IF 4.2 3区生物学

RNA Pub Date : 2024-09-16 DOI: 10.1261/rna.080066.124

Thiago Britto-Borges, Niels H Gehring, Volker Boehm, Christoph Dieterich

{"title":"NMDtxDB: data-driven identification and annotation of human NMD target transcripts.","authors":"Thiago Britto-Borges, Niels H Gehring, Volker Boehm, Christoph Dieterich","doi":"10.1261/rna.080066.124","DOIUrl":"10.1261/rna.080066.124","url":null,"abstract":"The nonsense-mediated RNA decay (NMD) pathway is a crucial mechanism of mRNA quality control. Current annotations of NMD substrate RNAs are rarely data-driven, but use generally established rules. We present a data set with four cell lines and combinations for SMG5, SMG6, and SMG7 knockdowns or SMG7 knockout. Based on this data set, we implemented a workflow that combines Nanopore and Illumina sequencing to assemble a transcriptome, which is enriched for NMD target transcripts. Moreover, we use coding sequence information (CDS) from Ensembl, Gencode consensus Ribo-seq ORFs, and OpenProt to enhance the CDS annotation of novel transcript isoforms. In summary, 302,889 transcripts were obtained from the transcriptome assembly process, out of which 24% are absent from Ensembl database annotations, 48,213 contain a premature stop codon, and 6433 are significantly upregulated in three or more comparisons of NMD active versus deficient cell lines. We present an in-depth view of these results through the NMDtxDB database, which is available at https://shiny.dieterichlab.org/app/NMDtxDB, and supports the study of NMD-sensitive transcripts. We open sourced our implementation of the respective web-application and analysis workflow at https://github.com/dieterich-lab/NMDtxDB and https://github.com/dieterich-lab/nmd-wf.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1277-1291"},"PeriodicalIF":4.2,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141879337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

IF 4.2 3区生物学

RNA Pub Date : 2024-09-16 DOI: 10.1261/rna.080011.124

Jingping Geng, Magdalena Chrabaszczewska, Karol Kurpiejewski, Anna Stankiewicz-Drogon, Marzena Jankowska-Anyszka, Edward Darzynkiewicz, Renata Grzela

{"title":"Cap-related modifications of RNA regulate binding to IFIT proteins.","authors":"Jingping Geng, Magdalena Chrabaszczewska, Karol Kurpiejewski, Anna Stankiewicz-Drogon, Marzena Jankowska-Anyszka, Edward Darzynkiewicz, Renata Grzela","doi":"10.1261/rna.080011.124","DOIUrl":"10.1261/rna.080011.124","url":null,"abstract":"All cells in our body are equipped with receptors to recognize pathogens and trigger a rapid defense response. As a result, foreign molecules are blocked, and cells are alerted to the danger. Among the many molecules produced in response to viral infection are interferon-induced proteins with tetratricopeptide repeats (IFITs). Their role is to recognize foreign mRNA and eliminate it from the translational pool of transcripts. In the present study, we used biophysical methods to characterize the interactions between the IFIT1 protein and its partners IFIT2 and IFIT3. IFIT1 interacts with IFIT3 with nanomolar binding affinity, which did not change significantly in the presence of the preformed IFIT2/3 complex. The interactions between IFIT2 and IFIT3 and IFIT1 and IFIT2 were one order of magnitude weaker. We also present kinetic data of the interactions between the IFIT protein complex and short RNA bearing various modifications at the 5' end. We show kinetic parameters for interaction between the IFIT complex and RNA with m6Am modification. The results show that the cap-adjacent m6Am modification is a stronger signature than cap1 alone. It blocks the formation of a complex between IFIT proteins and m7Gpppm6Am-RNA much more effectively than other cap modifications. In contrast, m6A in the 5'UTR is not recognized by IFIT proteins and does not contribute to translation repression by IFIT proteins. The data obtained are important for understanding the regulation of expression of genetic information. They indicate that 2'-O and m6Am modifications modulate the availability of mRNA molecules for proteins of innate immune response.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1292-1305"},"PeriodicalIF":4.2,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141620891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Boosting the toolbox for live imaging of translation. 改进翻译实时成像工具箱。

IF 4.2 3区生物学

RNA Pub Date : 2024-09-16 DOI: 10.1261/rna.080140.124

Maëlle Bellec, Ruoyu Chen, Jana Dhayni, Antonello Trullo, Damien Avinens, Hussein Karaki, Flavia Mazzarda, Helene Lenden-Hasse, Cyril Favard, Ruth Lehmann, Edouard Bertrand, Mounia Lagha, Jeremy Dufourt

