IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-03-24 DOI: 10.1080/15476286.2025.2478539

Lei Ji, Youguo Chen, Xiaoping Chen

{"title":"Circular RNA Circ_0002762 promotes cell migration and invasion in cervical squamous cell carcinoma via activating RelA/nuclear factor kappa B (Nf-kB) signalling pathway.","authors":"Lei Ji, Youguo Chen, Xiaoping Chen","doi":"10.1080/15476286.2025.2478539","DOIUrl":"10.1080/15476286.2025.2478539","url":null,"abstract":"Cervical cancer is a leading cause of cancer-related deaths, with cervical squamous cell carcinoma (CSCC) accounting for a majority of cases. Circular RNAs (circRNAs) have been repeatedly suggested as crucial effectors in modulating the development of multiple malignancies. The expression of circ_0002762 was predicted to be high in CSCC tissues in GEO dataset, but the functional role and underlying regulatory mechanism of circ_0002762 in CSCC was unclear. By series of functional assays and mechanism assays, supported by bioinformatics analysis, reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) analysis and western blot assays, we identified that circ_0002762 aberrantly up-regulated in CSCC, promoting CSCC cell migration and invasion. Mechanically, circ_0002762 was transcriptionally activated by Fork head box A1 (FOXA1). Moreover, the involvement of nuclear factor kappa B (NF-kB) signalling in circ_0002762 regulation mechanism in CSCC cells was ascertained. Additionally, circ_0002762, predominantly accumulated in cell cytoplasm, was proved to recruit Mov10 RISC complex RNA helicase (MOV10) to enhance RelA mRNA stability, thus affecting CSCC cell migration and invasion. In summary, FOXA1-mediated circ_0002762 up-regulation could enhance the migratory and invasive abilities of CSCC cells via the MOV10/RelA/NF-kB pathway.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-13"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625775","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 regulatory roles of RNA-binding proteins in the tumour immune microenvironment of gastrointestinal malignancies. rna结合蛋白在胃肠道恶性肿瘤肿瘤免疫微环境中的调控作用。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2024-12-24 DOI: 10.1080/15476286.2024.2440683

Dongqi Li, Xiangyu Chu, Weikang Liu, Yongsu Ma, Xiaodong Tian, Yinmo Yang

{"title":"The regulatory roles of RNA-binding proteins in the tumour immune microenvironment of gastrointestinal malignancies.","authors":"Dongqi Li, Xiangyu Chu, Weikang Liu, Yongsu Ma, Xiaodong Tian, Yinmo Yang","doi":"10.1080/15476286.2024.2440683","DOIUrl":"10.1080/15476286.2024.2440683","url":null,"abstract":"The crosstalk between the tumour immune microenvironment (TIME) and tumour cells promote immune evasion and resistance to immunotherapy in gastrointestinal (GI) tumours. Post-transcriptional regulation of genes is pivotal to GI tumours progression, and RNA-binding proteins (RBPs) serve as key regulators via their RNA-binding domains. RBPs may exhibit either anti-tumour or pro-tumour functions by influencing the TIME through the modulation of mRNAs and non-coding RNAs expression, as well as post-transcriptional modifications, primarily N6-methyladenosine (m6A). Aberrant regulation of RBPs, such as HuR and YBX1, typically enhances tumour immune escape and impacts prognosis of GI tumour patients. Further, while targeting RBPs offers a promising strategy for improving immunotherapy in GI cancers, the mechanisms by which RBPs regulate the TIME in these tumours remain poorly understood, and the therapeutic application is still in its early stages. This review summarizes current advances in exploring the roles of RBPs in regulating genes expression and their effect on the TIME of GI tumours, then providing theoretical insights for RBP-targeted cancer therapies.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-14"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142882916","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

Extracellular vesicle-derived MicroRNAs as potential therapies for spinal cord and peripheral nerve injuries. 细胞外囊泡衍生的microrna作为脊髓和周围神经损伤的潜在治疗方法。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-05-30 DOI: 10.1080/15476286.2025.2512618

