IF 4.2 3区生物学

RNA Pub Date : 2025-02-19 DOI: 10.1261/rna.080259.124

Liangliang Wang, Ralph R Weichselbaum, Chuan He

引用次数: 0

Trinucleotide repeat expansion and RNA dysregulation in fragile X syndrome: emerging therapeutic approaches. 脆性X综合征中的三核苷酸重复扩增和RNA失调：新兴的治疗方法。

IF 4.2 3区生物学

RNA Pub Date : 2025-02-19 DOI: 10.1261/rna.080270.124

Suna Jung, Joel D Richter

{"title":"Trinucleotide repeat expansion and RNA dysregulation in fragile X syndrome: emerging therapeutic approaches.","authors":"Suna Jung, Joel D Richter","doi":"10.1261/rna.080270.124","DOIUrl":"10.1261/rna.080270.124","url":null,"abstract":"Fragile X syndrome (FXS) is characterized by intellectual impairment caused by CGG repeat expansion in the FMR1 gene. When repeats exceed 200, they induce DNA methylation of the promoter and the repeat region, resulting in transcriptional silencing of the FMR1 gene and the subsequent loss of FMRP protein. In the past decade or so, research has focused on the role of FMRP as an RNA-binding protein involved in translation inhibition in the brain in FXS model mice, particularly by slowing or stalling ribosome translocation on mRNA. More recent advances have shown that FMRP has a profound role in RNA splicing, at least in some cases by modulating the translation of splicing factor mRNAs. In a surprise, the human FMR1 gene is transcribed in most cases even with a full CGG expansion. However, much of the FMR1 that is produced is misspliced, which can be corrected by splice-switching antisense oligonucleotide (ASO) administration. Other recent findings suggest that inhibition of multiple kinases can demethylate the FMR1 gene and induce the formation of an R-loop in the CGG repeat region, leading to contraction of the repeat and FMRP restoration. These insights are paving the way for possible future therapeutic approaches for this disorder. We highlight the importance of FMRP restoration by ASO-mediated splice switching or CGG repeat modulation as key advances that may lead to successful treatments for FXS.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"307-313"},"PeriodicalIF":4.2,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11874960/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142897134","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

Nuclear RNA-binding proteins meet cytoplasmic viruses. 核 RNA 结合蛋白与细胞质病毒相遇。

IF 4.2 3区生物学

RNA Pub Date : 2025-02-19 DOI: 10.1261/rna.080313.124

Alfredo Castello, Wael Kamel

引用次数: 0

A general RNA-templated RNA extension activity of E. coli RNA polymerase.

IF 4.2 3区生物学

RNA Pub Date : 2025-02-18 DOI: 10.1261/rna.080238.124

Drew Galls, Andreas U Mueller, Emily Greenwald, Andrew Fire

{"title":"A general RNA-templated RNA extension activity of E. coli RNA polymerase.","authors":"Drew Galls, Andreas U Mueller, Emily Greenwald, Andrew Fire","doi":"10.1261/rna.080238.124","DOIUrl":"https://doi.org/10.1261/rna.080238.124","url":null,"abstract":"Multi-subunit \"DNA-dependent\" RNA polymerases (RNAPs) have noncanonical RNA-directed RNA synthesis activity; this allows synthesis of complementary RNA from RNA templates. Such noncanonical RNAP activities are biologically significant, serving RNA pathogens such as hepatitis delta virus (HDV) and contributing to cellular gene regulation. Despite the broad biological implications of these processes, our understanding of the underlying RNAP mechanisms remains incomplete. Using E. coli RNAP, a multi-subunit RNAP, as a model, we describe here the general RNA-templated RNA extension activity of that enzyme. Our data argue that the 3' end of an added RNA template can fold back and pair with upstream bases in the template, creating an intramolecular primer-template duplex as short as 1-2 base pairs. The RNAP then extends this intramolecular duplex, incorporating nucleotides complementary to the template. RNA-templated RNA extension occurred in minutes and did not appear to be suppressed by the presence of a promoter-containing DNA template. Excepting oligonucleotides implicitly designed to prevent any possibility of 3' end self-priming, every RNA template we tested could be extended by the enzyme, highlighting the general nature of this reaction. These data define a general activity of a cellular RNAP. Unrestricted, this activity could contribute to emergence and replication of RNA-based agents such as HDV and viroids; if highly regulated, the activity could limit these same elements.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143450111","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

The PAZ domain of Aedes aegypti Dicer 2 is critical for accurate and high-fidelity size determination of virus-derived small interfering RNAs.