{"title":"Boosting the toolbox for live imaging of translation.","authors":"Maëlle Bellec, Ruoyu Chen, Jana Dhayni, Antonello Trullo, Damien Avinens, Hussein Karaki, Flavia Mazzarda, Helene Lenden-Hasse, Cyril Favard, Ruth Lehmann, Edouard Bertrand, Mounia Lagha, Jeremy Dufourt","doi":"10.1261/rna.080140.124","DOIUrl":"10.1261/rna.080140.124","url":null,"abstract":"Live imaging of translation based on tag recognition by a single-chain antibody is a powerful technique to assess translation regulation in living cells. However, this approach is challenging and requires optimization in terms of expression level and detection sensitivity of the system, especially in a multicellular organism. Here, we improved existing fluorescent tools and developed new ones to image and quantify nascent translation in the living Drosophila embryo and in mammalian cells. We tested and characterized five different green fluorescent protein variants fused to the single-chain fragment variable (scFv) and uncovered photobleaching, aggregation, and intensity disparities. Using different strengths of germline and somatic drivers, we determined that the availability of the scFv is critical in order to detect translation throughout development. We introduced a new translation imaging method based on a nanobody/tag system named ALFA-array, allowing the sensitive and simultaneous detection of the translation of several distinct mRNA species. Finally, we developed a largely improved RNA imaging system based on an MCP-tdStaygold fusion.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1374-1394"},"PeriodicalIF":4.2,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404453/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141767178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Study of the RNA splicing kinetics via in vivo 5-EU labeling. 通过体内 5-乙炔尿苷标记研究 RNA 剪接动力学。

IF 4.2 3区生物学

RNA Pub Date : 2024-09-16 DOI: 10.1261/rna.079937.123

Anastasiia K Bolikhova, Andrey I Buyan, Sofia S Mariasina, Alexander Y Rudenko, Daria S Chekh, Alexander M Mazur, Egor B Prokhortchouk, Olga A Dontsova, Petr V Sergiev

{"title":"Study of the RNA splicing kinetics via in vivo 5-EU labeling.","authors":"Anastasiia K Bolikhova, Andrey I Buyan, Sofia S Mariasina, Alexander Y Rudenko, Daria S Chekh, Alexander M Mazur, Egor B Prokhortchouk, Olga A Dontsova, Petr V Sergiev","doi":"10.1261/rna.079937.123","DOIUrl":"10.1261/rna.079937.123","url":null,"abstract":"Splicing is an important step of gene expression in all eukaryotes. Splice sites might be used with different efficiency, giving rise to alternative splicing products. At the same time, splice sites might be used at a variable rate. We used 5-ethynyl uridine labeling to sequence a nascent transcriptome of HeLa cells and deduced the rate of splicing for each donor and acceptor splice site. The following correlation analysis showed a correspondence of primary transcript features with the rate of splicing. Some dependencies we revealed were anticipated, such as a splicing rate decrease with a decreased complementarity of the donor splice site to U1 and acceptor sites to U2 snRNAs. Other dependencies were more surprising, like a negative influence of a distance to the 5' end on the rate of the acceptor splicing site utilization, or the differences in splicing rate between long, short, and RBM17-dependent introns. We also observed a deceleration of last intron splicing with an increase of the distance to the poly(A) site, which might be explained by the cooperativity of the splicing and polyadenylation. Additional analysis of splicing kinetics of SF3B4 knockdown cells suggested the impairment of a U2 snRNA recognition step. As a result, we deconvoluted the effects of several examined features on the splicing rate into a single regression model. The data obtained here are useful for further studies in the field, as they provide general splicing rate dependencies as well as help to justify the existence of slowly removed splice sites.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1356-1373"},"PeriodicalIF":4.2,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141760729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a. CRISPR-Cas12a结合和处理前crRNA的动力学剖析。

