IF 4.2 3区生物学

RNA Pub Date : 2024-12-16 DOI: 10.1261/rna.080273.124

Aniket Wahane, Vishal Kasina, Mounika Pathuri, Ciara Marro-Wilson, Anisha Gupta, Frank J Slack, Raman Bahal

{"title":"Development of bioconjugate-based delivery systems for nucleic acids.","authors":"Aniket Wahane, Vishal Kasina, Mounika Pathuri, Ciara Marro-Wilson, Anisha Gupta, Frank J Slack, Raman Bahal","doi":"10.1261/rna.080273.124","DOIUrl":"10.1261/rna.080273.124","url":null,"abstract":"Nucleic acids are a class of drugs that can modulate gene and protein expression by various mechanisms, namely, RNAi, mRNA degradation by RNase H cleavage, splice modulation, and steric blocking of protein binding or mRNA translation, thus exhibiting immense potential to treat various genetic and rare diseases. Unlike protein-targeted therapeutics, the clinical use of nucleic acids relies on Watson-Crick sequence recognition to regulate aberrant gene expression and impede protein translation. Though promising, targeted delivery remains a bottleneck for the clinical adoption of nucleic acid-based therapeutics. To overcome the delivery challenges associated with nucleic acids, various chemical modifications and bioconjugation-based delivery strategies have been explored. Currently, liver targeting by N-acetyl galactosamine (GalNAc) conjugation has been at the forefront for the treatment of rare and various metabolic diseases, which has led to FDA approval of four nucleic acid drugs. In addition, various other bioconjugation strategies have been explored to facilitate active organ and cell-enriched targeting. This review briefly covers the different classes of nucleic acids, their mechanisms of action, and their challenges. We also elaborate on recent advances in bioconjugation strategies in developing a diverse set of ligands for targeted delivery of nucleic acid drugs.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1-13"},"PeriodicalIF":4.2,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11648935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142547091","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

The oligonucleotides containing N7-regioisomer of guanosine: influence on thermodynamic properties and structure of RNA duplexes. 含有鸟苷 N7-regioisomer 的寡核苷酸。对 RNA 双链体热力学性质和结构的影响。

IF 4.2 3区生物学

RNA Pub Date : 2024-12-16 DOI: 10.1261/rna.080106.124

Aleksandra Jarmolowicz, Nivedita Dutta, Witold Andralojc, Joanna Sarzynska, Grzegorz Framski, Daniel Baranowski, Jerzy Boryski, Ansuman Lahiri, Zofia Gdaniec, Elzbieta Kierzek, Ryszard Kierzek

{"title":"The oligonucleotides containing N7-regioisomer of guanosine: influence on thermodynamic properties and structure of RNA duplexes.","authors":"Aleksandra Jarmolowicz, Nivedita Dutta, Witold Andralojc, Joanna Sarzynska, Grzegorz Framski, Daniel Baranowski, Jerzy Boryski, Ansuman Lahiri, Zofia Gdaniec, Elzbieta Kierzek, Ryszard Kierzek","doi":"10.1261/rna.080106.124","DOIUrl":"10.1261/rna.080106.124","url":null,"abstract":"During the chemical synthesis of the purine riboside, N7-regioisomer is kinetically formed, whereas N9-regioisomer is a thermodynamically formed product. We have studied the effect of substituting N9-regioisomer of guanosine with its N7-regioisomer (N7-guanosine, 7G) at a central position of several RNA duplexes. We found that this single substitution by 7G severely diminished their thermodynamic stabilities when 7G paired with C and U, but remarkably, led to a significant amount of stabilization in most of the duplexes when forming mismatches with G and A. The extent of stabilization was observed to be dependent on the sequence and orientation of neighboring base pairs of N7-guanosine. 1D and 2D NMR studies on the duplexes along with extensive molecular dynamics simulations revealed the conformational differences occurring due to the substitution of G by 7G, and it was observed that the thermodynamic results were largely explainable by considering the formation of stable noncanonical hydrogen bonding interactions, although other interactions such as stacking and electrostatic interactions could also play a role. These observations can have important applications in the design of RNA-based disease diagnostics and therapeutics.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"86-99"},"PeriodicalIF":4.2,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11648930/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522880","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

Conserved role for spliceosomal component PRPF40A in microexon splicing. 剪接体成分 PRPF40A 在微外显子剪接中的保守作用