IF 4.2 3区生物学

RNA Pub Date : 2025-02-13 DOI: 10.1261/rna.080149.124

Melinda Reuter, Rhys H Parry, Melanie McDonald, Rommel J Gestuveo, Rozeena Arif, Alexander A Khromykh, Benjamin Brennan, Margus Varjak, Alfredo Castello, Lars Redecke, Esther Schnettler, Alain Kohl

{"title":"The PAZ domain of Aedes aegypti Dicer 2 is critical for accurate and high-fidelity size determination of virus-derived small interfering RNAs.","authors":"Melinda Reuter, Rhys H Parry, Melanie McDonald, Rommel J Gestuveo, Rozeena Arif, Alexander A Khromykh, Benjamin Brennan, Margus Varjak, Alfredo Castello, Lars Redecke, Esther Schnettler, Alain Kohl","doi":"10.1261/rna.080149.124","DOIUrl":"https://doi.org/10.1261/rna.080149.124","url":null,"abstract":"The exogenous siRNA (exo-siRNA) pathway is a critical RNA interference response involved in controlling arbovirus replication in mosquito cells. It is initiated by the detection of viral long double-stranded RNA (dsRNA) by the RNase III enzyme Dicer 2 (Dcr2), which is processed into predominantly 21 nucleotide (nt) virus-derived small interfering RNAs, or vsiRNAs that are taken up by the Argonaute 2 (Ago2) protein to target viral single-stranded RNAs. The detailed understanding of Dicer structure, function and domains owes much to studies outside the context of viral infection and studies in model organisms, and as such how Dcr2 domains contribute to detecting viral dsRNA to mount antiviral responses in infected mosquito cells remains less well understood. Here, we used a Dcr2 reconstitution system in Aedes aegypti derived Dcr2 KO cells to assess the contribution of the PAZ domain to induction of the exo-siRNA pathway following infection with Semliki Forest virus (SFV; Togaviridae, Alphavirus). Amino acids critical for PAZ activity were identified, and loss of PAZ function affected the production of 21 nt vsiRNAs -with enrichment of 22 nt SFV-derived small RNAs observed- and silencing activity. This study establishes PAZ domain's functional contribution to Dcr2 processing of viral dsRNA to 21 nt vsiRNAs.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143415090","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

DIS3L, cytoplasmic exosome catalytic subunit, is essential for development but not cell viability in mice.

IF 4.2 3区生物学

RNA Pub Date : 2025-02-07 DOI: 10.1261/rna.080350.124

Michał Brouze, Marcin Szpila, Areta Magdalena Czerwińska, Wiktor Antczak, Seweryn Mroczek, Tomasz Kuliński, Anna Maria Hojka-Osińska, Dominik Cysewski, Olga Gewartowska, Dorota Adamska, Jakub Gruchota, Ewa Borsuk, Andrzej Dziembowski

{"title":"DIS3L, cytoplasmic exosome catalytic subunit, is essential for development but not cell viability in mice.","authors":"Michał Brouze, Marcin Szpila, Areta Magdalena Czerwińska, Wiktor Antczak, Seweryn Mroczek, Tomasz Kuliński, Anna Maria Hojka-Osińska, Dominik Cysewski, Olga Gewartowska, Dorota Adamska, Jakub Gruchota, Ewa Borsuk, Andrzej Dziembowski","doi":"10.1261/rna.080350.124","DOIUrl":"https://doi.org/10.1261/rna.080350.124","url":null,"abstract":"Among numerous enzymes involved in RNA decay, processive exoribonucleases are the most prominent group responsible for the degradation of the entire RNA molecules. The role of mammalian cytoplasmic 3'-5' exonuclease DIS3L at the organismal level remained unknown. Herein, we established knock-in and knock-out mouse models to study DIS3L functions in mice. DIS3L in mice is indeed a subunit of the cytoplasmic exosome complex, the disruption of which leads to severe embryo degeneration and death in mice soon after implantation. These changes could not be prevented by supplementing extraembryonic tissue with functional DIS3L through the construction of chimeric embryos. Preimplantation Dis3l-/- embryos were unaffected in their morphology and ability to produce functional embryonic stem cells, showing that DIS3L is not essential for cell viability. There were also no major changes at the transcriptome level for both embryonic stem cells and blastocysts, as revealed by RNA sequencing experiments. Notably, however, Dis3l knock-out led to inhibition of the global protein synthesis. These results point to the essential role of DIS3L in mRNA metabolism, which is crucial for proper protein synthesis during embryo development.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143371194","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

Cellular translational enhancer elements that recruit eukaryotic initiation factor 3. 招募真核起始因子的细胞翻译增强因子。