IF 4.2 3区生物学

RNA Pub Date : 2024-09-16 DOI: 10.1261/rna.080088.124

Selma Sinan, Nathan M Appleby, Chia-Wei Chou, Ilya J Finkelstein, Rick Russell

{"title":"Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a.","authors":"Selma Sinan, Nathan M Appleby, Chia-Wei Chou, Ilya J Finkelstein, Rick Russell","doi":"10.1261/rna.080088.124","DOIUrl":"10.1261/rna.080088.124","url":null,"abstract":"CRISPR-Cas12a binds and processes a single pre-crRNA during maturation, providing a simple tool for genome editing applications. Here, we constructed a kinetic and thermodynamic framework for pre-crRNA processing by Cas12a in vitro, and we measured the contributions of distinct regions of the pre-crRNA to this reaction. We find that the pre-crRNA binds rapidly and extraordinarily tightly to Cas12a (K d = 0.6 pM), such that pre-crRNA binding is fully rate limiting for processing and therefore determines the specificity of Cas12a for different pre-crRNAs. The guide sequence contributes 10-fold to the binding affinity of the pre-crRNA, while deletion of an upstream sequence has no significant effect. After processing, the mature crRNA remains very tightly bound to Cas12a with a comparable affinity. Strikingly, the affinity contribution of the guide region increases to 600-fold after processing, suggesting that additional contacts are formed and may preorder the crRNA for efficient DNA target recognition. Using a direct competition assay, we find that pre-crRNA-binding specificity is robust to changes in the guide sequence, addition of a 3' extension, and secondary structure within the guide region. However, stable secondary structure in the guide region can strongly inhibit DNA targeting, indicating that care should be taken in crRNA design. Together, our results provide a quantitative framework for pre-crRNA binding and processing by Cas12a and suggest strategies for optimizing crRNA design in genome editing applications.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1345-1355"},"PeriodicalIF":4.2,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141620892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Kinetic and structural insights into the requirement of fungal tRNA ligase for a 2'-phosphate end. 真菌 tRNA 连接酶对 2'-磷酸末端要求的动力学和结构见解。

IF 4.2 3区生物学

RNA Pub Date : 2024-09-16 DOI: 10.1261/rna.080120.124

Shreya Ghosh, Stewart Shuman

{"title":"Kinetic and structural insights into the requirement of fungal tRNA ligase for a 2'-phosphate end.","authors":"Shreya Ghosh, Stewart Shuman","doi":"10.1261/rna.080120.124","DOIUrl":"10.1261/rna.080120.124","url":null,"abstract":"Fungal RNA ligase (LIG) is an essential tRNA splicing enzyme that joins 3'-OH,2'-PO4 and 5'-PO4 RNA ends to form a 2'-PO4,3'-5' phosphodiester splice junction. Sealing entails three divalent cation-dependent adenylate transfer steps. First, LIG reacts with ATP to form a covalent ligase-(lysyl-Nζ)-AMP intermediate and displace pyrophosphate. Second, LIG transfers AMP to the 5'-PO4 RNA terminus to form an RNA-adenylate intermediate (A5'pp5'RNA). Third, LIG directs the attack of an RNA 3'-OH on AppRNA to form the splice junction and displace AMP. A defining feature of fungal LIG vis-à-vis canonical polynucleotide ligases is the requirement for a 2'-PO4 to synthesize a 3'-5' phosphodiester bond. Fungal LIG consists of an N-terminal adenylyltransferase domain and a unique C-terminal domain. The C-domain of Chaetomium thermophilum LIG (CthLIG) engages a sulfate anion thought to be a mimetic of the terminal 2'-PO4 Here, we interrogated the contributions of the C-domain and the conserved sulfate ligands (His227, Arg334, Arg337) to ligation of a pRNA2'p substrate. We find that the C-domain is essential for end-joining but dispensable for ligase adenylylation. Mutations H227A, R334A, and R337A slowed the rate of step 2 RNA adenylation by 420-fold, 120-fold, and 60-fold, respectively, vis-à-vis wild-type CthLIG. An R334A-R337A double-mutation slowed step 2 by 580-fold. These results fortify the case for the strictly conserved His-Arg-Arg triad as the enforcer of the 2'-PO4 end-specificity of fungal tRNA ligases and as a target for small molecule interdiction of fungal tRNA splicing.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1306-1314"},"PeriodicalIF":4.2,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404444/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141627579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural idiosyncrasies of glycyl T-box riboswitches among pathogenic bacteria. 致病细菌中甘氨酰 T-盒核糖开关的结构特异性。

IF 4.2 3区生物学

RNA Pub Date : 2024-09-16 DOI: 10.1261/rna.080071.124

Nikoleta Giarimoglou, Adamantia Kouvela, Jinwei Zhang, Vassiliki Stamatopoulou, Constantinos Stathopoulos

