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Erdmann K, Distler F, Gräfe S, Kwe J, Erb HHH, Fuessel S, Pahernik S, Thomas C, Borkowetz A. Transcript Markers from Urinary Extracellular Vesicles for Predicting Risk Reclassification of Prostate Cancer Patients on Active Surveillance. Cancers (Basel) 2024; 16:2453. [PMID: 39001515 PMCID: PMC11240337 DOI: 10.3390/cancers16132453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/25/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
Serum prostate-specific antigen (PSA), its derivatives, and magnetic resonance tomography (MRI) lack sufficient specificity and sensitivity for the prediction of risk reclassification of prostate cancer (PCa) patients on active surveillance (AS). We investigated selected transcripts in urinary extracellular vesicles (uEV) from PCa patients on AS to predict PCa risk reclassification (defined by ISUP 1 with PSA > 10 ng/mL or ISUP 2-5 with any PSA level) in control biopsy. Before the control biopsy, urine samples were prospectively collected from 72 patients, of whom 43% were reclassified during AS. Following RNA isolation from uEV, multiplexed reverse transcription, and pre-amplification, 29 PCa-associated transcripts were quantified by quantitative PCR. The predictive ability of the transcripts to indicate PCa risk reclassification was assessed by receiver operating characteristic (ROC) curve analyses via calculation of the area under the curve (AUC) and was then compared to clinical parameters followed by multivariate regression analysis. ROC curve analyses revealed a predictive potential for AMACR, HPN, MALAT1, PCA3, and PCAT29 (AUC = 0.614-0.655, p < 0.1). PSA, PSA density, PSA velocity, and MRI maxPI-RADS showed AUC values of 0.681-0.747 (p < 0.05), with accuracies for indicating a PCa risk reclassification of 64-68%. A model including AMACR, MALAT1, PCAT29, PSA density, and MRI maxPI-RADS resulted in an AUC of 0.867 (p < 0.001) with a sensitivity, specificity, and accuracy of 87%, 83%, and 85%, respectively, thus surpassing the predictive power of the individual markers. These findings highlight the potential of uEV transcripts in combination with clinical parameters as monitoring markers during the AS of PCa.
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Affiliation(s)
- Kati Erdmann
- Department of Urology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (S.G.); (J.K.); (H.H.H.E.); (C.T.); (A.B.)
- National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Florian Distler
- Department of Urology, Nuremberg General Hospital, Paracelsus Medical University, 90419 Nuremberg, Germany; (F.D.); (S.P.)
| | - Sebastian Gräfe
- Department of Urology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (S.G.); (J.K.); (H.H.H.E.); (C.T.); (A.B.)
- National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Jeremy Kwe
- Department of Urology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (S.G.); (J.K.); (H.H.H.E.); (C.T.); (A.B.)
| | - Holger H. H. Erb
- Department of Urology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (S.G.); (J.K.); (H.H.H.E.); (C.T.); (A.B.)
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Susanne Fuessel
- Department of Urology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (S.G.); (J.K.); (H.H.H.E.); (C.T.); (A.B.)
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sascha Pahernik
- Department of Urology, Nuremberg General Hospital, Paracelsus Medical University, 90419 Nuremberg, Germany; (F.D.); (S.P.)
| | - Christian Thomas
- Department of Urology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (S.G.); (J.K.); (H.H.H.E.); (C.T.); (A.B.)
- National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01307 Dresden, Germany
| | - Angelika Borkowetz
- Department of Urology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (K.E.); (S.G.); (J.K.); (H.H.H.E.); (C.T.); (A.B.)
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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Pan H, Wu T, Huang K, Guo Z, Liang H, Lyu P, Huang H, Feng X, Wang Q, Hu J, He Y, Guo Z, Yin M, Zhang Y. Reducing SULT2B1 promotes the interaction of LncRNAgga3-204 with SMAD4 to inhibit the macrophage inflammatory response and delay atherosclerosis progression. Transl Res 2024; 268:13-27. [PMID: 38286358 DOI: 10.1016/j.trsl.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/08/2024] [Accepted: 01/17/2024] [Indexed: 01/31/2024]
Abstract
Inflammation is a crucial pathophysiological mechanism in atherosclerosis (AS). This study aims to investigate the impact of sulfotransferase family 2b member 1 (SULT2B1) on the inflammatory response of macrophages and the progression of AS. Here, we reported that SULT2B1 expression increased with the progression of AS. In AS model mice, knockdown of Sult2b1 led to remission of AS and reduced inflammation levels. Further exploration of the downstream molecular mechanisms of SULT2B1 revealed that suppressing Sult2b1 in macrophages resulted in decreased levels of 25HC3S in the nucleus, elevated expression of Lxr, and increased the transcription of Lncgga3-204. In vivo, knockdown of Lncgga3-204 aggravated the inflammatory response and AS progression, while the simultaneous knockdown of both Sult2b1 and Lncgga3-204 exacerbated AS and the inflammatory response compared with knockdown of Sult2b1 alone. Increased binding of Lncgga3-204 to SMAD4 in response to oxidized-low density lipoprotein (ox-LDL) stimulation facilitated SMAD4 entry into the nucleus and regulated Smad7 transcription, which elevated SMAD7 expression, suppressed NF-κB entry into the nucleus, and ultimately attenuated the macrophage inflammatory response. Finally, we identified the presence of a single nucleotide polymorphism (SNP), rs2665580, in the SULT2B1 promoter region in monocytes from coronary artery disease (CAD) patients. The predominant GG/AG/AA genotypes were observed in the Asian population. Elevated SULT2B1 expression in monocytes with GG corresponded to elevated inflammatory factor levels and more unstable coronary plaques. To summarize, our study demonstrated that the critical role of SULT2B1/Lncgga3-204/SMAD4/NF-κB in AS progression. SULT2B1 serves as a novel biomarker indicating inflammatory status, thereby offering insights into potential therapeutic strategies for AS.
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Affiliation(s)
- Hangyu Pan
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China
| | - Tongwei Wu
- Department of Ultrasound, Nanfang Hospital of Southern Medical University, Guangzhou 510515, PR China
| | - Kang Huang
- Department of Cardiology, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou 570100, PR China
| | - Zhongzhou Guo
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, PR China
| | - Hongbin Liang
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China
| | - Ping Lyu
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China
| | - Hui Huang
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China
| | - Xinyi Feng
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China
| | - Qianqian Wang
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China
| | - Jing Hu
- Department of Cardiology, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, PR China
| | - Yihua He
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China
| | - Zhigang Guo
- Department of Cardiology, Huiqiao Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China.
| | - Mengzhuo Yin
- Department of Geriatrics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510515, PR China.
| | - Yanan Zhang
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China.
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Rishen Narayan Dev B, Kishan Raj SR, Chinni SV, Citartan M. Identification and Characterization of Non-protein Coding RNA Homologs in Serratia Marcescens by Comparative Transcriptomics. Indian J Microbiol 2024; 64:198-204. [PMID: 38468749 PMCID: PMC10924871 DOI: 10.1007/s12088-023-01160-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/16/2023] [Indexed: 03/13/2024] Open
Abstract
The Serratia marcescens is a Gram-negative bacterium from the Enterobacteriaceae family. Recently, S. marcescens have evolved to become a versatile and opportunistic pathogen. Furthermore, this bacterium is also a multi-drug resistant pathogen exhibiting Extended-Spectrum Beta-Lactamases (ESBL) activity. This bacterium is highly associated with infections in healthcare settings and even leads to death. Hence, an advanced approach based on non-protein coding RNA (npcRNA) of S. marcescens was considered in this study to understand its regulatory roles in virulence, pathogenesis, and the differential expression of these transcripts in various growth phases of the bacterium. BLASTn search of known npcRNAs from Salmonella typhi, Escherichia coli, and Yersinia pestis against S. marcescens was performed to discover putative conserved homologous transcripts. The novelty of these putative homologous npcRNAs was verified by screening through the Rfam web tool. The target mRNA for the homologs was predicted via the TargetRNA2 webtool to understand the possible regulatory roles of these transcripts. The npcRNA homologs, which were predicted to regulate virulence target mRNA were assessed for their expression profile at different growth stages via reverse transcription PCR and the band intensity was quantitatively analysed using the Image J tool. The known npcRNA ssrS, from S. typhi showed expression in S. marcescens during three growth stages (lag, log, and stationary). Expression was observed to be high during the lag phase followed by a similarly low-level expression during the log and no expression during stationary phase. This ssrS homolog was predicted to regulate mRNA that encodes for protein FliR, which is associated with virulence. This is a preliminary study that lay the foundation for further elucidation of more virulence-associated npcRNAs that are yet to be discovered from S. marcescens, which can be useful for diagnostics and therapeutic applications. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01160-y.
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Affiliation(s)
| | - Selva Raju Kishan Raj
- School of Biotechnology, Mila University, No 1, MIU Boulevard, Putra Nilai, 71800 Nilai, Negeri Sembilan Malaysia
| | - Suresh V. Chinni
- Department of Biochemistry, Faculty of Medicine, Bioscience, and Nursing, MAHSA University, Selangor 42610 Jenjarom, Malaysia
- Department of Periodontics, Saveetha Dental College, and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, 602105 India
| | - Marimuthu Citartan
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Bertam, Kepala Batas, Penang Malaysia
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Malgundkar SH, Tamimi Y. The pivotal role of long non-coding RNAs as potential biomarkers and modulators of chemoresistance in ovarian cancer (OC). Hum Genet 2024; 143:107-124. [PMID: 38276976 DOI: 10.1007/s00439-023-02635-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024]
Abstract
Ovarian cancer (OC) is a fatal gynecological disease that is often diagnosed at later stages due to its asymptomatic nature and the absence of efficient early-stage biomarkers. Previous studies have identified genes with abnormal expression in OC that couldn't be explained by methylation or mutation, indicating alternative mechanisms of gene regulation. Recent advances in human transcriptome studies have led to research on non-coding RNAs (ncRNAs) as regulators of cancer gene expression. Long non-coding RNAs (lncRNAs), a class of ncRNAs with a length greater than 200 nucleotides, have been identified as crucial regulators of physiological processes and human diseases, including cancer. Dysregulated lncRNA expression has also been found to play a crucial role in ovarian carcinogenesis, indicating their potential as novel and non-invasive biomarkers for improving OC management. However, despite the discovery of several thousand lncRNAs, only one has been approved for clinical use as a biomarker in cancer, highlighting the importance of further research in this field. In addition to their potential as biomarkers, lncRNAs have been implicated in modulating chemoresistance, a major problem in OC. Several studies have identified altered lncRNA expression upon drug treatment, further emphasizing their potential to modulate chemoresistance. In this review, we highlight the characteristics of lncRNAs, their function, and their potential to serve as tumor markers in OC. We also discuss a few databases providing detailed information on lncRNAs in various cancer types. Despite the promising potential of lncRNAs, further research is necessary to fully understand their role in cancer and develop effective strategies to combat this devastating disease.