Young-Ju Lim, Min-Soo Seo, Wook-Tae Park, Sangbum Park, Gun Woo Lee

引用次数: 0

The hidden power of antisense long non-coding RNAs: a dive into a novel regulatory layer mediated by double-stranded RNA formation. 反义长链非编码RNA的隐藏力量：双链RNA形成介导的新调控层。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-07-09 DOI: 10.1080/15476286.2025.2530797

Jan-Philipp Lamping, Heike Krebber

{"title":"The hidden power of antisense long non-coding RNAs: a dive into a novel regulatory layer mediated by double-stranded RNA formation.","authors":"Jan-Philipp Lamping, Heike Krebber","doi":"10.1080/15476286.2025.2530797","DOIUrl":"10.1080/15476286.2025.2530797","url":null,"abstract":"Over the past decade, non-coding RNAs (ncRNAs) have gained prominence in research due to their widespread presence in cells, yet their functions remain increasingly complex and less understood. Despite being initially deemed 'junk', many lncRNAs are now recognized as key regulators in cells and are often affected in disease contexts. Notably, numerous mRNAs have annotated antisense RNAs (asRNAs). Because asRNAs resemble the largest group of lncRNAs and were identified to serve a general function in Saccharomyces cerevisiae, they are the focus of this review. In S. cerevisiae, the absence of RNA interference (RNAi) enables unbiased study and allowed researchers to investigate their roles in gene regulation more directly with intriguing results, summarized here. Expression of asRNA leads to the formation of double-stranded RNAs (dsRNAs) with the regarding sense counterpart, resulting in enhanced gene expression through preferential nuclear export. Thus, these hidden leaders can boost gene expression and require future attention pivotal for elucidating their influence on biological processes and revealing disease mechanisms.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-16"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12247107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144592109","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 secret life of RNA and lipids. RNA和脂质的秘密生命。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-07-16 DOI: 10.1080/15476286.2025.2526903

Tomasz Czerniak, James P Saenz

{"title":"The secret life of RNA and lipids.","authors":"Tomasz Czerniak, James P Saenz","doi":"10.1080/15476286.2025.2526903","DOIUrl":"10.1080/15476286.2025.2526903","url":null,"abstract":"There is no life without RNA or lipids. But could there be life with only RNA and lipids? The discovery that RNA can catalyse reactions in addition to encoding information opened new directions for engineering life and the possibility of life emerging from an RNA World. But a key missing ingredient for RNA-based biochemical systems is a mechanism to organize RNAs and regulate their activity. Lipids, which are essential for life and one of the most ancient biomolecules, can spontaneously self-assemble to form membranous bilayers, theoretically providing a surface that can serve to concentrate, protect, and regulate RNAs. This review explores the interactions between RNA and lipids, including the chemical basis for their interactions, and the implications for synthetic biology, RNA World, and modern cell biology. We discuss observations that RNA can selectively bind to lipid membranes in a sequence-dependent manner, and entertain how these interactions might be employed to engineer RNA-based sensors and regulatory elements in synthetic systems. The emerging field of RNA-lipid interactions opens new possibilities for engineering orthogonal biochemistries for synthetic cells, innovations in RNA therapeutics, and discovering potentially new facets of cellular regulation.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-28"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12269668/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144560949","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

miR-4484 suppresses hepatocellular carcinoma progression via targeting KIF2C. miR-4484通过靶向KIF2C抑制肝细胞癌进展。

IF 3.4 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-10-04 DOI: 10.1080/15476286.2025.2569192