{"title":"Structural idiosyncrasies of glycyl T-box riboswitches among pathogenic bacteria.","authors":"Nikoleta Giarimoglou, Adamantia Kouvela, Jinwei Zhang, Vassiliki Stamatopoulou, Constantinos Stathopoulos","doi":"10.1261/rna.080071.124","DOIUrl":"10.1261/rna.080071.124","url":null,"abstract":"T-box riboswitches are widespread bacterial regulatory noncoding RNAs that directly interact with tRNAs and switch conformations to regulate the transcription or translation of genes related to amino acid metabolism. Recent studies in Bacilli have revealed the core mechanisms of T-boxes that enable multivalent, specific recognition of both the identity and aminoacylation status of the tRNA substrates. However, in-depth knowledge on a vast number of T-boxes in other bacterial species remains scarce, although a remarkable structural diversity, particularly among pathogens, is apparent. In the present study, analysis of T-boxes that control the transcription of glycyl-tRNA synthetases from four prominent human pathogens revealed significant structural idiosyncrasies. Nonetheless, these diverse T-boxes maintain functional T-box:tRNAGly interactions both in vitro and in vivo. Probing analysis not only validated recent structural observations, but also expanded our knowledge on the substantial diversities among T-boxes and suggest interesting distinctions from the canonical Bacilli T-boxes. Surprisingly, some glycyl T-boxes seem to redirect the T-box trajectory in the absence of recognizable K-turns or contain Stem II modules that are generally absent in glycyl T-boxes. These results consolidate the notion of a lineage-specific diversification and elaboration of the T-box mechanism and corroborate the potential of T-boxes as promising species-specific RNA targets for next-generation antibacterial compounds.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1328-1344"},"PeriodicalIF":4.2,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141564192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Thg1 family 3'-5' RNA polymerases as tools for targeted RNA synthesis. Thg1 家族 3'-5' RNA 聚合酶是定向 RNA 合成的工具。

IF 4.2 3区生物学

RNA Pub Date : 2024-09-16 DOI: 10.1261/rna.080156.124

Malithi I Jayasinghe, Krishna J Patel, Jane E Jackman

{"title":"Thg1 family 3'-5' RNA polymerases as tools for targeted RNA synthesis.","authors":"Malithi I Jayasinghe, Krishna J Patel, Jane E Jackman","doi":"10.1261/rna.080156.124","DOIUrl":"10.1261/rna.080156.124","url":null,"abstract":"Members of the 3'-5' RNA polymerase family, comprised of tRNAHis guanylyltransferase (Thg1) and Thg1-like proteins (TLPs), catalyze templated synthesis of RNA in the reverse direction to all other known 5'-3' RNA and DNA polymerases. The discovery of enzymes capable of this reaction raised the possibility of exploiting 3'-5' polymerases for posttranscriptional incorporation of nucleotides to the 5'-end of nucleic acids without ligation, and instead by templated polymerase addition. To date, studies of these enzymes have focused on nucleotide addition to highly structured RNAs, such as tRNA and other noncoding RNAs. Consequently, general principles of RNA substrate recognition and nucleotide preferences that might enable broader application of 3'-5' polymerases have not been elucidated. Here, we investigated the feasibility of using Thg1 or TLPs for multiple nucleotide incorporation to the 5'-end of a short duplex RNA substrate, using a templating RNA oligonucleotide provided in trans to guide 5'-end addition of specific sequences. Using optimized assay conditions, we demonstrated a remarkable capacity of certain TLPs to accommodate short RNA substrate-template duplexes of varying lengths with significantly high affinity, resulting in the ability to incorporate a desired nucleotide sequence of up to eight bases to 5'-ends of the model RNA substrates in a template-dependent manner. This work has further advanced our goals to develop this atypical enzyme family as a versatile nucleic acid 5'-end labeling tool.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1315-1327"},"PeriodicalIF":4.2,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404450/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141601427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Increasing MicroRNA Abundance by Targeting Biogenesis from the Primary Transcript with Steric-Blocking Antisense Oligonucleotides 利用立体阻断反义寡核苷酸靶向初级转录本的生物生成，提高 MicroRNA 的丰度