IF 4.2 3区生物学

RNA Pub Date : 2025-01-22 DOI: 10.1261/rna.080310.124

Jiří Koubek, Jaswinder Kaur, Shivani Bhandarkar, Cole J T Lewis, Rachel O Niederer, Andrei Stanciu, Colin Echeverría Aitken, Wendy V Gilbert

{"title":"Cellular translational enhancer elements that recruit eukaryotic initiation factor 3.","authors":"Jiří Koubek, Jaswinder Kaur, Shivani Bhandarkar, Cole J T Lewis, Rachel O Niederer, Andrei Stanciu, Colin Echeverría Aitken, Wendy V Gilbert","doi":"10.1261/rna.080310.124","DOIUrl":"10.1261/rna.080310.124","url":null,"abstract":"Translation initiation is a highly regulated process that broadly affects eukaryotic gene expression. Eukaryotic initiation factor 3 (eIF3) is a central player in canonical and alternative pathways for ribosome recruitment. Here, we have investigated how direct binding of eIF3 contributes to the large and regulated differences in protein output conferred by different 5'-untranslated regions (5' UTRs) of cellular mRNAs. Using an unbiased high-throughput approach to determine the affinity of budding yeast eIF3 for native 5' UTRs from 4252 genes, we demonstrate that eIF3 binds specifically to a subset of 5' UTRs that contain a short unstructured binding motif, AMAYAA. eIF3-binding mRNAs have higher ribosome density in growing cells and are preferentially translated under certain stress conditions, supporting the functional relevance of this interaction. Our results reveal a new class of translational enhancers and suggest a mechanism by which changes in core initiation factor activity enact mRNA-specific translation programs.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"193-207"},"PeriodicalIF":4.2,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142772143","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

An MST-based assay reveals new binding preferences of IFIT1 for canonically and noncanonically capped RNAs. 基于mst的分析揭示了IFIT1对常规和非常规封顶rna的新结合偏好。

IF 4.2 3区生物学

RNA Pub Date : 2025-01-22 DOI: 10.1261/rna.080089.124

Tomasz Spiewla, Katarzyna Grab, Anais Depaix, Kamil Ziemkiewicz, Marcin Warminski, Jacek Jemielity, Joanna Kowalska

{"title":"An MST-based assay reveals new binding preferences of IFIT1 for canonically and noncanonically capped RNAs.","authors":"Tomasz Spiewla, Katarzyna Grab, Anais Depaix, Kamil Ziemkiewicz, Marcin Warminski, Jacek Jemielity, Joanna Kowalska","doi":"10.1261/rna.080089.124","DOIUrl":"10.1261/rna.080089.124","url":null,"abstract":"IFITs (interferon-induced proteins with tetratricopeptide repeats) are components of the innate immune response that bind to viral and cellular RNA targets to inhibit translation and replication. The RNA target recognition is guided by molecular patterns, particularly at the RNA 5' ends. IFIT1 preferably binds RNAs modified with the m7G cap-0 structure, while RNAs with cap-1 structure are recognized with lower affinity. Less is known about the propensity of IFIT1 to recognize noncanonical RNA 5' ends, including hypermethylated and noncanonical RNA caps. Further insights into the structure-function relationship for IFIT1-RNA interactions are needed but require robust analytical methods. Here, we report a biophysical assay for quick, direct, in-solution affinity assessment of differently capped RNAs with IFIT1. The procedure, which relies on measuring microscale thermophoresis of fluorescently labeled protein as a function of increasing ligand concentration, is applicable to RNAs of various lengths and sequences without the need for their labeling or affinity tagging. Using the assay, we examined 13 canonically and noncanonically 5'-capped RNAs, revealing new binding preferences of IFIT1. The 5' terminal m6A mark in the m7G cap had a protective function against IFIT1, which was additive with the effect observed for the 2'-O position (m6Am cap-1). In contrast, an increased affinity for IFIT1 was observed for several noncanonical caps, including trimethylguanosine, unmethylated (G), and flavin-adenine dinucleotide caps. The results suggest new potential cellular targets of IFIT1 and may contribute to broadening the knowledge of the innate immune response mechanisms and the more effective design of chemically modified mRNAs.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"181-192"},"PeriodicalIF":4.2,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792360","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

Mitochondrial mRNA and the small subunit rRNA in budding yeasts undergo 3'-end processing at conserved species-specific elements. 芽殖酵母的线粒体 mRNA 和小亚基 rRNA 在保守的物种特异性元件上进行 3'- 末端加工。

IF 4.2 3区生物学

RNA Pub Date : 2025-01-22 DOI: 10.1261/rna.080254.124

Michael Anikin, Michael F Henry, Viktoria Hodorova, Hristo B Houbaviy, Jozef Nosek, Dimitri G Pestov, Dmitriy A Markov