IF 4.2 3区生物学

RNA Pub Date : 2024-12-16 DOI: 10.1261/rna.080142.124

Bikash Choudhary, Adam Norris

引用次数: 0

RNA fold prediction by Monte Carlo in graph space and the statistical mechanics of tertiary interactions. 通过蒙特卡罗图空间和三级相互作用的统计力学预测 RNA 折叠。

IF 4.2 3区生物学

RNA Pub Date : 2024-12-16 DOI: 10.1261/rna.080216.124

Ethan N H Phan, Chi H Mak

{"title":"RNA fold prediction by Monte Carlo in graph space and the statistical mechanics of tertiary interactions.","authors":"Ethan N H Phan, Chi H Mak","doi":"10.1261/rna.080216.124","DOIUrl":"10.1261/rna.080216.124","url":null,"abstract":"Using a graph representation of RNA structures, we have studied the ensembles of secondary and tertiary graphs of two sets of RNA with Monte Carlo simulations. The first consisted of 91 target ribozyme and riboswitch sequences of moderate lengths (<150 nt) having a variety of secondary, H-type pseudoknots and kissing loop interactions. The second set consisted of 71 more diverse sequences across many RNA families. Using a simple empirical energy model for tertiary interactions and only sequence information for each target as input, the simulations examined how tertiary interactions impact the statistical mechanics of the fold ensembles. The results show that the graphs proliferate enormously when tertiary interactions are possible, producing an entropic driving force for the ensemble to access folds having tertiary structures even though they are overall energetically unfavorable in the energy model. For each of the targets in the two test sets, we assessed the quality of the model and the simulations by examining how well the simulated structures were able to predict the native fold, and compared the results to fold predictions from ViennaRNA. Our model generated good or excellent predictions in a large majority of the targets. Overall, this method was able to produce predictions of comparable quality to Vienna, but it outperformed Vienna for structures with H-type pseudoknots. The results suggest that while tertiary interactions are predicated on real-space contacts, their impacts on the folded structure of RNA can be captured by graph space information for sequences of moderate lengths, using a simple tertiary energy model for the loops, the base pairs, and base stacks.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"14-31"},"PeriodicalIF":4.2,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11648927/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142507013","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

Quantification of influenza virus mini viral RNAs using Cas13. 利用 Cas13 对流感病毒微型病毒 RNA 进行定量。

IF 4.2 3区生物学

RNA Pub Date : 2024-12-16 DOI: 10.1261/rna.080174.124

Caitlin H Lamb, Emmanuelle M Pitré, Sean Ajufo, Charlotte V Rigby, Karishma Bisht, Michael S Oade, Hamid Jalal, Cameron Myhrvold, Aartjan J W Te Velthuis

{"title":"Quantification of influenza virus mini viral RNAs using Cas13.","authors":"Caitlin H Lamb, Emmanuelle M Pitré, Sean Ajufo, Charlotte V Rigby, Karishma Bisht, Michael S Oade, Hamid Jalal, Cameron Myhrvold, Aartjan J W Te Velthuis","doi":"10.1261/rna.080174.124","DOIUrl":"10.1261/rna.080174.124","url":null,"abstract":"Influenza A virus (IAV) RNA synthesis produces full-length and deletion-containing RNA molecules, which include defective viral genomes (DVG) and mini viral RNAs (mvRNA). Sequencing approaches have shown that DVG and mvRNA species may be present during infection, and that they can vary in size, segment origin, and sequence. Moreover, a subset of aberrant RNA molecules can bind and activate host-pathogen receptor retinoic acid-inducible gene I (RIG-I), leading to innate immune signaling and the expression of type I and III interferons. Measuring the kinetics and distribution of these immunostimulatory aberrant RNA sequences is important for understanding their function in IAV infection. Here, we explored if IAV mvRNA molecules can be detected and quantified using amplification-free, CRISPR-LbuCas13a-based detection. We show that CRISPR-LbuCas13a can be used to measure the copy numbers of specific mvRNAs in samples from infected tissue culture cells. However, to efficiently detect mvRNAs in other samples, promiscuous CRISPR guide RNAs are required that activate LbuCas13a in the presence of multiple mvRNA sequences. One crRNA was able to detect full-length IAV segment 5 without amplification, allowing it to be used for general IAV infection detection nasopharyngeal swabs. Using CRISPR-LbuCas13a, we confirm that mvRNAs are present in ferret upper and lower respiratory tract tissue, as well as clinical nasopharyngeal swab extracts of hospitalized patients. Overall, CRISPR-LbuCas13a-based RNA detection is a useful tool for studying deletion-containing viral RNAs, and it complements existing amplification-based approaches.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"126-138"},"PeriodicalIF":4.2,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11648933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142473667","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

