IF 4.5 3区生物学

RNA Pub Date : 2024-09-01 DOI: 10.1261/rna.080151.124

Chad D. Torgerson, David A. Hiller, Shira Stav, Scott A. Strobel

引用次数: 0

Corrigendum: Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity 更正：鸟苷-II 核糖开关的翻译调控在灵敏度、动态范围和明显的合作性方面具有高度可调性

IF 4.5 3区生物学

RNA Pub Date : 2024-09-01 DOI: 10.1261/rna.080150.124

Caroline M. Focht, David A. Hiller, Sabrina G. Grunseich, Scott A. Strobel

引用次数: 0

Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription. 腺苷修饰阻碍了 SARS-CoV-2 RNA 依赖性 RNA 转录。

IF 4.2 3区生物学

RNA Pub Date : 2024-08-16 DOI: 10.1261/rna.079991.124

Laura R Snyder, Ingrid Kilde, Artem Nemudryi, Blake Wiedenheft, Markos Koutmos, Kristin S Koutmou

{"title":"Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription.","authors":"Laura R Snyder, Ingrid Kilde, Artem Nemudryi, Blake Wiedenheft, Markos Koutmos, Kristin S Koutmou","doi":"10.1261/rna.079991.124","DOIUrl":"10.1261/rna.079991.124","url":null,"abstract":"SARS-CoV-2, the causative virus of the COVID-19 pandemic, follows SARS and MERS as recent zoonotic coronaviruses causing severe respiratory illness and death in humans. The recurrent impact of zoonotic coronaviruses demands a better understanding of their fundamental molecular biochemistry. Nucleoside modifications, which modulate many steps of the RNA life cycle, have been found in SARS-CoV-2 RNA, although whether they confer a pro- or antiviral effect is unknown. Regardless, the viral RNA-dependent RNA polymerase will encounter these modifications as it transcribes through the viral genomic RNA. We investigated the functional consequences of nucleoside modification on the pre-steady state kinetics of SARS-CoV-2 RNA-dependent RNA transcription using an in vitro reconstituted transcription system with modified RNA templates. Our findings show that N 6-methyladenosine and 2'-O-methyladenosine modifications slow the rate of viral transcription at magnitudes specific to each modification, which has the potential to impact SARS-CoV-2 genome maintenance.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1141-1150"},"PeriodicalIF":4.2,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331411/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141470603","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

Discrete measurements of RNA polymerase and reverse transcriptase fidelity reveal evolutionary tuning. 对 RNA 聚合酶和逆转录酶保真度的离散测量揭示了进化调整。

IF 4.2 3区生物学

RNA Pub Date : 2024-08-16 DOI: 10.1261/rna.080002.124

Vladimir Potapov, Stanislas Krudup, Sean Maguire, Irem Unlu, Shengxi Guan, Jackson A Buss, Benedict A Smail, Trevor van Eeuwen, Martin S Taylor, Kathleen H Burns, Jennifer L Ong, Robert J Trachman

{"title":"Discrete measurements of RNA polymerase and reverse transcriptase fidelity reveal evolutionary tuning.","authors":"Vladimir Potapov, Stanislas Krudup, Sean Maguire, Irem Unlu, Shengxi Guan, Jackson A Buss, Benedict A Smail, Trevor van Eeuwen, Martin S Taylor, Kathleen H Burns, Jennifer L Ong, Robert J Trachman","doi":"10.1261/rna.080002.124","DOIUrl":"10.1261/rna.080002.124","url":null,"abstract":"Direct methods for determining the fidelity of DNA polymerases are robust, with relatively little sample manipulation before sequencing. In contrast, methods for measuring RNA polymerase and reverse transcriptase fidelities are complicated by additional preparation steps that introduce ambiguity and error. Here, we describe a sequencing method, termed Roll-Seq, for simultaneously determining the individual fidelities of RNA polymerases and reverse transcriptases (RT) using Pacific Biosciences single molecule real-time sequencing. By using reverse transcriptases with high rolling-circle activity, Roll-Seq generates long concatemeric cDNA from a circular RNA template. To discern the origin of a mutation, errors are recorded and determined to occur within a single concatemer (reverse transcriptase error) or all concatemers (RNA polymerase error) over the cDNA strand. We used Roll-Seq to measure the fidelities of T7 RNA polymerases, a Group II intron-encoded RT (Induro), and two LINE RTs (Fasciolopsis buski R2-RT and human LINE-1). Substitution rates for Induro and R2-RT are the same for cDNA and second-strand synthesis while LINE-1 has 2.5-fold lower fidelity when performing second-strand synthesis. Deletion and insertion rates increase for all RTs during second-strand synthesis. In addition, we find that a structured RNA template impacts fidelity for both RNA polymerase and RT. The accuracy and precision of Roll-Seq enable this method to be applied as a complementary analysis to structural and mechanistic characterization of RNA polymerases and reverse transcriptases or as a screening method for RNAP and RT fidelity.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1246-1258"},"PeriodicalIF":4.2,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141470604","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

