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Contributions of folded and disordered domains to RNA binding by HNRNPR. 折叠和无序结构域对HNRNPR RNA结合的贡献。
IF 4.3 3区 生物学
RNA Pub Date : 2026-10-16 DOI: 10.1261/rna.081142.126
Bryan B Guzmán, Alli Jimenez, Grant A Goda, Justin G Martyr, Yue Hu, Francisco F Cavazos, Maria M Aleman, Daniel Dominguez
{"title":"Contributions of folded and disordered domains to RNA binding by HNRNPR.","authors":"Bryan B Guzmán, Alli Jimenez, Grant A Goda, Justin G Martyr, Yue Hu, Francisco F Cavazos, Maria M Aleman, Daniel Dominguez","doi":"10.1261/rna.081142.126","DOIUrl":"10.1261/rna.081142.126","url":null,"abstract":"<p><p>RNA binding proteins (RBPs) interact with and tightly regulate the fate of messenger RNAs, but how RNA targets are recognized remains a challenging question. RBPs often contain multiple domains known to directly bind RNA, such as RNA recognition motifs (RRMs), as well as domains whose RNA binding capacity remains incompletely understood, for example, low complexity domains (LCDs). Here, we dissect HNRNPR, an RBP with three RRMs and an arginine-glycine rich (RG-rich) LCD. We apply unbiased high-throughput biochemical approaches and identify critical RNA binding domains that confer specificity toward AU-rich RNA sequences. We show that not all RRMs contribute equally to binding and find that RRM3, along with a downstream C-terminal charged region, is required for RNA binding. HNRNPR also binds RNA G-quadruplexes (rG4s) and contains multiple rG4 binding sites, including the C-terminal charged region within RRM3 and RG-rich regions within the LCD. We dissect rG4 specificity for the full length HNRNPR and LCD using a newly created RNA pool focused on rG4s, reveal that binding is dependent on RNA folding, and find specific rG4 features that enhance HNRNPR-rG4 interactions. Our work highlights the complex interplay of folded and disordered regions within RBPs as mediators of RNA binding.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1729-1748"},"PeriodicalIF":4.3,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148713512","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
Improving RNA secondary structure prediction through expanded training data. 通过扩展训练数据改进RNA二级结构预测。
IF 4.3 3区 生物学
RNA Pub Date : 2026-10-16 DOI: 10.1261/rna.081259.126
Conner J Langeberg, Taehan Kim, Roma Nagle, Agni Rajinikanth, Charlotte Meredith, Dimple Amitha Garuadapuri, Jennifer A Doudna, Jamie H D Cate
{"title":"Improving RNA secondary structure prediction through expanded training data.","authors":"Conner J Langeberg, Taehan Kim, Roma Nagle, Agni Rajinikanth, Charlotte Meredith, Dimple Amitha Garuadapuri, Jennifer A Doudna, Jamie H D Cate","doi":"10.1261/rna.081259.126","DOIUrl":"10.1261/rna.081259.126","url":null,"abstract":"<p><p>In recent years, deep learning has revolutionized protein structure prediction, achieving remarkable speed and accuracy. RNA structure prediction, however, has lagged behind. Although several methods have shown moderate success in predicting RNA secondary and tertiary structures, none have reached the accuracy observed with contemporary protein models. The lack of success of these RNA structure prediction models has been proposed to be due to limited high-quality structural information that can be used as training data. To probe this proposed limitation, we developed a large and diverse data set comprising paired RNA sequences and their corresponding secondary structures. We assessed the utility of this enhanced data set by retraining a deep-learning model, SincFold. We find that SincFold exhibited improved performance on a set of previously unseen RNA families, enhancing its capability to predict accurate de novo RNA secondary structures. We additionally implemented Lyra-TransPred, which achieved the highest mean F1 and MCC among the evaluated models while requiring substantially less training time per epoch. The RNASSTR data set provides a substantial advance for RNA structure modeling, laying a strong foundation for the development of future RNA secondary structure prediction algorithms.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1687-1700"},"PeriodicalIF":4.3,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148876112","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
Improving the dynamic range of a trimethoprim-responsive self-amplifying RNA. 改进甲氧苄啶反应自扩增RNA的动态范围。
IF 4.3 3区 生物学
RNA Pub Date : 2026-10-16 DOI: 10.1261/rna.080982.126