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Affiliation(s)
- Shika Hanif Malgundkar
- Biochemistry Department, College of Medicine and Health Sciences, Sultan Qaboos University, PC 123, PO Box 35, Muscat, Sultanate of Oman
| | - Yahya Tamimi
- Biochemistry Department, College of Medicine and Health Sciences, Sultan Qaboos University, PC 123, PO Box 35, Muscat, Sultanate of Oman.
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Wang L, Fang X, Yang Z, Li X, Cheng M, Cheng L, Wang G, Li W, Liu L. LncRP11-675F6.3 responds to rapamycin treatment and reduces triglyceride accumulation via interacting with HK1 in hepatocytes by regulating autophagy and VLDL-related proteins. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1606-1617. [PMID: 37222534 PMCID: PMC10577451 DOI: 10.3724/abbs.2023091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/28/2023] [Indexed: 05/25/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have been widely proven to be involved in liver lipid homeostasis. Herein, we identify an upregulated lncRNA named lncRP11-675F6.3 in response to rapamycin treatment using a microarray in HepG2 cells. Knockdown of lncRP11-675F6. 3 leads to a significant reduction in apolipoprotein 100 (ApoB100), microsomal triglyceride transfer protein (MTTP), ApoE and ApoC3 with increased cellular triglyceride level and autophagy. Furthermore, we find that ApoB100 is obviously colocalized with GFP-LC3 in autophagosomes when lncRP11-675F6. 3 is knocked down, indicating that elevated triglyceride accumulation likely related to autophagy induces the degradation of ApoB100 and impairs very low-density lipoprotein (VLDL) assembly. We then identify and validate that hexokinase 1 (HK1) acts as the binding protein of lncRP11-675F6.3 and mediates triglyceride regulation and cell autophagy. More importantly, we find that lncRP11-675F6.3 and HK1 attenuate high fat diet induced nonalcoholic fatty liver disease (NAFLD) by regulating VLDL-related proteins and autophagy. In conclusion, this study reveals that lncRP11-675F6.3 is potentially involved in the downstream of mTOR signaling pathway and the regulatory network of hepatic triglyceride metabolism in cooperation with its interacting protein HK1, which may provide a new target for fatty liver disorder treatment.
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Affiliation(s)
- Lingling Wang
- Key Laboratory of Laboratory MedicineMinistry of Education of ChinaZhejiang Provincial Key Laboratory of Medical GeneticsSchool of Laboratory Medicine and Life SciencesWenzhou Medical UniversityWenzhou325035China
| | - Xiaojuan Fang
- Key Laboratory of Laboratory MedicineMinistry of Education of ChinaZhejiang Provincial Key Laboratory of Medical GeneticsSchool of Laboratory Medicine and Life SciencesWenzhou Medical UniversityWenzhou325035China
| | - Ziyou Yang
- Key Laboratory of Laboratory MedicineMinistry of Education of ChinaZhejiang Provincial Key Laboratory of Medical GeneticsSchool of Laboratory Medicine and Life SciencesWenzhou Medical UniversityWenzhou325035China
| | - Xueling Li
- Key Laboratory of Laboratory MedicineMinistry of Education of ChinaZhejiang Provincial Key Laboratory of Medical GeneticsSchool of Laboratory Medicine and Life SciencesWenzhou Medical UniversityWenzhou325035China
| | - Mengdi Cheng
- Key Laboratory of Laboratory MedicineMinistry of Education of ChinaZhejiang Provincial Key Laboratory of Medical GeneticsSchool of Laboratory Medicine and Life SciencesWenzhou Medical UniversityWenzhou325035China
| | - Liang Cheng
- Key Laboratory of Laboratory MedicineMinistry of Education of ChinaZhejiang Provincial Key Laboratory of Medical GeneticsSchool of Laboratory Medicine and Life SciencesWenzhou Medical UniversityWenzhou325035China
| | - Ganglin Wang
- Key Laboratory of Laboratory MedicineMinistry of Education of ChinaZhejiang Provincial Key Laboratory of Medical GeneticsSchool of Laboratory Medicine and Life SciencesWenzhou Medical UniversityWenzhou325035China
| | - Wei Li
- Key Laboratory of Laboratory MedicineMinistry of Education of ChinaZhejiang Provincial Key Laboratory of Medical GeneticsSchool of Laboratory Medicine and Life SciencesWenzhou Medical UniversityWenzhou325035China
| | - Lin Liu
- Key Laboratory of Laboratory MedicineMinistry of Education of ChinaZhejiang Provincial Key Laboratory of Medical GeneticsSchool of Laboratory Medicine and Life SciencesWenzhou Medical UniversityWenzhou325035China
- Zhuji Affiliated Hospital of Wenzhou Medical UniversityShaoxing311800China
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Hidalgo M, Ramos C, Zolla G. Analysis of lncRNAs in Lupinus mutabilis (Tarwi) and Their Potential Role in Drought Response. Noncoding RNA 2023; 9:48. [PMID: 37736894 PMCID: PMC10514842 DOI: 10.3390/ncrna9050048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 09/23/2023] Open
Abstract
Lupinus mutabilis is a legume with high agronomic potential and available transcriptomic data for which lncRNAs have not been studied. Therefore, our objective was to identify, characterize, and validate the drought-responsive lncRNAs in L. mutabilis. To achieve this, we used a multilevel approach based on lncRNA prediction, annotation, subcellular location, thermodynamic characterization, structural conservation, and validation. Thus, 590 lncRNAs were identified by at least two algorithms of lncRNA identification. Annotation with the PLncDB database showed 571 lncRNAs unique to tarwi and 19 lncRNAs with homology in 28 botanical families including Solanaceae (19), Fabaceae (17), Brassicaceae (17), Rutaceae (17), Rosaceae (16), and Malvaceae (16), among others. In total, 12 lncRNAs had homology in more than 40 species. A total of 67% of lncRNAs were located in the cytoplasm and 33% in exosomes. Thermodynamic characterization of S03 showed a stable secondary structure with -105.67 kcal/mol. This structure included three regions, with a multibranch loop containing a hairpin with a SECIS-like element. Evaluation of the structural conservation by CROSSalign revealed partial similarities between L. mutabilis (S03) and S. lycopersicum (Solyc04r022210.1). RT-PCR validation demonstrated that S03 was upregulated in a drought-tolerant accession of L. mutabilis. Finally, these results highlighted the importance of lncRNAs in tarwi improvement under drought conditions.
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Affiliation(s)
- Manuel Hidalgo
- Programa de Estudio de Medicina Humana, Universidad Privada Antenor Orrego, Av. América Sur 3145, Trujillo 13008, Peru; (M.H.); (C.R.)
| | - Cynthia Ramos
- Programa de Estudio de Medicina Humana, Universidad Privada Antenor Orrego, Av. América Sur 3145, Trujillo 13008, Peru; (M.H.); (C.R.)
| | - Gaston Zolla
- Laboratorio de Fisiología Molecular de Plantas del Programa de Cereales y Granos Nativos, Facultad de Agronomía, Universidad Nacional Agraria La Molina, Lima 12, Peru
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Feng H, Wang S, Wang Y, Ni X, Yang Z, Hu X, Sen Yang. LncCat: An ORF attention model to identify LncRNA based on ensemble learning strategy and fused sequence information. Comput Struct Biotechnol J 2023; 21:1433-1447. [PMID: 36824229 PMCID: PMC9941877 DOI: 10.1016/j.csbj.2023.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Background Long non-coding RNA (lncRNA) is one of the most essential forms of transcripts, playing crucial regulatory roles in the development of cancers and diseases without protein-coding ability. It was assumed that short ORFs (sORFs) in lncRNA were weak to translate proteins. However, recent research has shown that sORFs can encode peptides, which increases the difficulty to identify lncRNA. Therefore, identifying lncRNAs with sORFs facilitates finding novel regulatory factors. Results In this paper, we propose LncCat for identifying lncRNA based on category boosting (CatBoost) and ORF-attention features. LncCat combines five types of features to encode transcript sequences and employs CatBoost to build a prediction model. In addition, the visualization comparison reveals that the ORF-attention features between lncRNAs and protein-coding transcripts are significantly distinct. The comparison results show that LncCat outperforms competing methods on several benchmark datasets. For Matthew's Correlation Coefficient (MCC), LncCat achieves 0.9503, 0.9219, 0.8591, 0.8672, and 0.9047 on the human, mouse, zebrafish, wheat, and chicken datasets, with improvements ranging from 1.90% to 7.82%, 1.49-17.63%, 6.11-21.50%, 3.02-51.64% and 5.35-26.90%, respectively. Moreover, LncCat dramatically improves the MCC by at least 11.90%, 12.96% and 42.61% on sORF test datasets of human, mouse, and zebrafish, respectively. Conclusions Experiments indicate that LncCat performs better both on long ORF and sORF datasets, and ORF-attention features show positive effects on predicting lncRNA. In brief, LncCat is a reliable method for identifying lncRNA. Additionally, a user-friendly web server is developed for academics at http://cczubio.top/lnccat.
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Affiliation(s)
- Hongqi Feng
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou 213164, China
| | - Shaocong Wang
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou 213164, China
| | - Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
| | - Xinye Ni
- The Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University, Changzhou 213164, China
| | - Zexi Yang
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou 213164, China
| | - Xuemei Hu
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Sen Yang
- School of Computer Science and Artificial Intelligence Aliyun School of Big Data School of Software, Changzhou University, Changzhou 213164, China
- The Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University, Changzhou 213164, China
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8
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Synthetic Pathways and the Therapeutic Potential of Quercetin and Curcumin. Int J Mol Sci 2022; 23:ijms232214413. [PMID: 36430891 PMCID: PMC9696847 DOI: 10.3390/ijms232214413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
Polyphenols are considered popular ingredients in the pharmaceutical and medical fields due to their preventive and therapeutic properties. However, the potential effects and mechanisms of action of individual polyphenols remain largely unknown. Herein, we analyzed recent data on the synthetic pathways, features, and similarity of the properties of quercetin, as the most famous flavonoid, and curcumin, a representative of curcuminoids that despite their anti-oxidant activity, also have a pro-oxidant effect, depending on the concentration and the cellular environment. This review focuses on an analysis of their anti-cancer efficacy against various cancer cell lines via cell cycle arrest (regulation of p53/p21 and CDK/cyclins) and by triggering the mitochondrial intrinsic (Bcl-2/Bax/caspase 9) apoptotic pathway, as well as through the modulation of the signaling pathways (PI3K/Akt, Wnt/β-catenin, JAK/STAT, MAPK, p53, and NF-ĸB) and their influence on the non-coding RNAs involved in angiogenesis, invasion, migration, and metastasis. The therapeutic potential of quercetin and curcumin is discussed not only on the basis of their anti-cancer effects, but also with regard to their anti-diabetic, anti-obesity, anti-inflammatory, and anti-bacterial actions.