{"title":"Mitochondrial mRNA and the small subunit rRNA in budding yeasts undergo 3'-end processing at conserved species-specific elements.","authors":"Michael Anikin, Michael F Henry, Viktoria Hodorova, Hristo B Houbaviy, Jozef Nosek, Dimitri G Pestov, Dmitriy A Markov","doi":"10.1261/rna.080254.124","DOIUrl":"10.1261/rna.080254.124","url":null,"abstract":"Respiration in eukaryotes depends on mitochondrial protein synthesis, which is performed by organelle-specific ribosomes translating organelle-encoded mRNAs. Although RNA maturation and stability are central events controlling mitochondrial gene expression, many of the molecular details in this pathway remain elusive. These include cis- and trans-regulatory factors that generate and protect the 3' ends. Here, we mapped the 3' ends of mitochondrial mRNAs of yeasts classified into multiple families of the subphylum Saccharomycotina. We found that the processing of mitochondrial 15S rRNA and mRNAs involves species-specific sequence elements, which we term 3'-end RNA processing elements (3'-RPEs). In Saccharomyces cerevisiae, the 3'-RPE has long been recognized as a conserved dodecamer sequence, which recent studies have shown specifically interacts with the nuclear genome-encoded pentatricopeptide repeat protein Rmd9. We also demonstrate that, analogous to Rmd9 in S. cerevisiae, two Rmd9 orthologs from the Debaryomycetaceae family interact with their respective 3'-RPEs found in mRNAs and 15S rRNA. Thus, Rmd9-dependent processing of mitochondrial RNA precursors may be a common mechanism among the families of the Saccharomycotina subphylum. Surprisingly, we observed that 3'-RPEs often occur upstream of stop codons in complex I subunit mRNAs from yeasts of the CUG-Ser1 clade. We examined two of these mature mRNAs and found that their stop codons are indeed removed. Thus, translation of these stop-codon-less transcripts would require a noncanonical termination mechanism. Our findings highlight Rmd9 as a key evolutionarily conserved factor in both mitochondrial mRNA metabolism and mitoribosome biogenesis in a variety of yeasts.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"208-223"},"PeriodicalIF":4.2,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142688618","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

Microbial iCLIP2: enhanced mapping of RNA-protein interaction by promoting protein and RNA stability. 微生物iCLIP2：通过促进蛋白质和RNA的稳定性来增强RNA-蛋白相互作用的定位。

IF 4.2 3区生物学

RNA Pub Date : 2025-01-22 DOI: 10.1261/rna.080193.124

Nina Kim Stoffel, Srimeenakshi Sankaranarayanan, Kira Müntjes, Nadine Körtel, Anke Busch, Kathi Zarnack, Julian König, Michael Feldbrügge

{"title":"Microbial iCLIP2: enhanced mapping of RNA-protein interaction by promoting protein and RNA stability.","authors":"Nina Kim Stoffel, Srimeenakshi Sankaranarayanan, Kira Müntjes, Nadine Körtel, Anke Busch, Kathi Zarnack, Julian König, Michael Feldbrügge","doi":"10.1261/rna.080193.124","DOIUrl":"10.1261/rna.080193.124","url":null,"abstract":"The entire RNA life cycle, spanning from transcription to decay, is intricately regulated by RNA-binding proteins (RBPs). To understand their precise functions, it is crucial to identify direct targets, pinpoint their exact binding sites, and unravel the underlying specificity in vivo. Individual-nucleotide resolution UV cross-linking and immunoprecipitation 2 (iCLIP2) is a state-of-the-art technique that enables the identification of RBP-binding sites at single-nucleotide resolution. However, in the field of microbiology, optimized iCLIP protocols compared to mammalian systems are lacking. Here, we present the first microbial iCLIP2 approach using the multi-RRM domain protein Rrm4 from the fungus Ustilago maydis as an example. Key challenges, such as inherently high RNase and protease activity in fungi, were addressed by improving mechanical cell disruption and lysis buffer composition. Our modifications increased the yield of cross-link events and improved the identification of Rrm4-binding sites. Thereby, we were able to pinpoint that Rrm4 binds the stop codons of nuclear-encoded mRNAs of mitochondrial respiratory complexes I, III, and V-revealing an intimate link between endosomal mRNA transport and mitochondrial physiology. Thus, our study using U. maydis as an example might serve as a blueprint for optimizing iCLIP2 procedures in other microorganisms with high RNase/protease conditions.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"258-272"},"PeriodicalIF":4.2,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808020","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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