Pieter Vervaeke, Francis Combes, Niek N Sanders
{"title":"Improving the dynamic range of a trimethoprim-responsive self-amplifying RNA.","authors":"Pieter Vervaeke, Francis Combes, Niek N Sanders","doi":"10.1261/rna.080982.126","DOIUrl":"10.1261/rna.080982.126","url":null,"abstract":"<p><p>Self-amplifying mRNA (SAM) is a potential platform for protein replacement, as it enables recipients to transiently produce a therapeutic protein for 4-8 weeks. To obtain external control over the level and duration of protein expression, synthetic SAM constructs that switch OFF in the presence of a small molecule such as trimethoprim (TMP) have been developed in the past. Here, we increase the ON-state protein expression of such a TMP-responsive SAM by fusing the effector protein L7Ae to a TMP-responsive destabilizing domain (DD) on both terminals. We also lower the OFF-state by adding a duplicate of the SAM 3'UTR downstream from the <i>DD-L7Ae</i> subgenomic ORF. We demonstrate that fusing two DDs to L7Ae has a beneficial effect on the response rate and level of protein production after removal or addition of TMP. We further demonstrate that overexpression of DD-L7Ae results in microscopic abnormalities. These insights are implemented in a mechanistic model, and further improvements of the platform are highlighted.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1701-1713"},"PeriodicalIF":4.3,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148851536","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
Sense-antisense RNA duplexes mediate stress-responsive translational control in Plasmodium falciparum. 义-反义RNA双链介导恶性疟原虫应激反应性翻译控制。
IF 4.3 3区 生物学
RNA Pub Date : 2026-10-16 DOI: 10.1261/rna.081149.126
Rashim Malhotra, Kushankur Pandit, Pawan Malhotra, Krishanpal Karmodiya
{"title":"Sense-antisense RNA duplexes mediate stress-responsive translational control in <i>Plasmodium falciparum</i>.","authors":"Rashim Malhotra, Kushankur Pandit, Pawan Malhotra, Krishanpal Karmodiya","doi":"10.1261/rna.081149.126","DOIUrl":"10.1261/rna.081149.126","url":null,"abstract":"<p><p><i>Plasmodium falciparum</i>, the primary cause of human malaria, relies on tightly coordinated gene-expression programs to adapt to host-derived stress despite possessing a limited repertoire of canonical transcription factors. Antisense long noncoding RNAs have emerged as important regulators of parasite biology, including virulence gene regulation and sexual commitment; however, their prevalence, origin, and broader functional significance remain poorly understood. Here, we demonstrate that antisense transcription is a widespread, reproducible, and regulated feature of the <i>P. falciparum</i> transcriptome rather than a by-product of pervasive euchromatic transcription. Environmental stress, including febrile temperature exposure and artemisinin treatment, extensively remodeled antisense transcription, particularly at loci associated with virulence and stress adaptation, promoting widespread sense-antisense RNA duplex formation. Functional analyses of two stress-responsive chromatin regulators, <i>PfGCN5</i> and <i>PfHDAC1</i>, identified as antisense-expressing loci, revealed that increased antisense expression elevated steady-state mRNA abundance while reducing cognate protein levels. Mechanistically, sense-antisense RNA duplex formation stabilized complementary transcripts but suppressed translation. Integrated transcriptomic, RNA-RNA duplex profiling, ribosome sequencing, and proteomic analyses further showed that duplex-enriched transcripts exhibit reduced ribosome occupancy and reduced protein abundance, accompanied by localized antisense enrichment near transcription end sites and altered ribosome distribution consistent with impaired translational engagement. Collectively, our findings identify an antisense RNA-ribosome regulatory axis that couples RNA duplex formation to adaptive translational control, providing a previously unrecognized mechanism underlying stress adaptation and posttranscriptional gene regulation in <i>P. falciparum</i>.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1765-1786"},"PeriodicalIF":4.3,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148707564","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
Revisiting the in vivo functions of coilin in mice: requirement for snRNA modifications and formation of novel condensates in elongating spermatids. 重新审视小鼠体内卷曲蛋白的功能:细长精子中snRNA修饰和新凝聚物形成的需求。