IF 4.5 3区生物学

RNA Pub Date : 2024-09-10 DOI: 10.1261/rna.080021.124

Mallory A Havens, Anthony J Hinrich, Frank Rigo, Michelle L Hastings

{"title":"Increasing MicroRNA Abundance by Targeting Biogenesis from the Primary Transcript with Steric-Blocking Antisense Oligonucleotides","authors":"Mallory A Havens, Anthony J Hinrich, Frank Rigo, Michelle L Hastings","doi":"10.1261/rna.080021.124","DOIUrl":"https://doi.org/10.1261/rna.080021.124","url":null,"abstract":"MicroRNAs (miRNAs) are regulators of gene expression, and their dysregulation is linked to cancer and other diseases, making them important therapeutic targets. Several strategies for targeting and modulating miRNA activity are being explored. For example, steric blocking antisense oligonucleotides (ASOs) can reduce miRNA activity by either blocking binding sites on specific mRNAs or base-pairing to the miRNA itself to prevent its interaction with the target mRNAs. ASOs have been less explored as a tool to elevate miRNA levels, which could also be beneficial for treating disease. In this study, using the PKD1/miR-1225 gene locus as an example, where miR-1225 is located within a PKD1 intron, we demonstrate an ASO-based strategy that increases miRNA abundance by enhancing biogenesis from the primary miRNA transcript. Disruptions in PKD1 and miR-1225 are associated with autosomal dominant polycystic kidney disease (ADPKD) and various cancers, respectively, making them important therapeutic targets. We investigated PKD1 sequence variants reported in ADPKD that are located within the sequence shared by miR-1225 and PKD1, and identified one that causes a reduction in miR-1225 without affecting PKD1. We show that this reduction in miR-1225 can be recovered by treatment with a steric-blocking ASO. The ASO-induced increase in miR-1225 correlates with a decrease in the abundance of predicted miR-1225 cellular mRNA targets. This study demonstrates that miRNA abundance can be elevated using ASOs targeted to the primary transcript. This steric-blocking ASO-based approach has broad potential application as a therapeutic strategy for diseases that could be treated by modulating miRNA biogenesis.","PeriodicalId":21401,"journal":{"name":"RNA","volume":"169 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

tRNAVal allows four-way decoding with unmodified uridine at the wobble position in Lactobacillus casei 在干酪乳杆菌中，tRNAVal 可与位于摆动位置的未修饰尿苷进行四向解码

IF 4.5 3区生物学

RNA Pub Date : 2024-09-10 DOI: 10.1261/rna.080155.124

Riko Sugita, Vincent Guérineau, David Touboul, Satoko Yoshizawa, Kazuyuki Takai, Chie Tomikawa

{"title":"tRNAVal allows four-way decoding with unmodified uridine at the wobble position in Lactobacillus casei","authors":"Riko Sugita, Vincent Guérineau, David Touboul, Satoko Yoshizawa, Kazuyuki Takai, Chie Tomikawa","doi":"10.1261/rna.080155.124","DOIUrl":"https://doi.org/10.1261/rna.080155.124","url":null,"abstract":"Modifications at the wobble position (position 34) of tRNA facilitate interactions that enable or stabilize non-Watson-Crick basepairs. In bacterial tRNA, 5-hydroxyuridine (ho5U) derivatives xo5U [x: methyl (mo5U), carboxymethyl (cmo5U), and methoxycarbonylmethyl (mcmo5U)] present at the wobble positions of tRNAs are responsible for recognition of NYN codon families. These modifications of U34 allow basepairing not only with A and G but also with U and in some cases C. mo5U was originally found in Gram-positive bacteria, and cmo5U and mcmo5U were found in Gram-negative bacteria. tRNAs of Mycoplasma species, mitochondria, and chloroplasts adopt four-way decoding in which unmodified U34 recognizes codons ending in A, G, C, and U. Lactobacillus casei, Gram-positive bacteria and lactic acid bacteria, lacks the modification enzyme genes for xo5U biosynthesis. Nevertheless, L. casei has only one type of tRNAVal with the anticodon UAC [tRNAVal(UAC)]. However, the genome of L. casei encodes an undetermined tRNA (tRNAUnd) gene, and the sequence corresponding to the anticodon region is GAC. Here, we confirm that U34 in L. casei tRNAVal is unmodified and that there is no tRNAUnd expression in the cells. In addition, in vitro transcribed tRNAUnd was not aminoacylated by L. casei valyl-tRNA synthetase suggesting that tRNAUnd is not able to accept valine, even if expressed in cells. Correspondingly, native tRNAVal(UAC) with unmodified U34 bound to all four valine codons in the ribosome A site. This suggests that L. casei tRNAVal decodes all valine codons by four-way decoding, similarly to tRNAs from Mycoplasma species, mitochondria, and chloroplasts.","PeriodicalId":21401,"journal":{"name":"RNA","volume":"42 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142225103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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