Non-Coding RNA最新文献_第2页

Identification of Tumor-Suppressive miR-30a-3p Controlled Genes: ANLN as a Therapeutic Target in Breast Cancer. 肿瘤抑制miR-30a-3p控制基因的鉴定：ANLN作为乳腺癌的治疗靶点。

IF 3.6

Non-Coding RNA Pub Date : 2024-11-30 DOI: 10.3390/ncrna10060060

Reiko Mitsueda, Ayako Nagata, Hiroko Toda, Yuya Tomioka, Ryutaro Yasudome, Mayuko Kato, Yoshiaki Shinden, Akihiro Nakajo, Naohiko Seki

{"title":"Identification of Tumor-Suppressive miR-30a-3p Controlled Genes: ANLN as a Therapeutic Target in Breast Cancer.","authors":"Reiko Mitsueda, Ayako Nagata, Hiroko Toda, Yuya Tomioka, Ryutaro Yasudome, Mayuko Kato, Yoshiaki Shinden, Akihiro Nakajo, Naohiko Seki","doi":"10.3390/ncrna10060060","DOIUrl":"10.3390/ncrna10060060","url":null,"abstract":"Our recently created RNA-sequence-based microRNA (miRNA) expression signature in breast cancer clinical specimens revealed that some miR-30 family members were significantly downregulated in cancer tissues. Based on TCGA database analyses, we observed that among the miR-30 family members, miR-30a-3p (the passenger strand derived from pre-miR-30a) was significantly downregulated in breast cancer (BC) clinical specimens, and its low expression predicted worse prognoses. Ectopic expression assays showed that miR-30a-3p transfected cancer cells (MDA-MB-157 and MDA-MB-231) had their aggressive phenotypes significantly suppressed, e.g., their proliferation, migration, and invasion abilities. These data indicated that miR-30a-3p acted as a tumor-suppressive miRNA in BC cells. Our subsequent search for miR-30a-3p controlled molecular networks in BC cells yielded a total of 189 genes. Notably, among those 189 genes, cell-cycle-related genes (ANLN, MKI67, CCNB1, NCAPG, ZWINT, E2F7, PDS5A, RIF1, BIRC5, MAD2L1, CACUL1, KIF23, UBE2S, EML4, SEPT10, CLTC, and PCNP) were enriched according to a GeneCodis 4 database analysis. Moreover, the overexpression of four genes (ANLN, CCNB1, BIRC5, and KIF23) significantly predicted worse prognoses for patients with BC according to TCGA analyses. Finally, our assays demonstrated that the overexpression of ANLN had cancer-promoting functions in BC cells. The involvement of miR-30a-3p (the passenger strand) in BC molecular pathogenesis is a new concept in cancer research, and the outcomes of our study strongly indicate the importance of analyzing passenger strands of miRNAs in BC cells.","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"10 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11677261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SVALKA: A Long Noncoding Cis-Natural Antisense RNA That Plays a Role in the Regulation of the Cold Response of Arabidopsis thaliana. SVALKA：一个在拟南芥冷反应调控中起作用的长链非编码顺式天然反义RNA。