IF 4.3 3区 生物学
RNA Pub Date : 2026-10-16 DOI: 10.1261/rna.080484.125
Miyu Ichii, Yuma Ishigami, Xiao Yao, Jianxi Li, Josei Sato, Yuki Okada, Atsushi P Kimura, Mari Mito, Shintaro Iwasaki, Yasuyuki Kurihara, Taichi Noda, Kimi Araki, Masato Ohtsuka, Saki Ohazama, Hiroshi Maita, Tsutomu Suzuki, Shinichi Nakagawa
{"title":"Revisiting the in vivo functions of coilin in mice: requirement for snRNA modifications and formation of novel condensates in elongating spermatids.","authors":"Miyu Ichii, Yuma Ishigami, Xiao Yao, Jianxi Li, Josei Sato, Yuki Okada, Atsushi P Kimura, Mari Mito, Shintaro Iwasaki, Yasuyuki Kurihara, Taichi Noda, Kimi Araki, Masato Ohtsuka, Saki Ohazama, Hiroshi Maita, Tsutomu Suzuki, Shinichi Nakagawa","doi":"10.1261/rna.080484.125","DOIUrl":"10.1261/rna.080484.125","url":null,"abstract":"<p><p>Cajal bodies (CBs), first identified in the early 20th century, are classic nuclear structures organized primarily by the protein coilin. Although CBs have long been implicated in snRNA modification and maturation, their precise roles in mice remain unclear. Here, we revisit the functions of CBs by using genome editing to generate mice that lack nearly the entire coilin protein, retaining only the first seven amino acids. Mass-spectrometry analyses showed reduced 2'-<i>O</i>-methylation of U2 snRNA in <i>coilin</i> mutant liver; however, these reductions had minimal impact on overall gene expression and pre-mRNA splicing patterns. Additionally, detailed analysis recapitulated previously reported testicular size reductions and newly revealed decreased proportions of high-quality sperm. We also identified novel coilin-containing condensates distinct from genuine CBs in the nuclear pocket of elongating spermatids. Our findings imply that coilin orchestrates membraneless organelles in various compartments, playing multifunctional roles beyond classical CB formation.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1787-1804"},"PeriodicalIF":4.3,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148814017","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
Identification of cellular double-stranded RNAs in mammalian embryonic stem cells. 哺乳动物胚胎干细胞细胞双链rna的鉴定。
IF 4.3 3区 生物学
RNA Pub Date : 2026-10-16 DOI: 10.1261/rna.081048.126
Katharina J Kases, Pilar G Marchante, Jeroen Witteveldt, Guillermo Peris, Grzegorz Kudla, Sara R Heras, Sara Macias
{"title":"Identification of cellular double-stranded RNAs in mammalian embryonic stem cells.","authors":"Katharina J Kases, Pilar G Marchante, Jeroen Witteveldt, Guillermo Peris, Grzegorz Kudla, Sara R Heras, Sara Macias","doi":"10.1261/rna.081048.126","DOIUrl":"10.1261/rna.081048.126","url":null,"abstract":"<p><p>Antiviral defense mechanisms are typically activated upon sensing virus-derived nucleic acids. During replication, viruses generate double-stranded RNA (dsRNA) intermediates that the innate immune system can sense, triggering several defense pathways. Conversely, mammalian cells avoid accumulating their own endogenous dsRNA to prevent activating these defense mechanisms. However, we demonstrate that mammalian embryonic stem cells (ESCs) accumulate endogenous dsRNA without activating these responses, as they lack all classical dsRNA-mediated antiviral pathways. To identify these endogenous dsRNAs, we have developed a two-step purification method that includes an antibody-based immunoprecipitation followed by RNase I treatment to remove single-stranded RNA regions that do not contribute to dsRNA formation. RNase I treatment results in an enrichment of overlapping sense/antisense transcripts containing A-to-I editing sites, suggesting successful purification of cellular dsRNA. Our refined protocol reveals that transposable elements (TEs), including evolutionary young elements from the LINE and LTR classes, are the predominant source of dsRNA in ESCs. This approach will be useful for investigating the role of dsRNA in disease settings, such as autoimmunity or cancer, where endogenous dsRNA accumulation has also been observed.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1714-1728"},"PeriodicalIF":4.3,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148851498","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
Yeast Rai1p and the RAC complex (Ssz1p/Zuo1p) modulate uORF-mediated GCN4 translational control under stress conditions. 酵母Rai1p和RAC复合物(Ssz1p/Zuo1p)在逆境条件下调节uorf介导的GCN4翻译控制。
IF 4.3 3区 生物学
RNA Pub Date : 2026-10-16 DOI: 10.1261/rna.081039.126