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Singh D, Rai V, Agrawal DK. Non-Coding RNAs in Regulating Plaque Progression and Remodeling of Extracellular Matrix in Atherosclerosis. Int J Mol Sci 2022; 23:13731. [PMID: 36430208 PMCID: PMC9692922 DOI: 10.3390/ijms232213731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/31/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
Non-coding RNAs (ncRNAs) regulate cell proliferation, migration, differentiation, inflammation, metabolism of clinically important biomolecules, and other cellular processes. They do not encode proteins but are involved in the regulatory network of various proteins that are directly related to the pathogenesis of diseases. Little is known about the ncRNA-associated mechanisms of atherosclerosis and related cardiovascular disorders. Remodeling of the extracellular matrix (ECM) is critical in the pathogenesis of atherosclerosis and related disorders; however, its regulatory proteins are the potential subjects to explore with special emphasis on epigenetic regulatory components. The activity of regulatory proteins involved in ECM remodeling is regulated by various ncRNA molecules, as evident from recent research. Thus, it is important to critically evaluate the existing literature to enhance the understanding of nc-RNAs-regulated molecular mechanisms regulating ECM components, remodeling, and progression of atherosclerosis. This is crucial since deregulated ECM remodeling contributes to atherosclerosis. Thus, an in-depth understanding of ncRNA-associated ECM remodeling may identify novel targets for the treatment of atherosclerosis and other cardiovascular diseases.
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Affiliation(s)
| | | | - Devendra K. Agrawal
- Department of Translational Research, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
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10
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Navigating the Multiverse of Antisense RNAs: The Transcription- and RNA-Dependent Dimension. Noncoding RNA 2022; 8:ncrna8060074. [PMID: 36412909 PMCID: PMC9680235 DOI: 10.3390/ncrna8060074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 12/14/2022] Open
Abstract
Evidence accumulated over the past decades shows that the number of identified antisense transcripts is continuously increasing, promoting them from transcriptional noise to real genes with specific functions. Indeed, recent studies have begun to unravel the complexity of the antisense RNA (asRNA) world, starting from the multidimensional mechanisms that they can exert in physiological and pathological conditions. In this review, we discuss the multiverse of the molecular functions of asRNAs, describing their action through transcription-dependent and RNA-dependent mechanisms. Then, we report the workflow and methodologies to study and functionally characterize single asRNA candidates.
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Billakurthi K, Schulze S, Schulz ELM, Sage TL, Schreier TB, Hibberd JM, Ludwig M, Westhoff P. Shedding light on AT1G29480 of Arabidopsis thaliana-An enigmatic locus restricted to Brassicacean genomes. PLANT DIRECT 2022; 6:e455. [PMID: 36263108 PMCID: PMC9576117 DOI: 10.1002/pld3.455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/02/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
A key feature of C4 Kranz anatomy is the presence of an enlarged, photosynthetically highly active bundle sheath whose cells contain large numbers of chloroplasts. With the aim to identify novel candidate regulators of C4 bundle sheath development, we performed an activation tagging screen with Arabidopsis thaliana. The reporter gene used encoded a chloroplast-targeted GFP protein preferentially expressed in the bundle sheath, and the promoter of the C4 phosphoenolpyruvate carboxylase gene from Flaveria trinervia served as activation tag because of its activity in all chlorenchymatous tissues of A. thaliana. Primary mutants were selected based on their GFP signal intensity, and one stable mutant named kb-1 with a significant increase in GFP fluorescence intensity was obtained. Despite the increased GFP signal, kb-1 showed no alterations to bundle sheath anatomy. The causal locus, AT1G29480, is specific to the Brassicaceae with its second exon being conserved. Overexpression and reconstitution studies confirmed that AT1G29480, and specifically its second exon, were sufficient for the enhanced GFP phenotype, which was not dependent on translation of the locus or its parts into protein. We conclude, therefore, that the AT1G29480 locus enhances the GFP reporter gene activity via an RNA-based mechanism.
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Affiliation(s)
- Kumari Billakurthi
- Institute of Plant Molecular and Developmental BiologyUniversitätsstrasse 1, Heinrich‐Heine‐UniversityDuesseldorfGermany
- Cluster of Excellence on Plant Sciences ‘From Complex Traits Towards Synthetic Modules’Düsseldorf‐CologneGermany
- Department of Plant Sciences, Downing StreetUniversity of CambridgeCambridgeUK
| | - Stefanie Schulze
- Institute of Plant Molecular and Developmental BiologyUniversitätsstrasse 1, Heinrich‐Heine‐UniversityDuesseldorfGermany
| | - Eva Lena Marie Schulz
- Institute of Plant Molecular and Developmental BiologyUniversitätsstrasse 1, Heinrich‐Heine‐UniversityDuesseldorfGermany
| | - Tammy L. Sage
- Department of Ecology and Evolutionary BiologyThe University of TorontoTorontoOntarioCanada
| | - Tina B. Schreier
- Department of Plant Sciences, Downing StreetUniversity of CambridgeCambridgeUK
| | - Julian M. Hibberd
- Department of Plant Sciences, Downing StreetUniversity of CambridgeCambridgeUK
| | - Martha Ludwig
- School of Molecular SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Peter Westhoff
- Institute of Plant Molecular and Developmental BiologyUniversitätsstrasse 1, Heinrich‐Heine‐UniversityDuesseldorfGermany
- Cluster of Excellence on Plant Sciences ‘From Complex Traits Towards Synthetic Modules’Düsseldorf‐CologneGermany
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Identification of long non-coding RNAs in Verticillium dahliae following inoculation of cotton. Microbiol Res 2022; 257:126962. [PMID: 35042052 DOI: 10.1016/j.micres.2022.126962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 12/20/2021] [Accepted: 01/04/2022] [Indexed: 11/20/2022]
Abstract
Long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. However, these functions have not been assessed in Verticillium dahliae, a soil-borne fungal pathogen that causes devastating wilt diseases in many crops. The discovery and identity of novel lncRNAs and their association with virulence may contribute to an increased understanding of the regulation of virulence in V. dahliae. Here, we identified a total of 352 lncRNAs in V. dahliae. The lncRNAs were transcribed from all V. dahliae chromosomes, typically with shorter open reading frames, lower GC content, and fewer exons than protein-coding genes. In addition, 308 protein-coding genes located within 10 kb upstream and 10 kb downstream of lncRNAs were identified as neighboring genes, and which were considered as potential targets of lncRNA. These neighboring genes encode products involved in development, stress responses, and pathogenicity of V. dahliae, such as transcription factors (TF), kinase, and members of the secretome. Furthermore, 47 lncRNAs were significantly differentially expressed in V. dahliae following inoculation of susceptible cotton (Gossyoiumhisutum) cultivar Junmian No.1, suggesting that lncRNAs may be involved in the regulation of virulence in V. dahliae. Moreover, correlations in expression patterns between lncRNA and their neighboring genes were detected. Expression of lncRNA012077 and its neighboring gene was up-regulated 6 h following inoculation of cotton, while the expression of lncRNA007722 was down-regulated at 6 h but up-regulated at 24 h, in a pattern opposite to that of its neighboring gene. Overexpression of lncRNA012077 in wild-type strain (Vd991) enhanced its virulence on cotton while overexpression of lncRNA009491 reduced virulence. Identification of novel lncRNAs and their association with virulence may provide new targets for disease control.
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Antonaros F, Pitocco M, Abete D, Vione B, Piovesan A, Vitale L, Strippoli P, Caracausi M, Pelleri MC. Structural Characterization of the Highly Restricted Down Syndrome Critical Region on 21q22.13: New KCNJ6 and DSCR4 Transcript Isoforms. Front Genet 2021; 12:770359. [PMID: 34956324 PMCID: PMC8692863 DOI: 10.3389/fgene.2021.770359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/02/2021] [Indexed: 11/17/2022] Open
Abstract
Down syndrome (DS) is caused by trisomy of chromosome 21 and it is the most common genetic cause of intellectual disability (ID) in humans. Subjects with DS show a typical phenotype marked by facial dysmorphisms and ID. Partial trisomy 21 (PT21) is a rare genotype characterized by the duplication of a delimited chromosome 21 (Hsa21) portion and it may or may not be associated with DS diagnosis. The highly restricted Down syndrome critical region (HR-DSCR) is a region of Hsa21 present in three copies in all individuals with PT21 and a diagnosis of DS. This region, located on distal 21q22.13, is 34 kbp long and does not include characterized genes. The HR-DSCR is annotated as an intergenic region between KCNJ6-201 transcript encoding for potassium inwardly rectifying channel subfamily J member 6 and DSCR4-201 transcript encoding Down syndrome critical region 4. Two transcripts recently identified by massive RNA-sequencing (RNA-Seq) and automatically annotated on Ensembl database reveal that the HR-DSCR seems to be partially crossed by KCNJ6-202 and DSCR4-202 isoforms. KCNJ6-202 shares the coding sequence with KCNJ6-201 which is involved in many physiological processes, including heart rate in cardiac cells and circuit activity in neuronal cells. DSCR4-202 transcript has the first two exons in common with DSCR4-201, the only experimentally verified gene uniquely present in Hominidae. In this study, we performed in silico and in vitro analyses of the HR-DSCR. Bioinformatic data, obtained using Sequence Read Archive (SRA) and SRA-BLAST software, were confirmed by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and Sanger sequencing on a panel of human tissues. Our data demonstrate that the HR-DSCR cannot be defined as an intergenic region. Further studies are needed to investigate the functional role of the new transcripts, likely involved in DS phenotypes.