IF 3.6

Non-Coding RNA Pub Date : 2024-11-28 DOI: 10.3390/ncrna10060059

Nicholas M Kiger, Susan J Schroeder

{"title":"SVALKA: A Long Noncoding Cis-Natural Antisense RNA That Plays a Role in the Regulation of the Cold Response of Arabidopsis thaliana.","authors":"Nicholas M Kiger, Susan J Schroeder","doi":"10.3390/ncrna10060059","DOIUrl":"10.3390/ncrna10060059","url":null,"abstract":"RNA plays important roles in the regulation of gene expression in response to environmental stimuli. SVALKA, a long noncoding cis-natural antisense RNA, is a key component of regulating the response to cold temperature in Arabidopsis thaliana. There are three mechanisms through which SVALKA fine tunes the transcriptional response to cold temperatures. SVALKA regulates the expression of the CBF1 (C-Repeat Dehydration Binding Factor 1) transcription factor through a collisional transcription mechanism and a dsRNA and DICER mediated mechanism. SVALKA also interacts with Polycomb Repressor Complex 2 to regulate the histone methylation of CBF3. Both CBF1 and CBF3 are key components of the COLD REGULATED (COR) regulon that direct the plant's response to cold temperature over time, as well as plant drought adaptation, pathogen responses, and growth regulation. The different isoforms of SVALKA and its potential to form dynamic RNA conformations are important features in regulating a complex gene network in concert with several other noncoding RNA. This review will summarize the three mechanisms through which SVALKA participates in gene regulation, describe the ways that dynamic RNA structures support the function of regulatory noncoding RNA, and explore the potential for improving agricultural genetic engineering with a better understanding of the roles of noncoding RNA.","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"10 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11677326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142896483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Detection of miR-133a-5p Using a Molecular Beacon Probe for Investigating Postmortem Intervals. 使用分子信标探针检测miR-133a-5p用于研究死后间隔。

IF 3.6

Non-Coding RNA Pub Date : 2024-11-26 DOI: 10.3390/ncrna10060058

Eun Hye Lee, Mingyoung Jeong, Kwangmin Park, Dong Geon Lee, Eun Ju Lee, Haneul Lee, Ah Yeoung Kim, Jae Won Ahn, Hyun Jun Woo, Sunghyun Kim, Jaewon Lim, Jungho Kim

{"title":"Detection of miR-133a-5p Using a Molecular Beacon Probe for Investigating Postmortem Intervals.","authors":"Eun Hye Lee, Mingyoung Jeong, Kwangmin Park, Dong Geon Lee, Eun Ju Lee, Haneul Lee, Ah Yeoung Kim, Jae Won Ahn, Hyun Jun Woo, Sunghyun Kim, Jaewon Lim, Jungho Kim","doi":"10.3390/ncrna10060058","DOIUrl":"10.3390/ncrna10060058","url":null,"abstract":"Background: When a body is discovered at a crime or murder scene, it is crucial to examine the body and estimate its postmortem interval (PMI). Accurate estimation of PMI is vital for identifying suspects and providing clues to resolve the case. MicroRNAs (miRNAs or miRs) are small non-coding RNAs that remain relatively stable in the cell nucleus even after death-related changes occur. Objective: This study developed a molecular beacon probe for mmu-miR-133a-5p and assessed its use in mouse muscle tissue at temperatures of 4 °C and 21 °C to estimate the PMI. Methods: A total of 36 healthy adult male BALB/c mice were divided into 9 PMI time points (0, 2, 6, 8, and 10 days) with 3 mice per time point, and they were exposed to 4 °C and 21 °C. Next, the expression pattern of mmu-miR-133a in the skeletal muscle tissue over a 10-day PMI period was analyzed using the developed molecular beacon probe. Results: The molecular beacon (MB) probe was designed for optimal thermodynamic stability with a hairpin structure that opened in the presence of mmu-miR-133a-5p, thus separating the fluorophore from the quencher and resulting in a strong fluorescence signal at 495 nm. Fluorescence intensity increased with mmu-miR-133a-5p concentration from 1 ng/μL to 1000 ng/μL and exhibited a strong correlation (R2 = 0.9966) and a detection limit of 1 ng/μL. Subsequently, the expression level of mmu-miR-133a-5p was observed to be stable in mouse skeletal muscle tissue at both 4 °C and 21 °C. Conclusions: This user-friendly assay can complete measurements in just 30 min after RNA extraction and is suitable for point-of-care testing, and it possesses the potential to improve existing complex and time-consuming methods for PMI estimation.","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"10 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11676884/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142896484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