Kristína Jendruchová, Adriana Šubrtová, Leoš Shivaya Valášek
{"title":"Yeast Rai1p and the RAC complex (Ssz1p/Zuo1p) modulate uORF-mediated <i>GCN4</i> translational control under stress conditions.","authors":"Kristína Jendruchová, Adriana Šubrtová, Leoš Shivaya Valášek","doi":"10.1261/rna.081039.126","DOIUrl":"10.1261/rna.081039.126","url":null,"abstract":"<p><p>Translation reinitiation (REI) is one of the most important gene-specific regulatory mechanisms by which eukaryotic cells influence expression of main translons, for example, during highly conserved integrated stress response (ISR). In <i>Saccharomyces cerevisiae</i>, expression of the key stress response gene, <i>GCN4</i>, is controlled by an intricate interplay among four short upstream translons (uTranslons, formerly uORFs), resulting in high or low levels of REI at <i>GCN4</i> depending on the growth conditions. Under nutrient-rich conditions, <i>GCN4</i> expression is repressed, but upon amino acid starvation, it is derepressed, despite a general translational shutdown. Capitalizing on our screening reporter system, we identified three new factors influencing efficiency of REI after translation of <i>GCN4</i> uTranslons: Rai1p (an RNA quality control and processing factor), and Ssz1p and Zuo1p (members of the ribosome associated complex [RAC]). Importantly, we showed that depletion of these factors deregulated derepression of Gcn4p synthesis under starvation. Furthermore, we found that similar to RAC, Rai1p associates with 40S subunits and actively translating ribosomes. We also explored interactomes of these proteins. Collectively, we present three previously unknown factors that coregulate stress response to amino acid starvation in the budding yeast by unique mechanisms.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1805-1822"},"PeriodicalIF":4.3,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674258/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148797716","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
Seed pairing between a small regulatory RNA and target mRNA determines cleavage by an RNase E with a minimal C-terminal scaffold. 小调控RNA和目标mRNA之间的种子配对决定了RNase E与最小c端支架的切割。
IF 4.3 3区 生物学
RNA Pub Date : 2026-10-16 DOI: 10.1261/rna.080914.125
Carlos Vega Valle, Karine Prévost, David Lalaouna, Eric Massé
{"title":"Seed pairing between a small regulatory RNA and target mRNA determines cleavage by an RNase E with a minimal C-terminal scaffold.","authors":"Carlos Vega Valle, Karine Prévost, David Lalaouna, Eric Massé","doi":"10.1261/rna.080914.125","DOIUrl":"10.1261/rna.080914.125","url":null,"abstract":"<p><p>Small regulatory RNAs (sRNAs) can specifically bind to their target mRNAs to inhibit their expression, either by promoting degradation or by blocking translation. However, the molecular determinants that select which repression mode an sRNA employs remain poorly understood. To investigate this, we used the model target mRNA <i>hdeD</i>, which is repressed by two sRNAs, CyaR and RprA, both of which use distinct modes of repression. Whereas CyaR promotes the target mRNA <i>hdeD</i> degradation, the sRNA RprA specifically blocks <i>hdeD</i> translation initiation, leaving <i>hdeD</i> mRNA intact. We found that mutating two nucleotides in the seed pairing region of RprA with <i>hdeD</i> is sufficient to switch its mode of repression from translation inhibition to degradation by recruiting RNase E. We investigated this further by using various RNase E deletion mutants of the C-terminal domain (CTD). Among these was an RNase E mutant deleted to contain a minimal C-terminal scaffold (<i>rne</i> 701), a form which typically fails to promote sRNA-induced mRNA degradation. Our data indicated that even with a minimal scaffold, the mutated RprA sRNA still promoted <i>hdeD</i> mRNA degradation, whereas the native sRNA CyaR could not. Our data suggested that the mutated RprA sRNA relies primarily on the arginine-rich RNA-binding (ARRBD) domain of RNase E to induce target mRNA <i>hdeD</i> degradation. This suggests that the mutated RprA sRNA requires fewer components of the CTD of RNase E and RNA degradosome to induce target mRNA degradation.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1749-1764"},"PeriodicalIF":4.3,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148797649","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 moonlighting functions of SEC13 in nonsense-mediated mRNA decay and the regulation of ER stress. SEC13在无义介导的mRNA衰变和内质网应激调控中的兼职功能。