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Affiliation(s)
- Francesca Antonaros
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Margherita Pitocco
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Domenico Abete
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Beatrice Vione
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Allison Piovesan
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Lorenza Vitale
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Pierluigi Strippoli
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Caracausi
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Chiara Pelleri
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
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HSV-1 small non-coding RNA (sncRNA) 1 and 2 activate the Herpes virus entry mediator (HVEM) promoter. J Virol 2021; 96:e0198521. [PMID: 34851143 DOI: 10.1128/jvi.01985-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HSV-1 latency associated transcript (LAT) plays a significant role in efficient establishment of latency and reactivation. LAT has antiapoptotic activity and downregulates expression of components of the Type I interferon pathway. LAT also specifically activates expression of the herpesvirus entry mediator (HVEM), one of seven known receptors used by HSV-1 for cell entry that is crucial for latency and reactivation. However, the mechanism by which LAT regulates HVEM expression is not known. LAT encodes two sncRNAs that are not miRNAs, within its 1.5 kb stable transcript, which also have antiapoptotic activity. These sncRNAs may encode short peptides, but experimental evidence is lacking. Here, we demonstrate that these two sncRNAs control HVEM expression by activating its promoter. Both sncRNAs are required for WT level of activation of HVEM and sncRNA1 is more important in HVEM activation than sncRNA2. Disruption of a putative start codon in sncRNA1 and sncRNA2 sequences reduced HVEM promoter activity, suggesting that sncRNAs may encode a protein. However, we did not detect peptide binding using two chromatin immunoprecipitation (ChIP) approaches and a web-based algorithm predicts low probability that the putative peptides bind to DNA. In addition, computational modeling predicts that sncRNA molecules bind with high affinity to the HVEM promoter and deletion of these binding sites to sncRNA1, sncRNA2 or both reduced HVEM promoter activity. Together, our data suggests that sncRNAs exert their function as RNA molecules, not as proteins, and we provide a model for the predicted binding affinities and binding sites of sncRNA1 and sncRNA2 in the HVEM promoter. IMPORTANCE HSV-1 causes recurrent ocular infections, which is the leading cause of corneal scarring and blindness. Corneal scarring is caused by the host immune response to repeated reactivation events. LAT functions by regulating latency and reactivation, in part by inhibiting apoptosis and activating HVEM expression. However, the mechanism used by LAT to control of HVEM expression is unclear. Here, we demonstrate that two sncRNAs encoded within the 1.5 kb LAT transcript activate HVEM expression by binding to two regions of its promoter. Interfering with these interactions may reduce latency and thereby eye disease associated with reactivation.
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Comparative genomic identification and characterization of npcRNA homologs in Proteus vulgaris. J Biosci 2021. [DOI: 10.1007/s12038-021-00230-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Long noncoding RNA landscapes specific to benign and malignant thyroid neoplasms of distinct histological subtypes. Sci Rep 2021; 11:16728. [PMID: 34408227 PMCID: PMC8373968 DOI: 10.1038/s41598-021-96149-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/04/2021] [Indexed: 01/14/2023] Open
Abstract
The main types of thyroid neoplasms, follicular adenoma (FA), follicular thyroid carcinoma (FTC), classical and follicular variants of papillary carcinoma (clPTC and fvPTC), and anaplastic thyroid carcinoma (ATC), differ in prognosis, progression rate and metastatic behaviour. Specific patterns of lncRNAs involved in the development of clinical and morphological features can be presumed. LncRNA landscapes within distinct benign and malignant histological variants of thyroid neoplasms were not investigated. The aim of the study was to discover long noncoding RNA landscapes common and specific to major benign and malignant histological subtypes of thyroid neoplasms. LncRNA expression in FA, FTC, fvPTC, clPTC and ATC was analysed with comprehensive microarray and RNA-Seq datasets. Putative biological functions were evaluated via enrichment analysis of coexpressed coding genes. In the results, lncRNAs common and specific to FTC, clPTC, fvPTC, and ATC were identified. The discovered lncRNAs are putatively involved in L1CAM interactions, namely, pre-mRNA processing (lncRNAs specific to FTC); PCP/CE and WNT pathways (lncRNAs specific to fvPTC); extracellular matrix organization (lncRNAs specific to clPTC); and the cell cycle (lncRNAs specific to ATC). Known oncogenic and suppressor lncRNAs (RMST, CRNDE, SLC26A4-AS1, NR2F1-AS1, and LINC00511) were aberrantly expressed in thyroid carcinomas. These findings enhance the understanding of lncRNAs in the development of subtype-specific features in thyroid cancer.
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Chorostecki U, Saus E, Gabaldón T. Structural characterization of NORAD reveals a stabilizing role of spacers and two new repeat units. Comput Struct Biotechnol J 2021; 19:3245-3254. [PMID: 34141143 PMCID: PMC8192489 DOI: 10.1016/j.csbj.2021.05.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) can perform a variety of key cellular functions by interacting with proteins and other RNAs. Recent studies have shown that the functions of lncRNAS are largely mediated by their structures. However, our structural knowledge for most lncRNAS is limited to sequence-based computational predictions. Non-coding RNA activated by DNA damage (NORAD) is an atypical lncRNA due to its abundant expression and high sequence conservation. NORAD regulates genomic stability by interacting with proteins and microRNAs. Previous sequence-based characterization has identified a modular organization of NORAD composed of several NORAD repeat units (NRUs). These units comprise the protein-binding elements and are separated by regular spacers. Here, we experimentally determine for the first time the secondary structure of NORAD using the nextPARS approach. Our results suggest that the spacer regions provide structural stability to NRUs. Furthermore, we uncover two previously unreported NRUs, and determine the core structural motifs conserved across NRUs. Overall, these findings will help to elucidate the function and evolution of NORAD.
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Affiliation(s)
- Uciel Chorostecki
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, 29. 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ester Saus
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, 29. 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, 29. 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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18
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Vijayan M, Reddy PH. Non-Coding RNAs Based Molecular Links in Type 2 Diabetes, Ischemic Stroke, and Vascular Dementia. J Alzheimers Dis 2021; 75:353-383. [PMID: 32310177 DOI: 10.3233/jad-200070] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This article reviews recent advances in the study of microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and their functions in type 2 diabetes mellitus (T2DM), ischemic stroke (IS), and vascular dementia (VaD). miRNAs and lncRNAs are gene regulation markers that both regulate translational aspects of a wide range of proteins and biological processes in healthy and disease states. Recent studies from our laboratory and others have revealed that miRNAs and lncRNAs expressed differently are potential therapeutic targets for neurological diseases, especially T2DM, IS, VaD, and Alzheimer's disease (AD). Currently, the effect of aging in T2DM, IS, and VaD and the cellular and molecular pathways are largely unknown. In this article, we highlight results from the works on the molecular connections between T2DM and IS, and IS and VaD. In each disease, we also summarize the pathophysiology and the differential expressions of miRNAs and lncRNAs. Based on current research findings, we hypothesize that 1) T2DM bi-directionally and age-dependently induces IS and VaD, and 2) these changes are precursors to the onset of dementia in elderly people. Research into these hypotheses is required to examine further whether research efforts on reducing T2DM, IS, and VaD may affect dementia and/or delay the AD disease process in the aged population.
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Affiliation(s)
- Murali Vijayan
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Speech, Language and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Public Health, Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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Tassinari M, Richter SN, Gandellini P. Biological relevance and therapeutic potential of G-quadruplex structures in the human noncoding transcriptome. Nucleic Acids Res 2021; 49:3617-3633. [PMID: 33721024 PMCID: PMC8053107 DOI: 10.1093/nar/gkab127] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 12/11/2022] Open
Abstract
Noncoding RNAs are functional transcripts that are not translated into proteins. They represent the largest portion of the human transcriptome and have been shown to regulate gene expression networks in both physiological and pathological cell conditions. Research in this field has made remarkable progress in the comprehension of how aberrations in noncoding RNA drive relevant disease-associated phenotypes; however, the biological role and mechanism of action of several noncoding RNAs still need full understanding. Besides fulfilling its function through sequence-based mechanisms, RNA can form complex secondary and tertiary structures which allow non-canonical interactions with proteins and/or other nucleic acids. In this context, the presence of G-quadruplexes in microRNAs and long noncoding RNAs is increasingly being reported. This evidence suggests a role for RNA G-quadruplexes in controlling microRNA biogenesis and mediating noncoding RNA interaction with biological partners, thus ultimately regulating gene expression. Here, we review the state of the art of G-quadruplexes in the noncoding transcriptome, with their structural and functional characterization. In light of the existence and further possible development of G-quadruplex binders that modulate G-quadruplex conformation and protein interactions, we also discuss the therapeutic potential of G-quadruplexes as targets to interfere with disease-associated noncoding RNAs.
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Affiliation(s)
- Martina Tassinari
- Department of Biosciences, University of Milan, via G. Celoria 26, 20133 Milano, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padova, Italy
| | - Paolo Gandellini
- Department of Biosciences, University of Milan, via G. Celoria 26, 20133 Milano, Italy
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Studies on the Regulatory Roles and Related Mechanisms of lncRNAs in the Nervous System. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6657944. [PMID: 33791072 PMCID: PMC7984887 DOI: 10.1155/2021/6657944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/19/2020] [Accepted: 02/15/2021] [Indexed: 11/25/2022]
Abstract
Long noncoding RNAs (lncRNAs) have attracted extensive attention due to their regulatory role in various cellular processes. Emerging studies have indicated that lncRNAs are expressed to varying degrees after the growth and development of the nervous system as well as injury and degeneration, thus affecting various physiological processes of the nervous system. In this review, we have compiled various reported lncRNAs related to the growth and development of central and peripheral nerves and pathophysiology (including advanced nerve centers, spinal cord, and peripheral nervous system) and explained how these lncRNAs play regulatory roles through their interactions with target-coding genes. We believe that a full understanding of the regulatory function of lncRNAs in the nervous system will contribute to understand the molecular mechanism of changes after nerve injury and will contribute to discover new diagnostic markers and therapeutic targets for nerve injury diseases.
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21
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The Expanding Regulatory Mechanisms and Cellular Functions of Long Non-coding RNAs (lncRNAs) in Neuroinflammation. Mol Neurobiol 2021; 58:2916-2939. [PMID: 33555549 DOI: 10.1007/s12035-020-02268-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022]
Abstract
LncRNAs have emerged as important regulatory molecules in biological processes. They serve as regulators of gene expression pathways through interactions with proteins, RNA, and DNA. LncRNA expression is altered in several diseases of the central nervous system (CNS), such as neurodegenerative disorders, stroke, trauma, and infection. More recently, it has become clear that lncRNAs contribute to regulating both pro-inflammatory and anti-inflammatory pathways in the CNS. In this review, we discuss the molecular pathways involved in the expression of lncRNAs, their role and mechanism of action during gene regulation, cellular functions, and use of lncRNAs as therapeutic targets during neuroinflammation in CNS disorders.