LNC-ing Genetics in Mitochondrial Disease. 线粒体疾病的 LNC-ing 遗传学。

IF 3.6

Non-Coding RNA Pub Date : 2024-11-15 DOI: 10.3390/ncrna10060057

Rick Kamps, Emma Louise Robinson

{"title":"LNC-ing Genetics in Mitochondrial Disease.","authors":"Rick Kamps, Emma Louise Robinson","doi":"10.3390/ncrna10060057","DOIUrl":"10.3390/ncrna10060057","url":null,"abstract":"Primary mitochondrial disease (MD) is a group of rare genetic diseases reported to have a prevalence of 1:5000 and is currently without a cure. This group of diseases includes mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS), maternally inherited diabetes and deafness (MIDD), Leber's hereditary optic neuropathy (LHON), Leigh syndrome (LS), Kearns-Sayre syndrome (KSS), and myoclonic epilepsy and ragged-red fiber disease (MERRF). Additionally, secondary mitochondrial dysfunction has been implicated in the most common current causes of mortality and morbidity, including cardiovascular disease (CVD) and cancer. Identifying key genetic contributors to both MD and secondary mitochondrial dysfunction may guide clinicians to assess the most effective treatment course and prognosis, as well as informing family members of any hereditary risk of disease transmission. Identifying underlying genetic causes of primary and secondary MD involves either genome sequencing (GS) or small targeted panel analysis of known disease-causing nuclear- or mitochondrial genes coding for mitochondria-related proteins. Due to advances in GS, the importance of long non-coding RNA (lncRNA) as functional contributors to the pathophysiology of MD is being unveiled. A limited number of studies have thus far reported the importance of lncRNAs in relation to MD causation and progression, and we are entering a new area of attention for clinical geneticists in specific rare malignancies. This commentary provides an overview of what is known about the role of lncRNAs as genetic and molecular contributors to disease pathophysiology and highlights an unmet need for a deeper understanding of mitochondrial dysfunction in serious human disease burdens.","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"10 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11587075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Androgen Receptor and Non-Coding RNAs' Interaction in Renal Cell Carcinoma. 肾细胞癌中雄激素受体与非编码 RNA 的相互作用

IF 3.6

Non-Coding RNA Pub Date : 2024-11-12 DOI: 10.3390/ncrna10060056

Manal A Hussain, Noha M Elemam, Iman M Talaat

{"title":"Androgen Receptor and Non-Coding RNAs' Interaction in Renal Cell Carcinoma.","authors":"Manal A Hussain, Noha M Elemam, Iman M Talaat","doi":"10.3390/ncrna10060056","DOIUrl":"10.3390/ncrna10060056","url":null,"abstract":"Renal cell carcinoma (RCC), the most prevalent among the urogenital cancers, accounts for around 3% of new cancer cases worldwide. Significantly, the incidence of RCC has doubled in developed world countries, ranking it as the sixth most common cancer in males, who represent two-thirds of RCC cases. Males with RCC exhibit a higher mortality rate and tend to develop a more aggressive form of the disease than females. Sex-related risk factors, including lifestyle and biological variations, explain this difference. The androgen receptor (AR) oncogenic signaling pathway has been extensively studied among the biological factors that affect RCC. Recent advancements in high-throughput RNA sequencing techniques have underscored the significant roles played by noncoding-RNAs (ncRNAs), previously dismissed as \"junk\". The oncogenic potential of AR is manifested through its dysregulation of the ncRNAs' availability and function, promoting RCC tumorigenesis. This review offers a summary of the most recent findings on the role and molecular mechanisms of the AR in dysregulating the ncRNAs that play a role in the progression of RCC and the possibility of utilizing ncRNAs to target AR as a potential therapeutic strategy.","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"10 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11587015/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparison of Three Computational Tools for the Prediction of RNA Tertiary Structures. 用于预测 RNA 三级结构的三种计算工具的比较。