Jianyang Lin, Yun Cai, Zhihong Chen, Jichun Ma, Kun Zhao

{"title":"miR-4484 suppresses hepatocellular carcinoma progression via targeting KIF2C.","authors":"Jianyang Lin, Yun Cai, Zhihong Chen, Jichun Ma, Kun Zhao","doi":"10.1080/15476286.2025.2569192","DOIUrl":"10.1080/15476286.2025.2569192","url":null,"abstract":"Aberrantly expressed microRNA-4484 (miR-4484) has recently garnered attention for its involvement in human diseases, but its specific role in hepatocellular carcinoma (HCC) remains largely unexplored. This study investigates the function of miR-4484 in HCC progression and its regulatory interaction with KIF2C. Analysis of the data from the TCGA-LIHC database revealed that miR-4484 expression is significantly downregulated in HCC tissues, with lower levels correlating with worse prognosis. In vitro experiments confirmed that miR-4484 expression is lower in HCC cell lines compared to a normal liver cell line. Functional assays demonstrated that miR-4484 overexpression via a miR-4484 mimic suppressed cell proliferation and induced G1 phase arrest, whereas miR-4484 inhibition promoted proliferation and facilitated cell cycle progression from G1 to S and G2 phases. Additionally, KIF2C expression was significantly upregulated in HCC tissues and cell lines, exhibiting an inverse correlation with miR-4484 levels. Dual-Luciferase Reporter Assays confirmed that miR-4484 directly binds to KIF2C, thereby regulating its expression and influencing cell proliferation and cell cycle progression. In vivo, subcutaneous intratumoral injection of the miR-4484 mimic in nude mice significantly inhibited HCC tumour growth. These findings highlight miR-4484 as a potential tumour suppressor in HCC through its direct targeting of KIF2C, underscoring its promise as a therapeutic target for HCC treatment.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-20"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12498537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145207525","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

Altering rRNA 2'O-methylation pattern during neuronal differentiation is regulated by FMRP. 神经元分化过程中rRNA 2' o甲基化模式的改变受FMRP调控。

IF 3.4 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-10-03 DOI: 10.1080/15476286.2025.2563986

Michelle Ninochka D'Souza, Naveen Kumar Chandappa Gowda, Nivedita Hariharan, Syed Wasifa Qadri, Dasaradhi Palakodeti, Ravi S Muddashetty

{"title":"Altering rRNA 2'O-methylation pattern during neuronal differentiation is regulated by FMRP.","authors":"Michelle Ninochka D'Souza, Naveen Kumar Chandappa Gowda, Nivedita Hariharan, Syed Wasifa Qadri, Dasaradhi Palakodeti, Ravi S Muddashetty","doi":"10.1080/15476286.2025.2563986","DOIUrl":"10.1080/15476286.2025.2563986","url":null,"abstract":"The Fragile X Messenger Ribonucleoprotein (FMRP) is a selective RNA-binding protein that localizes to the cytoplasm and the nucleus. The loss of FMRP results in Fragile X Syndrome (FXS), an autism spectrum disorder. FMRP interacts with ribosomes and regulates the translation of mRNAs essential for neuronal development and synaptic plasticity. However, the biochemical nature of this translation regulation is unknown. Here, we report that a potential feature of FMRP-mediated translation regulation during neuronal differentiation is the modulation of 2'-O-methylation of ribosomal RNA. 2'O-methylation, facilitated by C/D box snoRNAs in the nucleus, is a major epitranscriptome mark on rRNA, essential for ribosome assembly and function. We found that FMRP influences a distinct rRNA 2'O-Methylation pattern across neuronal differentiation. We show that in H9 ESCs, FMRP interacts with a selected set of C/D box snoRNA in the nucleus, resulting in the generation of ribosomes with a distinct pattern of rRNA 2'O-Methylation. This epitranscriptome pattern on rRNA undergoes a significant change during the differentiation of ESCs to neuronal precursors and cortical neurons. ESCs exhibit substantial levels of hypomethylated residues on rRNA, which progressively decrease in neuronal precursors and post-mitotic cortical neurons. This reduction correlates with changes in global protein synthesis across different stages of differentiation. Importantly, this stepwise change in the 2'O-methylation pattern during neuronal differentiation is altered in the absence of FMRP, which could impact neuronal development and contribute to dysregulated protein synthesis observed in Fragile X Syndrome.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-22"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12498540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145213567","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

tRNA modifications: greasing the wheels of translation and beyond. tRNA修饰：润滑翻译的车轮和超越。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2024-12-26 DOI: 10.1080/15476286.2024.2442856

Minjie Zhang, Zhipeng Lu

引用次数: 0

Prp16 enables efficient splicing of introns with diverse exonic consensus elements in the short-intron rich Cryptococcus neoformans transcriptome. 在富含短内含子的新型隐球菌转录组中，Prp16能够有效地剪接具有多种外显子一致元件的内含子。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-03-13 DOI: 10.1080/15476286.2025.2477844