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22
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Alfaifi M, Ali Beg MM, Alshahrani MY, Ahmad I, Alkhathami AG, Joshi PC, Alshehri OM, Alamri AM, Verma AK. Circulating long non-coding RNAs NKILA, NEAT1, MALAT1, and MIAT expression and their association in type 2 diabetes mellitus. BMJ Open Diabetes Res Care 2021; 9:9/1/e001821. [PMID: 33436407 PMCID: PMC7805373 DOI: 10.1136/bmjdrc-2020-001821] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/07/2020] [Accepted: 11/21/2020] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) is a multifactorial disorder that leads to alterations in gene regulation. Long non-coding RNAs (lncRNAs) have become a major research topic as they are involved in metabolic disorders. METHODS This study included a total of 400 study subjects; 200 were subjects with T2DM and 200 were healthy subjects. Extracted RNA was used to synthesize cDNA by quantitative real time. Serum analysis was carried out to determine differences in biochemical parameters. Recorded data were used to evaluate associations with expression of lncRNAs NF-kappaB interacting lncRNA (NKILA), nuclear enriched abundant transcript 1 (NEAT1), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), and myocardial infarction-associated transcript (MIAT) in T2DM cases. RESULTS Compared with healthy controls, patients with T2DM showed an overall increase in expression of lncRNAs NKILA, NEAT, MALAT1, and MIAT by 3.94-fold, 5.28-fold, 4.46-fold, and 6.35-fold, respectively. Among patients with T2DM, higher expression of lncRNA NKILA was associated with hypertension (p=0.001), smoking (p<0.0001), and alcoholism (p<0.0001). Altered NEAT1 expression was significantly associated with weight loss (p=0.04), fatigue (p=0.01), slow wound healing (p=0.002), blurred vision (p=0.008), loss of appetite (p=0.007), smoking (p<0.0001), and alcoholism (p<0.0001). Higher expression of lncRNA MALAT1 was significantly linked with weight loss (p=0.003), blurred vision (p=0.01), smoking (p<0.0001), and alcoholism (p<0.0001). Expression of lncRNA MIAT was associated with only blurred vision (p<0.0001), smoking (p<0.0001), and alcoholism (p<0.0001). Positive correlations of lncRNA NKILA with lncRNAs NEAT1 (r=0.42, p<0.0001), MALAT (r=0.36, p<0.0001) and MIAT (r=0.42, p<0.0001) were observed among patients with T2DM. Significant positive correlations of lncRNA NEAT with lncRNAs MALAT and MIAT were observed among patients with T2DM. A positive correlation between lncRNAs MALAT and MIAT was also observed among patients with T2DM. CONCLUSION Increased circulating NKILA, NEAT1, MALAT, and MIAT expression in patients with T2DM, which is linked with poor patient outcomes and significantly linked with alcoholism and smoking, may influence the degree and severity of disease among patients with T2DM. These lncRNAs may contribute to the progression of T2DM disease or other related diabetes-related complications.
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Affiliation(s)
- Mohammed Alfaifi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mirza Masroor Ali Beg
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi, Delhi, India
- Department of Biochemistry, Maulana Azad Medical College, New Delhi, India
| | - Mohammed Yahya Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Ali Gaithan Alkhathami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Prakash C Joshi
- Department of Zoology and Environmental Sciences, Gurukula Kangri University, Haridwar, Uttarakhand, India
| | - Osama M Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | | | - Amit Kumar Verma
- Department of Zoology and Environmental Sciences, Gurukula Kangri University, Haridwar, Uttarakhand, India
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, Delhi, India
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23
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FOXM1/LINC00152 feedback loop regulates proliferation and apoptosis in rheumatoid arthritis fibroblast-like synoviocytes via Wnt/β-catenin signaling pathway. Biosci Rep 2020; 40:221642. [PMID: 31854447 PMCID: PMC6974425 DOI: 10.1042/bsr20191900] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/29/2019] [Accepted: 12/18/2019] [Indexed: 12/14/2022] Open
Abstract
Rheumatoid arthritis (RA), a chronic systemic disease, is featured with inflammatory synovitis, which can lead to destruction on bone and cartilage and even cause disability. Emerging studies demonstrated that Fibroblast-like synoviocytes (FLS) is a vital cellular participant in RA progression. Long non-coding RNAs (lncRNAs) are also reported to participate in the pathogenesis of RA. In our present study, lncRNA microarray analysis was applied to screen out lncRNAs differentially expressed in RA FLS. Among which, cytoskeleton regulator RNA (LINC00152) presented biggest fold change. Gain- or loss-of function assays were further carried out in RA FLS, and the results revealed that LINC00152 promoted proliferation but induced apoptosis in RA FLS. Furthermore, up-regulation of LINC00152 may induce promotion of Wnt/β-catenin signaling pathway in RA FLS. Mechanistically, we found that forkhead box M1 (FOXM1) transcriptionally activated LINC00152 in RA FLS. Additionally, LINC00152 positively regulated FOXM1 via sponging miR-1270. In conclusion, the present study focused on elucidating the function of FOXM1/LINC00152 positive feedback loop in RA FLS and its association with Wnt/β-catenin signaling.
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24
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Hung SY, Lin CC, Hsu CL, Yao CY, Wang YH, Tsai CH, Hou HA, Chou WC, Tien HF. The expression levels of long non-coding RNA KIAA0125 are associated with distinct clinical and biological features in myelodysplastic syndromes. Br J Haematol 2020; 192:589-598. [PMID: 33249572 DOI: 10.1111/bjh.17231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022]
Abstract
Long non-coding RNAs (lncRNAs) have important functions in cancer biology. Among them, lncRNA KIAA0125 is one of the genes proposed to play a critical role in leukaemia stem cell (LSC). In this study, we aimed to investigate the clinical relevance of the expression levels of lncRNA KIAA0125 in myelodysplastic syndromes (MDS), a disease with highly heterogeneous clinical and biological features. Using RNA arrays, we measured the expression of KIAA0125 in 176 primary MDS patients. We found that higher KIAA0125 expression was associated with higher risk MDS, based on the revised International Prognostic Scoring System (IPSS-R), mutations in ASXL1 and NRAS, and predicted poorer overall survival (OS) and leukaemia-free survival (LFS). Multivariate analysis revealed that higher KIAA0125 expression was an independent, unfavourable prognostic factor for OS and LFS, irrespective of IPSS-R and mutation status. Further global gene expression profile analysis suggested a close association of higher KIAA0125 expressions with LSC signatures. The expression of KIAA0125 may be a potential biomarker to guide the treatment choice in MDS patients, especially those with lower risk subtypes, in whom palliative treatment is usually used.
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Affiliation(s)
- Sheng-Yu Hung
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | - Chien-Chin Lin
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei, Taiwan.,Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-Lang Hsu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Chi-Yuan Yao
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei, Taiwan.,Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Hung Wang
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Cheng-Hong Tsai
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Chien Chou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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25
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Xia W, Dou Y, Liu R, Gong S, Huang D, Fan H, Xiao Y. Genome-wide discovery and characterization of long noncoding RNAs in African oil palm ( Elaeis guineensis Jacq.). PeerJ 2020; 8:e9585. [PMID: 33194332 PMCID: PMC7643553 DOI: 10.7717/peerj.9585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 06/30/2020] [Indexed: 01/04/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are an important class of genes and play important roles in a range of biological processes. However, few reports have described the identification of lncRNAs in oil palm. In this study, we applied strand specific RNA-seq with rRNA removal to identify 1,363 lncRNAs from the equally mixed tissues of oil palm spear leaf and six different developmental stages of mesocarp (8–24 weeks). Based on strand specific RNA-seq data and 18 released oil palm transcriptomes, we systematically characterized the expression patterns of lncRNA loci and their target genes. A total of 875 uniq target genes for natural antisense lncRNAs (NAT-lncRNA, 712), long intergenic noncoding RNAs (lincRNAs, 92), intronic-lncRNAs (33), and sense-lncRNAs (52) were predicted. A majority of lncRNA loci (77.8%–89.6%) had low expression in 18 transcriptomes, while only 89 lncRNA loci had medium to high expression in at least one transcriptome. Coexpression analysis between lncRNAs and their target genes indicated that 6% of lncRNAs had expression patterns positively correlated with those of target genes. Based on single nucleotide polymorphism (SNP) markers derived from our previous research, 6,882 SNPs were detected for lncRNAs and 28 SNPs belonging to 21 lncRNAs were associated with the variation of fatty acid contents. Moreover, seven lncRNAs showed expression patterns positively correlated expression pattern with those of genes in de novo fatty acid synthesis pathways. Our study identified a collection of lncRNAs for oil palm and provided clues for further research into lncRNAs that may regulate mesocarp development and lipid metabolism.
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Affiliation(s)
- Wei Xia
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yajing Dou
- College of Tropical Crops, Hainan University, Haikou, China
| | - Rui Liu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Shufang Gong
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Dongyi Huang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Haikuo Fan
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yong Xiao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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26
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Das T, Deb A, Parida S, Mondal S, Khatua S, Ghosh Z. LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients. RNA Biol 2020; 18:1136-1151. [PMID: 33112702 DOI: 10.1080/15476286.2020.1833529] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of multiple species other than Human and Mouse. LncRBase V.2 hosts information of 549,648 lncRNAs corresponding to six additional species besides Human and Mouse, viz. Rat, Fruitfly, Zebrafish, Chicken, Cow and C.elegans. It provides additional distinct features such as (i) Transcription Factor Binding Site (TFBS) in the lncRNA promoter region, (ii) sub-cellular localization pattern of lncRNAs (iii) lnc-pri-miRNAs (iv) Possible small open reading frames (sORFs) within lncRNA. (v) Manually curated information of interacting target molecules and disease association of lncRNA genes (vi) Distribution of lncRNAs across multiple tissues of all species. Moreover, we have hosted ClinicLSNP within LncRBase V.2. ClinicLSNP has a comprehensive catalogue of lncRNA variants present within breast, ovarian, and cervical cancer inferred from 561 RNA-Seq data corresponding to these cancers. Further, we have checked whether these lncRNA variants overlap with (i)Repeat elements,(ii)CGI, (iii)TFBS within lncRNA loci (iv)SNP localization in trait-associated Linkage Disequilibrium(LD) region, (v)predicted the potentially pathogenic variants and (vi)effect of SNP on lncRNA secondary structure. Overall, LncRBaseV.2 is a user-friendly database to survey, search and retrieve information about multi-species lncRNAs. Further, ClinicLSNP will serve as a useful resource for cancer specific lncRNA variants and their related information. The database is freely accessible and available at http://dibresources.jcbose.ac.in/zhumur/lncrbase2/.
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Affiliation(s)
- Troyee Das
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Aritra Deb
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Sibun Parida
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Sudip Mondal
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Sunirmal Khatua
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
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27
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Saw PE, Xu X, Chen J, Song EW. Non-coding RNAs: the new central dogma of cancer biology. SCIENCE CHINA-LIFE SCIENCES 2020; 64:22-50. [PMID: 32930921 DOI: 10.1007/s11427-020-1700-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
The central dogma of molecular biology states that the functions of RNA revolve around protein translation. Until the last decade, most researches were geared towards characterization of RNAs as intermediaries in protein translation, namely, messenger RNAs (mRNAs) as temporary copies of genetic information, ribosomal RNAs (rRNAs) as a main component of ribosome, or translators of codon sequence (tRNAs). The statistical reality, however, is that these processes account for less than 2% of the genome, and insufficiently explain the functionality of 98% of transcribed RNAs. Recent discoveries have unveiled thousands of unique non-coding RNAs (ncRNAs) and shifted the perception of them from being "junk" transcriptional products to "yet to be elucidated"-and potentially monumentally important-RNAs. Most ncRNAs are now known as key regulators in various networks in which they could lead to specific cellular responses and fates. In major cancers, ncRNAs have been identified as both oncogenic drivers and tumor suppressors, indicating a complex regulatory network among these ncRNAs. Herein, we provide a comprehensive review of the various ncRNAs and their functional roles in cancer, and the pre-clinical and clinical development of ncRNA-based therapeutics. A deeper understanding of ncRNAs could facilitate better design of personalized therapeutics.