IF 4.3 3区 生物学
RNA Pub Date : 2026-10-16 DOI: 10.1261/rna.081099.126
Laura Monaghan, Chetan Srinath, Abigail R Mann, Nila Roy Choudhury, Graeme R Grimes, Dasa Longman, Javier F Cáceres
{"title":"The moonlighting functions of SEC13 in nonsense-mediated mRNA decay and the regulation of ER stress.","authors":"Laura Monaghan, Chetan Srinath, Abigail R Mann, Nila Roy Choudhury, Graeme R Grimes, Dasa Longman, Javier F Cáceres","doi":"10.1261/rna.081099.126","DOIUrl":"10.1261/rna.081099.126","url":null,"abstract":"<p><p>The nonsense-mediated decay pathway (NMD) is an RNA quality control mechanism that regulates the stability of target RNAs. We previously identified the ER-localized SEC13 protein as a novel NMD factor in <i>Caenorhabditis elegans</i> and in HeLa cells; raising the possibility that it could be involved in regulating the stability of mRNAs translated at the ER. SEC13 is a component of several cellular complexes, including te COPII vesicle coat, the nuclear pore complex (NPC) and the nutrient sensing GATOR2 complex. Here, we show that SEC13 interacts with core NMD factors, and using a newly developed dual-color fluorescent NMD sensor in U2OS cells, we assessed SEC13 NMD activity at a single-cell level. Transcriptomic profiling revealed that unlike the previously described ER-NMD factor, NBAS, SEC13 co-regulates the stability of substrates translated both in the cytoplasm and at the ER. We also show that SEC13 function in NMD is largely independent of its function in other cellular complexes. Altogether, these results show that SEC13 is a bona fide NMD factor in mammalian cells. Finally, we utilized an ER stress-activated indicator (ERAI) in U2OS cells to demonstrate that SEC13, together with canonical NMD factors, has a role in the regulation of the unfolded protein response (UPR) at the ER. Thus, the moonlighting functions of SEC13 include a role in the NMD pathway and the regulation of ER stress.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1837-1856"},"PeriodicalIF":4.3,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148881453","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
Cellular signal-responsive m5C editing by an inducible split CRISPR platform. 诱导分裂CRISPR平台的细胞信号响应性m5C编辑。
IF 4.3 3区 生物学
RNA Pub Date : 2026-10-16 DOI: 10.1261/rna.081049.126
Chanjuan Dong, Ying Xu, Kellie Wu, Nathan Mu, Satendra Kumar, Fu-Sen Liang
{"title":"Cellular signal-responsive m<sup>5</sup>C editing by an inducible split CRISPR platform.","authors":"Chanjuan Dong, Ying Xu, Kellie Wu, Nathan Mu, Satendra Kumar, Fu-Sen Liang","doi":"10.1261/rna.081049.126","DOIUrl":"10.1261/rna.081049.126","url":null,"abstract":"<p><p>RNA 5-methylcytidine (m<sup>5</sup>C) modification plays an essential role in regulating RNA metabolism and functions in cellular processes. Tools to achieve temporal and transcript-specific m<sup>5</sup>C editing for functional studies are still limited. Furthermore, methods enabling m<sup>5</sup>C editing triggered by specific cellular signals to study m<sup>5</sup>C functions are currently lacking. Here, we present a temporally and conditionally controlled m<sup>5</sup>C writing platform engineered through integrating abscisic acid (ABA)-mediated chemically induced proximity with split-dCas13b-NSUN2/NSUN6 technology. This system enables the writing of m<sup>5</sup>C by reconstituting the split dCas13b-based m<sup>5</sup>C editing complex at the guide RNA (gRNA)-targeted RNA transcript sites under the control of the inducer ABA. The deposition of m<sup>5</sup>C is inducible, reversible and selective. The deposited m<sup>5</sup>C is biologically active and influences the stability of endogenous mRNA transcripts. Moreover, by incorporating ABA prodrugs, the m<sup>5</sup>C writing can be triggered by signals associated with distinct physiological or disease conditions (e.g., tumor microenvironment and senescence). This conditional m<sup>5</sup>C editing strategy provides a new programmable tool for studying m<sup>5</sup>C biology in a context-dependent manner and expands the repertoire of RNA modification editing technologies.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1823-1836"},"PeriodicalIF":4.3,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674257/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148876037","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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