Widespread destabilization of Caenorhabditis elegans microRNAs by the E3 ubiquitin ligase EBAX-1. E3泛素连接酶EBAX-1广泛破坏秀丽隐杆线虫microRNA的稳定性。

IF 4.2 3区生物学

RNA Pub Date : 2024-12-16 DOI: 10.1261/rna.080276.124

Michael W Stubna, Aditi Shukla, David P Bartel

{"title":"Widespread destabilization of Caenorhabditis elegans microRNAs by the E3 ubiquitin ligase EBAX-1.","authors":"Michael W Stubna, Aditi Shukla, David P Bartel","doi":"10.1261/rna.080276.124","DOIUrl":"10.1261/rna.080276.124","url":null,"abstract":"MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to form complexes that direct mRNA repression. miRNAs are also the subject of regulation. For example, some miRNAs are destabilized through a pathway in which pairing to specialized transcripts recruits the ZSWIM8 E3 ubiquitin ligase, which polyubiquitinates AGO, leading to its degradation and exposure of the miRNA to cellular nucleases. Here, we found that 22 miRNAs in Caenorhabditis elegans are sensitive to loss of EBAX-1, the ZSWIM8 ortholog in nematodes, implying that these 22 miRNAs might be subject to this pathway of target-directed miRNA degradation (TDMD). The impact of EBAX-1 depended on the developmental stage, with the greatest effect on the miRNA pool (14.5%) observed in L1 larvae, and the greatest number of different miRNAs affected (17) observed in germline-depleted adults. The affected miRNAs included the miR-35-42 family, as well as other miRNAs among the least stable in the worm, suggesting that TDMD is a major miRNA-destabilization pathway in the worm. The excess miR-35-42 molecules that accumulated in ebax-1 mutants caused increased repression of their predicted target mRNAs and underwent 3' trimming over time. In general, however, miRNAs sensitive to EBAX-1 loss had no consistent pattern of either trimming or tailing. Replacement of the 3' region of miR-43 substantially reduced EBAX-1 sensitivity, a result that differed from that observed previously for miR-35. Together, these findings broaden the implied biological scope of TDMD-like regulation of miRNA stability in animals, and indicate that a role for miRNA 3' sequences is variable in the worm.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"51-66"},"PeriodicalIF":4.2,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11648932/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142473684","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

Template switching enables chemical probing of native RNA structures. 通过模板切换，可对原生 RNA 结构进行化学探测。

IF 4.2 3区生物学

RNA Pub Date : 2024-12-16 DOI: 10.1261/rna.079926.123

Ian Hall, Martin O'Steen, Sophie Gold, Sarah C Keane, Chase A Weidmann

{"title":"Template switching enables chemical probing of native RNA structures.","authors":"Ian Hall, Martin O'Steen, Sophie Gold, Sarah C Keane, Chase A Weidmann","doi":"10.1261/rna.079926.123","DOIUrl":"10.1261/rna.079926.123","url":null,"abstract":"RNAs are often studied in nonnative sequence contexts to facilitate structural studies. However, seemingly innocuous changes to an RNA sequence may perturb the native structure and generate inaccurate or ambiguous structural models. To facilitate the investigation of native RNA secondary structure by selective 2' hydroxyl acylation analyzed by primer extension (SHAPE), we engineered an approach that couples minimal enzymatic steps to RNA chemical probing and mutational profiling (MaP) reverse transcription (RT) methods-a process we call template switching and mutational profiling (Switch-MaP). In Switch-MaP, RT templates and additional library sequences are added postprobing through ligation and template switching, capturing reactivities for every nucleotide. For a candidate SAM-I riboswitch, we compared RNA structure models generated by the Switch-MaP approach to those of traditional primer-based MaP, including RNAs with or without appended structure cassettes. Primer-based MaP masked reactivity data in the 5' and 3' ends of the RNA, producing ambiguous ensembles inconsistent with the conserved SAM-I riboswitch secondary structure. Structure cassettes enabled unambiguous modeling of an aptamer-only construct but introduced nonnative interactions in the full-length riboswitch. In contrast, Switch-MaP provided reactivity data for all nucleotides in each RNA and enabled unambiguous modeling of secondary structure, consistent with the conserved SAM-I fold. Switch-MaP is a straightforward alternative approach to primer-based and cassette-based chemical probing methods that precludes primer masking and the formation of alternative secondary structures due to nonnative sequence elements.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"113-125"},"PeriodicalIF":4.2,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11648929/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142507014","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