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Affiliation(s)
- Phei Er Saw
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Xiaoding Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Jianing Chen
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Er-Wei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China. .,Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
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28
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Jones AN, Pisignano G, Pavelitz T, White J, Kinisu M, Forino N, Albin D, Varani G. An evolutionarily conserved RNA structure in the functional core of the lincRNA Cyrano. RNA (NEW YORK, N.Y.) 2020; 26:1234-1246. [PMID: 32457084 PMCID: PMC7430676 DOI: 10.1261/rna.076117.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/18/2020] [Indexed: 05/08/2023]
Abstract
The wide prevalence and regulated expression of long noncoding RNAs (lncRNAs) highlight their functional roles, but the molecular basis for their activities and structure-function relationships remains to be investigated, with few exceptions. Among the relatively few lncRNAs conserved over significant evolutionary distances is the long intergenic noncoding RNA (lincRNA) Cyrano (orthologous to human OIP5-AS1), which contains a region of 300 highly conserved nucleotides within tetrapods, which in turn contains a functional stretch of 26 nt of deep conservation. This region binds to and facilitates the degradation of the microRNA miR-7, a short ncRNA with multiple cellular functions, including modulation of oncogenic expression. We probed the secondary structure of Cyrano in vitro and in cells using chemical and enzymatic probing, and validated the results using comparative sequence analysis. At the center of the functional core of Cyrano is a cloverleaf structure maintained over the >400 million years of divergent evolution that separates fish and primates. This strikingly conserved motif provides interaction sites for several RNA-binding proteins and masks a conserved recognition site for miR-7. Conservation in this region strongly suggests that the function of Cyrano depends on the formation of this RNA structure, which could modulate the rate and efficiency of degradation of miR-7.
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Affiliation(s)
- Alisha N Jones
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Giuseppina Pisignano
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR) and Oncology Institute of Southern Switzerland (IOSI), Bellinzona CH-6500, Switzerland
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Thomas Pavelitz
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Jessica White
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Martin Kinisu
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Nicholas Forino
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Dreycey Albin
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
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29
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Abstract
Long noncoding RNAs (lncRNAs) are a group of noncoding RNAs that are longer than 200 nucleotides without protein-coding potential. Becasuse of which these RNAs have no significant protein-coding potential, they were initially considered as "junk-products" of transcription without biological meaning. Nevertheless, recent research advancements have shown that lncRNAs are involved in many physiological processes such as cell cycle regulation, cell apoptosis and survival, cancer migration and metabolism. This review described the function of lncRNAs and the potential underlying mechanism involved in diabetes and diabetic microvascular complications. The roles of lncRNAs in the pathogenesis of type 2 diabetes mellitus have only recently been recognized, involving hepatic glucose production and insulin resistance. We further investigated the mechanisms of lncRNAs in diabetic nephropathy (DN), including the roles of lncRNAs in mesangial cells (MCs) proliferation and fibrosis, inflammatory processes, extracellular matrix accumulation in the glomeruli and tubular injury. We also discussed the potential mechanism of lncRNAs in diabetic retinopathy (DR), including aberrant neovascularization and neuronal dysfunction. This review summarized the current knowledge of the functions and underlying mechanisms of lncRNAs in type 2 diabetes mellitus and related renal and retinal complications. Accumulating evidence suggests the potential of lncRNAs as therapeutic targets for clinical applications in the management of diabetes.
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Affiliation(s)
- Yanxia Chen
- Department of Endocrinology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, PR China
| | - Yinxi He
- Department of Orthopaedic Trauma, The Third Hospital of Shijiazhuang, Shijiazhuang, Hebei, 050000, PR China
| | - Hong Zhou
- Department of Endocrinology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, PR China
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30
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Fasolo F, Di Gregoli K, Maegdefessel L, Johnson JL. Non-coding RNAs in cardiovascular cell biology and atherosclerosis. Cardiovasc Res 2020; 115:1732-1756. [PMID: 31389987 DOI: 10.1093/cvr/cvz203] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/14/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Atherosclerosis underlies the predominant number of cardiovascular diseases and remains a leading cause of morbidity and mortality worldwide. The development, progression and formation of clinically relevant atherosclerotic plaques involves the interaction of distinct and over-lapping mechanisms which dictate the roles and actions of multiple resident and recruited cell types including endothelial cells, vascular smooth muscle cells, and monocyte/macrophages. The discovery of non-coding RNAs (ncRNAs) including microRNAs, long non-coding RNAs, and circular RNAs, and their identification as key mechanistic regulators of mRNA and protein expression has piqued interest in their potential contribution to atherosclerosis. Accruing evidence has revealed ncRNAs regulate pivotal cellular and molecular processes during all stages of atherosclerosis including cell invasion, growth, and survival; cellular uptake and efflux of lipids, expression and release of pro- and anti-inflammatory intermediaries, and proteolytic balance. The expression profile of ncRNAs within atherosclerotic lesions and the circulation have been determined with the aim of identifying individual or clusters of ncRNAs which may be viable therapeutic targets alongside deployment as biomarkers of atherosclerotic plaque progression. Consequently, numerous in vivo studies have been convened to determine the effects of moderating the function or expression of select ncRNAs in well-characterized animal models of atherosclerosis. Together, clinicopathological findings and studies in animal models have elucidated the multifaceted and frequently divergent effects ncRNAs impose both directly and indirectly on the formation and progression of atherosclerosis. From these findings' potential novel therapeutic targets and strategies have been discovered which may pave the way for further translational studies and possibly taken forward for clinical application.
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Affiliation(s)
- Francesca Fasolo
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar-Technical University Munich, Biedersteiner Strasse 29, Munich, Germany
| | - Karina Di Gregoli
- Laboratory of Cardiovascular Pathology, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lars Maegdefessel
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar-Technical University Munich, Biedersteiner Strasse 29, Munich, Germany.,Molecular Vascular Medicine, Karolinska Institute, Center for Molecular Medicine L8:03, 17176 Stockholm, Sweden.,German Center for Cardiovascular Research (DZHK), Partner Site Munich (Munich Heart Alliance), Munich, Germany
| | - Jason L Johnson
- Laboratory of Cardiovascular Pathology, Bristol Medical School, University of Bristol, Bristol, UK
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Pereira IT, Spangenberg L, Cabrera G, Dallagiovanna B. Polysome-associated lncRNAs during cardiomyogenesis of hESCs. Mol Cell Biochem 2020; 468:35-45. [PMID: 32125578 DOI: 10.1007/s11010-020-03709-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/22/2020] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been found to be involved in many biological processes, including the regulation of cell differentiation, but a complete characterization of lncRNA is still lacking. Additionally, there is evidence that lncRNAs interact with ribosomes, raising questions about their functions in cells. Here, we used a developmentally staged protocol to induce cardiogenic commitment of hESCs and then investigated the differential association of lncRNAs with polysomes. Our results identified lncRNAs in both the ribosome-free and polysome-bound fractions during cardiogenesis and showed a very well-defined temporal lncRNA association with polysomes. Clustering of lncRNAs was performed according to the gene expression patterns during the five timepoints analyzed. In addition, differential lncRNA recruitment to polysomes was observed when comparing the differentially expressed lncRNAs in the ribosome-free and polysome-bound fractions or when calculating the polysome-bound vs ribosome-free ratio. The association of lncRNAs with polysomes could represent an additional cytoplasmic role of lncRNAs, e.g., in translational regulation of mRNA expression.
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Affiliation(s)
- Isabela Tiemy Pereira
- Basic Stem-Cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil
| | - Lucia Spangenberg
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Guillermo Cabrera
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Bruno Dallagiovanna
- Basic Stem-Cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil.
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32
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Aziz NB, Mahmudunnabi RG, Umer M, Sharma S, Rashid MA, Alhamhoom Y, Shim YB, Salomon C, Shiddiky MJA. MicroRNAs in ovarian cancer and recent advances in the development of microRNA-based biosensors. Analyst 2020; 145:2038-2057. [DOI: 10.1039/c9an02263e] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ovarian cancer is the most aggressive of all gynaecological malignancies and is the leading cause of cancer-associated mortality worldwide.
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Affiliation(s)
- Nahian Binte Aziz
- School of Environment and Science
- Griffith University
- Nathan Campus
- Australia
- School of Chemistry & Molecular Biosciences
| | - Rabbee G. Mahmudunnabi
- Department of Molecular Science Technology and Institute of BioPhysio Sensor Technology (IBST)
- Pusan National University
- Busan 46241
- Republic of Korea
| | - Muhammad Umer
- Queensland Micro and nanotechnology Centre
- Griffith University
- Nathan Campus
- Australia
| | - Shayna Sharma
- Exosome Biology Laboratory
- Centre for Clinical Diagnostics
- University of Queensland Centre for Clinical Research
- Royal Brisbane and Women's Hospital
- The University of Queensland
| | - Md Abdur Rashid
- Department of Pharmaceutics
- College of Pharmacy
- King Khalid University
- Abha
- Kingdom of Saudi Arabia
| | - Yahya Alhamhoom
- Department of Pharmaceutics
- College of Pharmacy
- King Khalid University
- Abha
- Kingdom of Saudi Arabia
| | - Yoon-Bo Shim
- Department of Chemistry and Institute of BioPhysio Sensor Technology (IBST)
- Pusan National University
- Busan 46241
- Republic of Korea
| | - Carlos Salomon
- Exosome Biology Laboratory
- Centre for Clinical Diagnostics
- University of Queensland Centre for Clinical Research
- Royal Brisbane and Women's Hospital
- The University of Queensland
| | - Muhammad J. A. Shiddiky
- School of Environment and Science
- Griffith University
- Nathan Campus
- Australia
- Queensland Micro and nanotechnology Centre
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33
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Gudenas BL, Wang J, Kuang SZ, Wei AQ, Cogill SB, Wang LJ. Genomic data mining for functional annotation of human long noncoding RNAs. J Zhejiang Univ Sci B 2019; 20:476-487. [PMID: 31090273 DOI: 10.1631/jzus.b1900162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Life may have begun in an RNA world, which is supported by increasing evidence of the vital role that RNAs perform in biological systems. In the human genome, most genes actually do not encode proteins; they are noncoding RNA genes. The largest class of noncoding genes is known as long noncoding RNAs (lncRNAs), which are transcripts greater in length than 200 nucleotides, but with no protein-coding capacity. While some lncRNAs have been demonstrated to be key regulators of gene expression and 3D genome organization, most lncRNAs are still uncharacterized. We thus propose several data mining and machine learning approaches for the functional annotation of human lncRNAs by leveraging the vast amount of data from genetic and genomic studies. Recent results from our studies and those of other groups indicate that genomic data mining can give insights into lncRNA functions and provide valuable information for experimental studies of candidate lncRNAs associated with human disease.