Structure and sequence at an RNA template 5' end influence insertion of transgenes by an R2 retrotransposon protein. RNA 模板 5' 端的结构和序列会影响 R2 逆转录质子蛋白插入转基因。

IF 4.2 3区生物学

RNA Pub Date : 2024-08-16 DOI: 10.1261/rna.080031.124

Sarah M Palm, Connor A Horton, Xiaozhu Zhang, Kathleen Collins

{"title":"Structure and sequence at an RNA template 5' end influence insertion of transgenes by an R2 retrotransposon protein.","authors":"Sarah M Palm, Connor A Horton, Xiaozhu Zhang, Kathleen Collins","doi":"10.1261/rna.080031.124","DOIUrl":"10.1261/rna.080031.124","url":null,"abstract":"R2 non-long terminal repeat retrotransposons insert site-specifically into ribosomal RNA genes (rDNA) in a broad range of multicellular eukaryotes. R2-encoded proteins can be leveraged to mediate transgene insertion at 28S rDNA loci in cultured human cells. This strategy, precise RNA-mediated insertion of transgenes (PRINT), relies on the codelivery of an mRNA encoding R2 protein and an RNA template encoding a transgene cassette of choice. Here, we demonstrate that the PRINT RNA template 5' module, which as a complementary DNA 3' end will generate the transgene 5' junction with rDNA, influences the efficiency and mechanism of gene insertion. Iterative design and testing identified optimal 5' modules consisting of a hepatitis delta virus-like ribozyme fold with high thermodynamic stability, suggesting that RNA template degradation from its 5' end may limit transgene insertion efficiency. We also demonstrate that transgene 5' junction formation can be either precise, formed by annealing the 3' end of first-strand complementary DNA with the upstream target site, or imprecise, by end-joining, but this difference in junction formation mechanism is not a major determinant of insertion efficiency. Sequence characterization of imprecise end-joining events indicates surprisingly minimal reliance on microhomology. Our findings expand the current understanding of the role of R2 retrotransposon transcript sequence and structure, and especially the 5' ribozyme fold, for retrotransposon mobility and RNA-templated gene synthesis in cells.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1227-1245"},"PeriodicalIF":4.2,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141498880","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

Loss of ADAR1 protein induces changes in small RNA landscape in hepatocytes. ADAR1 蛋白的缺失会诱导肝细胞中的小 RNA 结构发生变化。

IF 4.2 3区生物学

RNA Pub Date : 2024-08-16 DOI: 10.1261/rna.080097.124

Kristina Roučová, Václav Vopálenský, Tomáš Mašek, Edgar Del Llano, Jan Provazník, Jonathan J M Landry, Nayara Azevedo, Edvard Ehler, Vladimír Beneš, Martin Pospíšek