IF 3.6

Non-Coding RNA Pub Date : 2024-11-08 DOI: 10.3390/ncrna10060055

Frank Yiyang Mao, Mei-Juan Tu, Gavin McAllister Traber, Ai-Ming Yu

{"title":"Comparison of Three Computational Tools for the Prediction of RNA Tertiary Structures.","authors":"Frank Yiyang Mao, Mei-Juan Tu, Gavin McAllister Traber, Ai-Ming Yu","doi":"10.3390/ncrna10060055","DOIUrl":"10.3390/ncrna10060055","url":null,"abstract":"Understanding the structures of noncoding RNAs (ncRNAs) is important for the development of RNA-based therapeutics. There are inherent challenges in employing current experimental techniques to determine the tertiary (3D) structures of RNAs with high complexity and flexibility in folding, which makes computational methods indispensable. In this study, we compared the utilities of three advanced computational tools, namely RNAComposer, Rosetta FARFAR2, and the latest AlphaFold 3, to predict the 3D structures of various forms of RNAs, including the small interfering RNA drug, nedosiran, and the novel bioengineered RNA (BioRNA) molecule showing therapeutic potential. Our results showed that, while RNAComposer offered a malachite green aptamer 3D structure closer to its crystal structure, the performances of RNAComposer and Rosetta FARFAR2 largely depend upon the secondary structures inputted, and Rosetta FARFAR2 predictions might not even recapitulate the typical, inverted \"L\" shape tRNA 3D structure. Overall, AlphaFold 3, integrating molecular dynamics principles into its deep learning framework, directly predicted RNA 3D structures from RNA primary sequence inputs, even accepting several common post-transcriptional modifications, which closely aligned with the experimentally determined structures. However, there were significant discrepancies among three computational tools in predicting the distal loop of human pre-microRNA and larger BioRNA (tRNA fused pre-miRNA) molecules whose 3D structures have not been characterized experimentally. While computational predictions show considerable promise, their notable strengths and limitations emphasize the needs for experimental validation of predictions besides characterization of more RNA 3D structures.","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"10 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11587127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Extracellular Vesicle lncRNAs as Key Biomolecules for Cell-to-Cell Communication and Circulating Cancer Biomarkers. 细胞外囊泡 lncRNAs 是细胞间通信和循环癌症生物标志物的关键生物分子。

IF 3.6

Non-Coding RNA Pub Date : 2024-11-05 DOI: 10.3390/ncrna10060054

Panagiotis Papoutsoglou, Antonin Morillon

{"title":"Extracellular Vesicle lncRNAs as Key Biomolecules for Cell-to-Cell Communication and Circulating Cancer Biomarkers.","authors":"Panagiotis Papoutsoglou, Antonin Morillon","doi":"10.3390/ncrna10060054","DOIUrl":"10.3390/ncrna10060054","url":null,"abstract":"Extracellular vesicles (EVs) are secreted by almost every cell type and are considered carriers of active biomolecules, such as nucleic acids, proteins, and lipids. Their content can be uptaken and released into the cytoplasm of recipient cells, thereby inducing gene reprogramming and phenotypic changes in the acceptor cells. Whether the effects of EVs on the physiology of recipient cells are mediated by individual biomolecules or the collective outcome of the total transferred EV content is still under debate. The EV RNA content consists of several types of RNA, such as messenger RNA (mRNA), microRNA (miRNA), and long non-coding RNA (lncRNA), the latter defined as transcripts longer than 200 nucleotides that do not code for proteins but have important established biological functions. This review aims to update our insights on the functional roles of EV and their cargo non-coding RNA during cancer progression, to highlight the utility of EV RNA as novel diagnostic or prognostic biomarkers in cancer, and to tackle the technological advances and limitations for EV RNA identification, integrity assessment, and preservation of its functionality.","PeriodicalId":19271,"journal":{"name":"Non-Coding RNA","volume":"10 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11587107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cardiomyopathies: The Role of Non-Coding RNAs. 心肌病：非编码 RNA 的作用。

IF 3.6

Non-Coding RNA Pub Date : 2024-10-23 DOI: 10.3390/ncrna10060053

Nicole Carabetta, Chiara Siracusa, Isabella Leo, Giuseppe Panuccio, Antonio Strangio, Jolanda Sabatino, Daniele Torella, Salvatore De Rosa

引用次数: 0

MicroRNA Biogenesis, Gene Regulation Mechanisms, and Availability in Foods. MicroRNA 的生物生成、基因调控机制和食品中的可用性。

IF 3.6

Non-Coding RNA Pub Date : 2024-10-11 DOI: 10.3390/ncrna10050052

Amilton S de Mello, Bradley S Ferguson, Erica L Shebs-Maurine, Francine M Giotto

引用次数: 0

Interplay of microRNAs and circRNAs in Epithelial Ovarian Cancer. 上皮性卵巢癌中 microRNA 与 circRNA 的相互作用