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Affiliation(s)
- Brian L Gudenas
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Jun Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Shu-Zhen Kuang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - An-Qi Wei
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Steven B Cogill
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Liang-Jiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
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34
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RNAdemocracy: an ensemble method for RNA secondary structure prediction using consensus scoring. Comput Biol Chem 2019; 83:107151. [DOI: 10.1016/j.compbiolchem.2019.107151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 06/05/2019] [Accepted: 10/15/2019] [Indexed: 11/18/2022]
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35
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Soda N, Rehm BHA, Sonar P, Nguyen NT, Shiddiky MJA. Advanced liquid biopsy technologies for circulating biomarker detection. J Mater Chem B 2019; 7:6670-6704. [PMID: 31646316 DOI: 10.1039/c9tb01490j] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Liquid biopsy is a new diagnostic concept that provides important information for monitoring and identifying tumor genomes in body fluid samples. Detection of tumor origin biomolecules like circulating tumor cells (CTCs), circulating tumor specific nucleic acids (circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), microRNAs (miRNAs), long non-coding RNAs (lnRNAs)), exosomes, autoantibodies in blood, saliva, stool, urine, etc. enables cancer screening, early stage diagnosis and evaluation of therapy response through minimally invasive means. From reliance on painful and hazardous tissue biopsies or imaging depending on sophisticated equipment, cancer management schemes are witnessing a rapid evolution towards minimally invasive yet highly sensitive liquid biopsy-based tools. Clinical application of liquid biopsy is already paving the way for precision theranostics and personalized medicine. This is achieved especially by enabling repeated sampling, which in turn provides a more comprehensive molecular profile of tumors. On the other hand, integration with novel miniaturized platforms, engineered nanomaterials, as well as electrochemical detection has led to the development of low-cost and simple platforms suited for point-of-care applications. Herein, we provide a comprehensive overview of the biogenesis, significance and potential role of four widely known biomarkers (CTCs, ctDNA, miRNA and exosomes) in cancer diagnostics and therapeutics. Furthermore, we provide a detailed discussion of the inherent biological and technical challenges associated with currently available methods and the possible pathways to overcome these challenges. The recent advances in the application of a wide range of nanomaterials in detecting these biomarkers are also highlighted.
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Affiliation(s)
- Narshone Soda
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery (GRIDD), Griffith University, Nathan, QLD 4111, Australia
| | - Prashant Sonar
- School of Chemistry, Physics and Mechanical Engineering, Molecular Design and Synthesis, Queensland University of Technology (QUT), Brisbane, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
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36
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Liu Q, Xiao Y, Cai P, Li J, Li D. Long noncoding RNA DINO (damage induced noncoding) represses the development of gastric cancer by modulating p21 and Bcl-2 Associated X Protein (Bax) expression. J Cell Biochem 2019; 120:11190-11195. [PMID: 30775800 DOI: 10.1002/jcb.28394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/26/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
lncRNAs are responsible for a variety of diseases, including gastric cancer (GC). Many recent studies have reported that lncRNAs can serve as crucial regulators of various genes. Nevertheless, the biological function of lncRNA damage induced noncoding (DINO) remained poorly investigated in GC. Therefore, in our present study, the detailed role of DINO was investigated. It was manifested that DINO was significantly downregulated in GC tissues. Then, DINO was modulated by infecting LV-DINO or by LV-shRNA in BGC-823 and MGC-803 cells. Moreover, it was displayed that GC cell proliferation was suppressed by DINO overexpression, whereas silencing DINO increased cell proliferation significantly. For another, it was indicated that DINO dramatically induced apoptotic ratios of BGC-823 and MGC-803 cells, whereas the decrease of DINO depressed GC cell apoptosis. Apart from these, GC cell cycle progression was greatly blocked by LV-DINO. Furthermore, Western blot results displayed that upregulation of DINO elevated p21 expression and Bax expression. Oppositely, inhibition of DINO greatly suppressed p21 and Bax protein expression level. Taken these, DINO might exert a tumor inhibitory role in the progression of GC through modulating p21 and Bax.
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Affiliation(s)
- Qinqiang Liu
- Department of General Surgery, Xuzhou Hospital of Traditional Chinese medicine, Xuzhou, Jiangsu, China
| | - Yan Xiao
- Anaesthesiology department, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, China
| | - Peng Cai
- Department of General Surgery, Xuzhou Hospital of Traditional Chinese medicine, Xuzhou, Jiangsu, China
| | - Jun Li
- Department of General Surgery, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Dawei Li
- Department of General Surgery, Xuzhou Hospital of Traditional Chinese medicine, Xuzhou, Jiangsu, China
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37
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Wang S, Zuo H, Jin J, Lv W, Xu Z, Fan Y, Zhang J, Zuo B. Long noncoding RNA Neat1 modulates myogenesis by recruiting Ezh2. Cell Death Dis 2019; 10:505. [PMID: 31243262 PMCID: PMC6594961 DOI: 10.1038/s41419-019-1742-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/02/2019] [Accepted: 06/13/2019] [Indexed: 12/14/2022]
Abstract
Neat1 is widely expressed in many tissues and cells and exerts pro-proliferation effects on many cancer cells. However, little is known about the function of Neat1 in myogenesis. Here we characterized the roles of Neat1 in muscle cell formation and muscle regeneration. Gain- or loss-of-function studies in C2C12 cells demonstrated that Neat1 accelerates myoblast proliferation but suppresses myoblast differentiation and fusion. Further, knockdown of Neat1 in vivo increased the cross-sectional area of muscle fibers but impaired muscle regeneration. Mechanically, Neat1 physically interacted with Ezh2 mainly through the core binding region (1001–1540 bp) and recruited Ezh2 to target gene promoters. Neat1 promoted myoblast proliferation mainly by decreasing the expression of the cyclin-dependent kinase inhibitor P21 gene but inhibited myoblast differentiation by suppressing the transcription of myogenic marker genes, such as Myog, Myh4, and Tnni2. Altogether, we uncover a previously unknown function of Neat1 in muscle development and the molecular mechanism by which Neat1 regulates myogenesis.
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Affiliation(s)
- Shanshan Wang
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Hao Zuo
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Jianjun Jin
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Wei Lv
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Zaiyan Xu
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Department of Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Yonghui Fan
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Jiali Zhang
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Bo Zuo
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China. .,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China. .,The Cooperative Innovation Center for Sustainable Pig Production, 430070, Wuhan, People's Republic of China.
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lncRNA PSORS1C3 is regulated by glucocorticoids and fine-tunes OCT4 expression in non-pluripotent cells. Sci Rep 2019; 9:8370. [PMID: 31182783 PMCID: PMC6557835 DOI: 10.1038/s41598-019-44827-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 05/20/2019] [Indexed: 11/29/2022] Open
Abstract
OCT4 is a transcription factor known for its regulatory roles in stemness, tumorigenesis and stress response. Considering its versatile functions, expression of OCT4 is regulated at different levels. PSORS1C3, a long non-coding RNA overlapped with OCT4, has a putative association with immune mediated diseases; however, its exact functions remained to be elucidated. Here, we demonstrated that PSORS1C3 is regulated by glucocorticoids (GC), has two endogenously active promoters, promoter 0 and 1, and two sets of transcripts, short and long variants. According to our findings, PSORS1C3 promoters behaved differently during neural differentiation of NT2 cells and glucocorticoid receptor (GR) activation. In both processes the expression pattern of short variants differed from that of long variants and was similar to OCT4 expression. Furthermore, our data revealed that PSORS1C3’s promoter 0 could act as an enhancer for OCT4 in non-pluripotent cells, where its deletion caused a significant decrease in OCT4 expression. Meanwhile, during GR activation promoter 0 functioned as a negative regulator and alleviated transcription induction of OCT4 after GC treatment. Altogether, our work clarified the structure and regulation of PSORS1C3, explained its relation to immune-related disease through GR signaling and introduced it as a novel fine-tuner of OCT4 expression in non-pluripotent cells.
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Zhang L, Meng X, Zhu XW, Yang DC, Chen R, Jiang Y, Xu T. Long non-coding RNAs in Oral squamous cell carcinoma: biologic function, mechanisms and clinical implications. Mol Cancer 2019; 18:102. [PMID: 31133028 PMCID: PMC6535863 DOI: 10.1186/s12943-019-1021-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 04/22/2019] [Indexed: 01/17/2023] Open
Abstract
There is growing evidence that regions of the genome that cannot encode proteins play an important role in diseases. These regions are usually transcribed into long non-coding RNAs (lncRNAs). LncRNAs, little or no coding potential, are defined as capped transcripts longer than 200 nucleotides. New sequencing technologies have shown that a large number of aberrantly expressed lncRNAs are associated with multiple cancer types and indicated they have emerged as an important class of pervasive genes during the development and progression of cancer. However, the underlying mechanism in cancer is still unknown. Therefore, it is necessary to elucidate the lncRNA function. Notably, many lncRNAs dysregulation are associated with Oral squamous cell carcinoma (OSCC) and affect various aspects of cellular homeostasis, including proliferation, survival, migration or genomic stability. This review expounds the up- or down-regulation of lncRNAs in OSCC and the molecular mechanisms by which lncRNAs perform their function in the malignant cell. Finally, the potential of lncRNAs as non-invasive biomarkers for OSCC diagnosis are also described. LncRNAs hold promise as prospective novel therapeutic targets, but more research is needed to gain a better understanding of their biologic function.
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Affiliation(s)
- Lei Zhang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China.,Department of Periodontology, College and Hospital of Stomatology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Xiang Meng
- School of Stomatology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Xin-Wei Zhu
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China.,Outpatient Department of Binhu District, College and Hospital of Stomatology, Anhui Medical University, Hefei, 230601, Anhui Province, China
| | - Deng-Cheng Yang
- School of Stomatology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Ran Chen
- School of Stomatology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Yong Jiang
- Department of Stomatology, The Fourth Affiliated Hospital of Anhui Medical University, 372 Tunxi Road, Hefei, 230000, Anhui Province, China.
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui Province, China. .,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui Province, China.