{"title":"Loss of ADAR1 protein induces changes in small RNA landscape in hepatocytes.","authors":"Kristina Roučová, Václav Vopálenský, Tomáš Mašek, Edgar Del Llano, Jan Provazník, Jonathan J M Landry, Nayara Azevedo, Edvard Ehler, Vladimír Beneš, Martin Pospíšek","doi":"10.1261/rna.080097.124","DOIUrl":"10.1261/rna.080097.124","url":null,"abstract":"In recent years, numerous evidence has been accumulated about the extent of A-to-I editing in human RNAs and the key role ADAR1 plays in the cellular editing machinery. It has been shown that A-to-I editing occurrence and frequency are tissue-specific and essential for some tissue development, such as the liver. To study the effect of ADAR1 function in hepatocytes, we have created Huh7.5 ADAR1 KO cell lines. Upon IFN treatment, the Huh7.5 ADAR1 KO cells show rapid arrest of growth and translation, from which they do not recover. We analyzed translatome changes by using a method based on sequencing of separate polysome profile RNA fractions. We found significant changes in the transcriptome and translatome of the Huh7.5 ADAR1 KO cells. The most prominent changes include negatively affected transcription by RNA polymerase III and the deregulation of snoRNA and Y RNA levels. Furthermore, we observed that ADAR1 KO polysomes are enriched in mRNAs coding for proteins pivotal in a wide range of biological processes such as RNA localization and RNA processing, whereas the unbound fraction is enriched mainly in mRNAs coding for ribosomal proteins and translational factors. This indicates that ADAR1 plays a more relevant role in small RNA metabolism and ribosome biogenesis.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1164-1183"},"PeriodicalIF":4.2,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141284673","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

Function and mechanism of action of the small regulatory RNA ArcZ in Enterobacterales. 肠杆菌小调控 RNA ArcZ 的功能和作用机制

IF 4.2 3区生物学

RNA Pub Date : 2024-08-16 DOI: 10.1261/rna.080010.124

Quentin Dubois, Typhaine Brual, Charlotte Oriol, Pierre Mandin, Guy Condemine, Erwan Gueguen

{"title":"Function and mechanism of action of the small regulatory RNA ArcZ in Enterobacterales.","authors":"Quentin Dubois, Typhaine Brual, Charlotte Oriol, Pierre Mandin, Guy Condemine, Erwan Gueguen","doi":"10.1261/rna.080010.124","DOIUrl":"10.1261/rna.080010.124","url":null,"abstract":"ArcZ is a small regulatory RNA conserved in Enterobacterales It is an Hfq-dependent RNA that is cleaved by RNase E in a processed form of 55-60 nucleotides. This processed form is highly conserved for controlling the expression of target mRNAs. ArcZ expression is induced by abundant oxygen levels and reaches its peak during the stationary growth phase. This control is mediated by the oxygen-responsive two-component system ArcAB, leading to the repression of arcZ transcription under low-oxygen conditions in most bacteria in which it has been studied. ArcZ displays multiple targets, and it can control up to 10% of a genome and interact directly with more than 300 mRNAs in Escherichia coli and Salmonella enterica ArcZ displays a multifaceted ability to regulate its targets through diverse mechanisms such as RNase recruitment, modulation of ribosome accessibility on the mRNA, and interaction with translational enhancing regions. By influencing stress response, motility, and virulence through the regulation of master regulators such as FlhDC or RpoS, ArcZ emerges as a major orchestrator of cell physiology within Enterobacterales.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1107-1121"},"PeriodicalIF":4.2,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141262745","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

Modeling the structure and DAP5-binding site of the FGF-9 5'-UTR RNA utilized in cap-independent translation. 建立 FGF-9 5' UTR RNA 结构和 DAP5 结合位点的模型，该 RNA 在 Cap 依赖性翻译中使用。

