, 7:793–810. doi:10.1002/wrna.1378 ; The research leading to this work has received funding from the European Union Seventh Framework Programme (FP7/2007-2013), through the European Research Council, under grant agreement RIBOMYLOME_309545 (Gian Gaetano Tartaglia), and from the Spanish Ministry of Economy and Competitiveness (BFU2014-55054-P). We also acknowledge support from AGAUR (2014 SGR 00685) and the Spanish Ministry of Economy and Competitiveness 'Centro de Excelencia Severo Ochoa 2013–2017' (SEV-2012-0208).

Transcription and genome architecture are interdependent, but it is still unclear how nucleosomes in the chromatin fiber interact with nascent RNA, and which is the relative nuclear distribution of these RNAs and elongating RNA polymerase II (RNAP II). Using super-resolution (SR) microscopy, we visualized the nascent transcriptome, in both nucleoplasm and nucleolus, with nanoscale resolution. We found that nascent RNAs organize in structures we termed RNA nanodomains, whose characteristics are independent of the number of transcripts produced over time. Dual-color SR imaging of nascent RNAs, together with elongating RNAP II and H2B, shows the physical relation between nucleosome clutches, RNAP II, and RNA nanodomains. The distance between nucleosome clutches and RNA nanodomains is larger than the distance measured between elongating RNAP II and RNA nanodomains. Elongating RNAP II stands between nascent RNAs and the small, transcriptionally active, nucleosome clutches. Moreover, RNA factories are small and largely formed by few RNAP II. Finally, we describe a novel approach to quantify the transcriptional activity at an individual gene locus. By measuring local nascent RNA accumulation upon transcriptional activation at single alleles, we confirm the measurements made at the global nuclear level. ; Innovative Team Program of Guangzhou Regenerative Medicine and Health Guangdong Laboratory [2018GZR110103001 to M.P.C.]; Guangzhou Key Projects of Brain Science and Brain-Like Intelligence Technology [20200730009 to M.P.C.]; National Natural Science Foundation of China [31971177 to M.P.C.]; Science and Technology Program of Guangzhou, China [202002030146 to M.P.C.]; European Union's Horizon 2020 Research and Innovation Programme [CellViewer No. 686637 to M.P.C. and M.L.]; Ministerio de Ciencia e Innovación [BFU2017-86760-P (AEI/FEDER, UE) to M.P.C.]; AGAUR grant from Secretaria d'Universitats i Recerca del Departament d'Empresa I Coneixement de la Generalitat de Catalunya [2017 SGR 689 to M.P.C.]; Centro de Excelencia Severo Ochoa [2013–2017 to M.P.C.]; CERCA Programme/Generalitat de Catalunya [to M.P.C.]; People Program (Marie Curie Actions) FP7/2007–2013 under REA grant [608959 to M.V.N.]; Spanish Ministry of Science and Innovation to the European Molecular Biology Laboratory (EMBL) partnership [to M.P.C.]; Juan de la Cierva-Incorporación 2017 [to M.V.N.]. Funding for open access charge: National Natural Science Foundation of China (NSFC) grant [31971177 to M.P.C].

RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining the secondary structures of RNAs is central to understanding their function and evolution. In recent years several sequencing-based approaches have been developed that allow probing structural features of thousands of RNA molecules present in a sample. Here, we describe nextPARS, a novel Illumina-based implementation of in vitro parallel probing of RNA structures. Our approach achieves comparable accuracy to previous implementations, while enabling higher throughput and sample multiplexing. ; This work was supported by the Spanish Ministry of Economy and Competitiveness grants "Centro de Excelencia Severo Ochoa 2013–2017" (SEV-2012-0208); the European Regional Development Fund (ERDF) from the European Union and European Research Council (ERC) Seventh Framework Programme (FP7/2007–2013) (ERC-2012-StG-310325); and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement (H2020-MSCA-ITN-2014-642095).

RNA and DNA flipons in health and disease
Flipons are the next step in DNA research. What they are, their role in DNA and RNA coding, their impact on medical science, and their relation to the immune system are discussed here. Flipons are DNA and RNA sequences that adopt alternative forms inside our bodies. These different ways of folding nucleic acids were first discovered after Watson and Crick proposed their famous model for DNA called the 'secret of life'. They were considered mere curiosities until the first crystal structure of DNA revealed that the DNA helix was wound in a left-handed direction rather than the expected right-handed twist of B-DNA.

[EN] In most eukaryotes, RNA silencing is an adaptive immune system regulating key biological processes including antiviral defense. To evade this response, viruses of plants, worms and insects have evolved viral suppressors of RNA silencing proteins (VSRs). Various VSRs, such as P1 from Sweet potato mild mottle virus (SPMMV), inhibit the activity of RNA-induced silencing complexes (RISCs) including an ARGONAUTE (AGO) protein loaded with a small RNA. However, the specific mechanisms explaining this class of inhibition are unknown. Here, we show that SPMMV P1 interacts with AGO1 and AGO2 from Arabidopsis thaliana, but solely interferes with AGO1 function. Moreover, a mutational analysis of a newly identified zinc finger domain in P1 revealed that this domain could represent an effector domain as it is required for P1 suppressor activity but not for AGO1 binding. Finally, a comparative analysis of the target RNA binding capacity of AGO1 in the presence of wild-type or suppressor-defective P1 forms revealed that P1 blocks target RNA binding to AGO1. Our results describe the negative regulation of RISC, the small RNA containing molecular machine. ; Hungarian Scientific Research Fund (OTKA) [K91042, NN107787, NN11024 to L.L.]; European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska Curie [655841 to A.C.]. Funding for open access charge: OTKA [NN11024] ; Kenesi, E.; Carbonell, A.; Lozsa, R.; Vertessy, B.; Lakatos, L. (2017). A viral suppressor of RNA silencing inhibits ARGONAUTE 1 function by precluding target RNA binding to pre-assembled RISC. Nucleic Acids Research. 45(13):7736-7750. https://doi.org/10.1093/nar/gkx379 ; S ; 7736 ; 7750 ; 45 ; 13 ; Sayed, D., & Abdellatif, M. (2011). MicroRNAs in Development and Disease. Physiological Reviews, 91(3), 827-887. doi:10.1152/physrev.00006.2010 ; Martin, R. C., Liu, P.-P., Goloviznina, N. A., & Nonogaki, H. (2010). microRNA, seeds, and Darwin?: diverse function of miRNA in seed biology and plant responses to stress. Journal of ...