Manendra Singh Negi, Vishnu Priya Krishnan, Niharika Saraf, Usha Vijayraghavan

{"title":"Prp16 enables efficient splicing of introns with diverse exonic consensus elements in the short-intron rich Cryptococcus neoformans transcriptome.","authors":"Manendra Singh Negi, Vishnu Priya Krishnan, Niharika Saraf, Usha Vijayraghavan","doi":"10.1080/15476286.2025.2477844","DOIUrl":"10.1080/15476286.2025.2477844","url":null,"abstract":"DEAH box splicing helicase Prp16 in budding yeast governs spliceosomal remodelling from the branching conformation (C complex) to the exon ligation conformation (C* complex). In this study, we examined the genome-wide functions of Prp16 in the short intron-rich genome of the basidiomycete yeast Cryptococcus neoformans. The presence of multiple introns per transcript with intronic features that are more similar to those of higher eukaryotes makes it a promising model for studying spliceosomal splicing. Using a promoter-shutdown conditional Prp16 knockdown strain, we uncovered genome-wide but substrate-specific roles in C. neoformans splicing. The splicing functions of Prp16 are dependent on helicase motifs I and II, which are conserved motifs for helicase activity. A small subset of introns spliced independent of Prp16 activity was investigated to discover that exonic sequences at the 5' splice site (5'SS) and 3' splice site (3'SS) with stronger affinity for U5 loop 1 are a common feature in these introns. Furthermore, short (60-100nts) and ultrashort introns (<60nts) prevalent in the C. neoformans transcriptome were more sensitive to Prp16 knockdown than longer introns, indicating that Prp16 is required for the efficient splicing of short and ultrashort introns. We propose that stronger U5 snRNA-pre-mRNA interactions enable efficient transition of the spliceosome from the first to the second catalytic confirmation in Prp16 knockdown, particularly for short introns and introns with suboptimal features. This study provides insights into fine-tuning spliceosomal helicase function with variations in cis-element features.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-14"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11913375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143597670","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 oncogenic microRNA miR-222 promotes human LINE-1 retrotransposition. 致癌microRNA miR-222促进人类LINE-1逆转录转位。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-06-03 DOI: 10.1080/15476286.2025.2511318

Tomer Friehmann, Yamama Abu Mohsen, Yehuda Schlesinger, Lucy Ghantous, Lika Gamaev, Chavah Landau Zenilman, Avi Harazi, Eithan Galun, Daniel S Goldenberg

{"title":"The oncogenic microRNA miR-222 promotes human LINE-1 retrotransposition.","authors":"Tomer Friehmann, Yamama Abu Mohsen, Yehuda Schlesinger, Lucy Ghantous, Lika Gamaev, Chavah Landau Zenilman, Avi Harazi, Eithan Galun, Daniel S Goldenberg","doi":"10.1080/15476286.2025.2511318","DOIUrl":"10.1080/15476286.2025.2511318","url":null,"abstract":"The Long Interspersed Element-1 (LINE-1) contributes significantly to carcinogenesis and to tumour heterogeneity in many cancer types, including hepatocellular carcinoma (HCC), by its autonomous retrotransposition (RTP) and by its ability to retrotranspose some non-autonomous transposable elements. Previously, multiple proteins and a few microRNAs (miRs) were described as regulators of LINE-1 RTP. Here, we demonstrate that miR-222, which is oncogenic in HCC, promotes LINE-1 RTP in human HCC and some other cell lines in vitro, and that both miR-222-3p and miR-222-5p activate LINE-1 RTP in a cell-type specific manner. We generated miR-222-knockout mutants of the Huh7 and FLC4 hCC cell lines, and performed RNA-seq analysis of Huh7/miR-222-knockout cells and global proteomics analysis of both Huh7 and FLC4 miR-222-knockout mutants. We demonstrate that miR-222 decreases let-7c expression in both Huh7 and FLC4 cells, and that this decrease contributes to promotion of LINE-1 RTP by miR-222 in Huh7 cells.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-15"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151352","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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