IF 4.2 3区生物学

RNA Pub Date : 2024-08-16 DOI: 10.1261/rna.080013.124

Amanda Whittaker, Dixie J Goss

{"title":"Modeling the structure and DAP5-binding site of the FGF-9 5'-UTR RNA utilized in cap-independent translation.","authors":"Amanda Whittaker, Dixie J Goss","doi":"10.1261/rna.080013.124","DOIUrl":"10.1261/rna.080013.124","url":null,"abstract":"Cap-independent or eukaryotic initiation factor (eIF) 4E-independent, translation initiation in eukaryotes requires scaffolding protein eIF4G or its homolog, death-associated protein 5 (DAP5). eIF4G associates with the 40S ribosomal subunit, recruiting the ribosome to the RNA transcript. A subset of RNA transcripts, such as fibroblast growth factor 9 (FGF-9), contain 5' untranslated regions (5' UTRs) that directly bind DAP5 or eIF4GI. For viral mRNA, eIF recruitment usually utilizes RNA structure, such as a pseudoknot or stem-loops, and the RNA-helicase eIF4A is required for DAP5- or 4G-mediated translation, suggesting these 5' UTRs are structured. However, for cellular IRES-like translation, no consensus RNA structures or sequences have yet been identified for eIF binding. However, the DAP5-binding site within the FGF-9 5' UTR is unknown. Moreover, DAP5 binds to other, dissimilar 5' UTRs, some of which require an unpaired, accessible 5' end to stimulate cap-independent translation. Using SHAPE-seq, we modeled the 186 nt FGF-9 5'-UTR RNA's complex secondary structure in vitro. Further, DAP5 footprinting, toeprinting, and UV cross-linking experiments identify DAP5-RNA interactions. Modeling of FGF-9 5'-UTR tertiary structure aligns DAP5-interacting nucleotides on one face of the predicted structure. We propose that RNA structure involving tertiary folding, rather than a conserved sequence or secondary structure, acts as a DAP5-binding site. DAP5 appears to contact nucleotides near the start codon. Our findings offer a new perspective in the hunt for cap-independent translational enhancers. Structural, rather than sequence-specific, eIF-binding sites may act as attractive chemotherapeutic targets or as dosage tools for mRNA-based therapies.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1184-1198"},"PeriodicalIF":4.2,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141311607","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

Conformational dynamics of the hepatitis C virus 3'X RNA. 丙型肝炎病毒 3'X RNA 的构象动力学。

IF 4.2 3区生物学

RNA Pub Date : 2024-08-16 DOI: 10.1261/rna.079983.124

Parker D Sperstad, Erik D Holmstrom

引用次数: 0

Small molecule telomerase inhibitors are also potent inhibitors of telomeric C-strand synthesis. 小分子端粒酶抑制剂也是端粒 C 链合成的有效抑制剂。

IF 4.2 3区生物学

RNA Pub Date : 2024-08-16 DOI: 10.1261/rna.080043.124

Kaitlin Johnson, Julia M Seidel, Thomas R Cech

{"title":"Small molecule telomerase inhibitors are also potent inhibitors of telomeric C-strand synthesis.","authors":"Kaitlin Johnson, Julia M Seidel, Thomas R Cech","doi":"10.1261/rna.080043.124","DOIUrl":"10.1261/rna.080043.124","url":null,"abstract":"Telomere replication is essential for continued proliferation of human cells, such as stem cells and cancer cells. Telomerase lengthens the telomeric G-strand, while C-strand replication is accomplished by CST-polymerase α-primase (CST-PP). Replication of both strands is inhibited by formation of G-quadruplex (GQ) structures in the G-rich single-stranded DNA. TMPyP4 and pyridostatin (PDS), which stabilize GQ structures in both DNA and RNA, inhibit telomerase in vitro, and in human cells they cause telomere shortening that has been attributed to telomerase inhibition. Here, we show that TMPyP4 and PDS also inhibit C-strand synthesis by stabilizing DNA secondary structures and thereby preventing CST-PP from binding to telomeric DNA. We also show that these small molecules inhibit CST-PP binding to a DNA sequence containing no consecutive guanine residues, which is unlikely to form GQs. Thus, while these \"telomerase inhibitors\" indeed inhibit telomerase, they are also robust inhibitors of telomeric C-strand synthesis. Furthermore, given their binding to GQ RNA and their limited specificity for GQ structures, they may disrupt many other protein-nucleic acid interactions in human cells.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1213-1226"},"PeriodicalIF":4.2,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141451407","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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