Corrigendum: Specific roles for the Ccr4-Not complex subunits in expression of the genome. 勘误：Ccr4-Not复杂亚基在基因组表达中的特殊作用。

IF 4.2 3区生物学

RNA Pub Date : 2024-12-16 DOI: 10.1261/rna.080301.124

Nowel Azzouz, Olesya O Panasenko, Cécile Deluen, Julien Hsieh, Grégory Theiler, Martine A Collart

引用次数: 0

Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis. 通过网络分析研究 RNA 结合蛋白 Ssd1 在非整倍体耐受性中的作用

IF 4.2 3区生物学

RNA Pub Date : 2024-12-16 DOI: 10.1261/rna.080199.124

H Auguste Dutcher, Audrey P Gasch

{"title":"Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis.","authors":"H Auguste Dutcher, Audrey P Gasch","doi":"10.1261/rna.080199.124","DOIUrl":"10.1261/rna.080199.124","url":null,"abstract":"RNA-binding proteins (RBPs) play critical cellular roles by mediating various stages of RNA life cycles. Ssd1, an RBP with pleiotropic effects, has been implicated in aneuploidy tolerance in Saccharomyces cerevisiae but its mechanistic role remains unclear. Here, we used a network-based approach to inform on Ssd1's role in aneuploidy tolerance, by identifying and experimentally perturbing a network of RBPs that share mRNA targets with Ssd1. We identified RBPs whose bound mRNA targets significantly overlap with Ssd1 targets. For 14 identified RBPs, we then used a genetic approach to generate all combinations of genotypes for euploid and aneuploid yeast with an extra copy of chromosome XII, with and without SSD1 and/or the RBP of interest. Deletion of 10 RBPs either exacerbated or alleviated the sensitivity of wild-type and/or ssd1Δ cells to chromosome XII duplication, in several cases indicating genetic interactions with SSD1 in the context of aneuploidy. We integrated these findings with results from a global overexpression screen that identified genes whose duplication complements ssd1Δ aneuploid sensitivity. The resulting network points to a subgroup of proteins with shared roles in translational repression and P-body formation, implicating these functions in aneuploidy tolerance. Our results reveal a role for new RBPs in aneuploidy tolerance and support a model in which Ssd1 mitigates translation-related stresses in aneuploid cells.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"100-112"},"PeriodicalIF":4.2,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11648931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142547092","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

Bioinformatics-driven refinement of the commonly used TPI nonsense-mediated decay reporter system. 生物信息学驱动的常用 TPI 无义衰变报告系统的改进

IF 4.2 3区生物学

RNA Pub Date : 2024-12-16 DOI: 10.1261/rna.080134.124

Laura Peter, Lara Walotka, Johannes Ptok, Caroline Meyer, Dominik Schüller, Heiner Schaal, Lisa Müller

{"title":"Bioinformatics-driven refinement of the commonly used TPI nonsense-mediated decay reporter system.","authors":"Laura Peter, Lara Walotka, Johannes Ptok, Caroline Meyer, Dominik Schüller, Heiner Schaal, Lisa Müller","doi":"10.1261/rna.080134.124","DOIUrl":"10.1261/rna.080134.124","url":null,"abstract":"The cellular nonsense-mediated decay (NMD) pathway recognizes and degrades mRNAs with unusual structural features, such as long 3' UTRs or overlapping reading frames, and therefore serves as a transcript quality control mechanism. A broad spectrum of today's knowledge about the nonsense-mediated mRNA decay pathway has been discovered using NMD reporter systems, mostly consisting of multiple exons, with a wild-type and a premature termination codon-containing variant. In a preliminary NMD study, we used the seven-exon triose phosphate isomerase (TPI) reporter and observed that in this well-known NMD reporter, surprisingly, not all splice sites are used constitutively, but additional cryptic splice sites are used. As this is more frequently observed in the construction of minigenes, especially when unknown splicing regulatory elements (SREs) are removed, for example, by shortening introns, this may affect the reliability of such reporters. To demonstrate how such minigenes can be improved in general with respect to constitutive splice site recognition, we restored an intron length in the TPI reporter or made bioinformatic adjustments to SREs or intrinsic strength of the splice sites themselves. As a result, this NMD reporter could be made more robust and specific for the evaluation of NMD sensitivity within a single transcript. The modifications of the TPI reporter shown here as examples can generally be used for the transfer of cellular multiexon transcripts to minigenes.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"32-42"},"PeriodicalIF":4.2,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11648928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142473666","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

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