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40
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Zhang Y, Tao Y, Liao Q. Long noncoding RNA: a crosslink in biological regulatory network. Brief Bioinform 2019; 19:930-945. [PMID: 28449042 DOI: 10.1093/bib/bbx042] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 01/17/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) had been defined as a novel class of functional RNAs longer than 200 nucleotides around a decade ago. It is widely acknowledged that lncRNAs play a significant role in regulation of gene expression, but the biological and molecular mechanisms are diverse and complex, and remain to be determined. Especially, the regulatory network of lncRNAs associated with other biological molecules is still a controversial matter, thus becoming a new frontier of the studies on transcriptome. Recent advance in high-throughput sequencing technologies and bioinformatics approaches may be an accelerator to lift the mysterious veil. In this review, we will outline well-known associations between lncRNAs and other biological molecules, demonstrate the diverse bioinformatics approaches applied in prediction and analysis of lncRNA interaction and perform a case study for lncRNA linc00460 to concretely decipher the lncRNA regulatory network.
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Affiliation(s)
- Yuwei Zhang
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Yang Tao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Qi Liao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
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41
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Sarfi M, Abbastabar M, Khalili E. Long noncoding RNAs biomarker-based cancer assessment. J Cell Physiol 2019; 234:16971-16986. [PMID: 30835829 DOI: 10.1002/jcp.28417] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/04/2019] [Accepted: 02/14/2019] [Indexed: 12/18/2022]
Abstract
Cancer diagnosis have mainly relied on the incorporation of molecular biomarkers as part of routine diagnostic tool. The molecular alteration ranges from those involving DNA, RNA, noncoding RNAs (microRNAs and long noncoding RNAs [lncRNAs]) and proteins. lncRNAs are recently discovered noncoding endogenous RNAs that critically regulates the development, invasion, and metastasis of cancer cells. They are dysregulated in different types of malignancies and have the potential to serve as diagnostic markers for cancer. The expression of noncoding RNAs is altered following many diseases, and besides, some of them can be secreted from the cells into the circulation following the apoptotic and necrotic cell death. These secreted noncoding RNAs are known as cell free RNA. These RNAs can be secreted from the cell through the apoptotic body, extracellular vesicles including microvesicle and exosome, and bind to proteins. Since, lncRNAs display high organ and cell specificity, can be found in the blood, urine, tumor tissue, or other tissues or bodily fluids of some patients with cancer, this review summarizes the most significant and up-to-date findings of research on lncRNAs involvement in different cancers, focusing on the potential of cancer-related lncRNAs as biomarkers for diagnosis, prognosis, and therapy.
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Affiliation(s)
- Mohammad Sarfi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Students Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Abbastabar
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Students Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ehsan Khalili
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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42
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Yu T, Tzeng DTW, Li R, Chen J, Zhong S, Fu D, Zhu B, Luo Y, Zhu H. Genome-wide identification of long non-coding RNA targets of the tomato MADS box transcription factor RIN and function analysis. ANNALS OF BOTANY 2019; 123:469-482. [PMID: 30376036 PMCID: PMC6377105 DOI: 10.1093/aob/mcy178] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 10/08/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS In recent years, increasing numbers of long non-coding RNAs (lncRNAs) have been identified in humans, animals and plants, and several of them have been shown to play important roles in diverse biological processes. However, little work has been performed on the regulation mechanism of lncRNA biogenesis and expression, especially in plants. Compared with studies of tomato MADS-box transcription factor RIPENING INHIBITOR (RIN) target coding genes, there are few reports on its relationship to non-coding RNAs. The aim of the present study was to identify and explore the specific role of RIN target lncRNAs in tomato fruit development and ripening. METHODS lncRNA targets of RIN were identified by chromatin immunoprecipitation sequencing (ChIP-seq) combined with RNA deep sequencing analysis. Six selected lncRNA targets were validated by quantitative real-time PCR, ChIP and electrophoretic mobility shift assays, and we further confirmed differential expression between wild-type and ripening-deficient mutant fruit, and RIN direct binding in the promoter regions. By means of virus-induced gene silencing (VIGS) assays and a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome editing strategy, the ripening-related function of a specific target lncRNA (lncRNA2155) was studied. KEY RESULTS We identified 187 lncRNAs as direct RIN targets, which exhibited RIN binding sites in their promoters and showed different expression between the wild-type and rin mutant. Six target lncRNAs were shown to bind with RIN directly in their promoters in vivo and in vitro. Moreover, using CRISPR/Cas9 technology to knock out the locus of the target lncRNA2155 indicated that it delayed fruit ripening in tomato. CONCLUSIONS Collectively, these findings provide new insight into RIN in the transcriptional regulation of lncRNAs and suggest that lncRNAs will contribute to a better understanding of the RIN regulatory network that controls fruit ripening.
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Affiliation(s)
- Tongtong Yu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - David T W Tzeng
- EG12 Science Centre School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Ran Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jianye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bio resources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou, China
| | - Silin Zhong
- EG12 Science Centre School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Daqi Fu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Benzhong Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yunbo Luo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- For correspondence: and
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- For correspondence: and
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43
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Valanne S, Salminen TS, Järvelä-Stölting M, Vesala L, Rämet M. Immune-inducible non-coding RNA molecule lincRNA-IBIN connects immunity and metabolism in Drosophila melanogaster. PLoS Pathog 2019; 15:e1007504. [PMID: 30633769 PMCID: PMC6345493 DOI: 10.1371/journal.ppat.1007504] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 01/24/2019] [Accepted: 12/05/2018] [Indexed: 01/09/2023] Open
Abstract
Non-coding RNAs have important roles in regulating physiology, including immunity. Here, we performed transcriptome profiling of immune-responsive genes in Drosophila melanogaster during a Gram-positive bacterial infection, concentrating on long non-coding RNA (lncRNA) genes. The gene most highly induced by a Micrococcus luteus infection was CR44404, named Induced by Infection (lincRNA-IBIN). lincRNA-IBIN is induced by both Gram-positive and Gram-negative bacteria in Drosophila adults and parasitoid wasp Leptopilina boulardi in Drosophila larvae, as well as by the activation of the Toll or the Imd pathway in unchallenged flies. We show that upon infection, lincRNA-IBIN is expressed in the fat body, in hemocytes and in the gut, and its expression is regulated by NF-κB signaling and the chromatin modeling brahma complex. In the fat body, overexpression of lincRNA-IBIN affected the expression of Toll pathway -mediated genes. Notably, overexpression of lincRNA-IBIN in unchallenged flies elevated sugar levels in the hemolymph by enhancing the expression of genes important for glucose retrieval. These data show that lncRNA genes play a role in Drosophila immunity and indicate that lincRNA-IBIN acts as a link between innate immune responses and metabolism.
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Affiliation(s)
- Susanna Valanne
- Laboratory of Experimental Immunology, BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Tiina S. Salminen
- Laboratory of Experimental Immunology, BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Mirva Järvelä-Stölting
- Laboratory of Experimental Immunology, BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Laura Vesala
- Laboratory of Experimental Immunology, BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Mika Rämet
- Laboratory of Experimental Immunology, BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
- PEDEGO Research Unit, and Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
- * E-mail:
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44
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Akiyama M, Sato K, Sakakibara Y. A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model. J Bioinform Comput Biol 2019; 16:1840025. [PMID: 30616476 DOI: 10.1142/s0219720018400255] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A popular approach for predicting RNA secondary structure is the thermodynamic nearest-neighbor model that finds a thermodynamically most stable secondary structure with minimum free energy (MFE). For further improvement, an alternative approach that is based on machine learning techniques has been developed. The machine learning-based approach can employ a fine-grained model that includes much richer feature representations with the ability to fit the training data. Although a machine learning-based fine-grained model achieved extremely high performance in prediction accuracy, a possibility of the risk of overfitting for such a model has been reported. In this paper, we propose a novel algorithm for RNA secondary structure prediction that integrates the thermodynamic approach and the machine learning-based weighted approach. Our fine-grained model combines the experimentally determined thermodynamic parameters with a large number of scoring parameters for detailed contexts of features that are trained by the structured support vector machine (SSVM) with the [Formula: see text] regularization to avoid overfitting. Our benchmark shows that our algorithm achieves the best prediction accuracy compared with existing methods, and heavy overfitting cannot be observed. The implementation of our algorithm is available at https://github.com/keio-bioinformatics/mxfold .
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Affiliation(s)
- Manato Akiyama
- Department of Biosciences and Informatics, Keio University, 3–14–1 Hiyoshi, Kohoku-ku, Yokohama 223–8522, Japan
| | - Kengo Sato
- Department of Biosciences and Informatics, Keio University, 3–14–1 Hiyoshi, Kohoku-ku, Yokohama 223–8522, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, 3–14–1 Hiyoshi, Kohoku-ku, Yokohama 223–8522, Japan
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45
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Kramer MC, Gregory BD. Using Protein Interaction Profile Sequencing (PIP-seq) to Identify RNA Secondary Structure and RNA-Protein Interaction Sites of Long Noncoding RNAs in Plants. Methods Mol Biol 2019; 1933:343-361. [PMID: 30945196 DOI: 10.1007/978-1-4939-9045-0_21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
From the moment of transcription, RNA molecules are continuously bound by RNA-binding proteins (RBPs). While the majority of research has focused on how these RBPs regulate posttranscriptional gene regulation of messenger RNAs (mRNAs), the majority of cellular RNAs do not code for proteins, such as ribosomal RNAs, transfer RNAs, and microRNAs. Since these RNAs do not code for protein, their function is mainly determined by their interactions with RBPs as well as their intramolecular base pairing, or RNA secondary structure. One class of noncoding RNAs termed long noncoding RNAs (lncRNAs) have recently become the subject of intense research interest. To study the function of lncRNAs in eukaryotic cells, it is important to examine both their interactions with RBPs as well as their RNA secondary structure. Protein interaction profile sequencing (PIP-seq) is a genome-wide method that uses structure-specific ribonucleases (RNases) to identify regions of double-stranded and single-stranded RNA as well as regions that are protected from these RNases, which represent sites of RBP binding. This method is a very powerful way to examine RNA-protein interactions and RNA secondary structure of all lncRNAs expressed in cells and tissues and can reveal cell-type-specific or tissue-specific patterns of these RNA features. Here, we give a step-by-step account of performing this technique for comprehensively analyzing RNA-protein interactions and RNA secondary structure in plant transcriptomes.
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Affiliation(s)
- Marianne C Kramer
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
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47
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Moqtaderi Z, Geisberg JV, Struhl K. Extensive Structural Differences of Closely Related 3' mRNA Isoforms: Links to Pab1 Binding and mRNA Stability. Mol Cell 2018; 72:849-861.e6. [PMID: 30318446 PMCID: PMC6289678 DOI: 10.1016/j.molcel.2018.08.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/05/2018] [Accepted: 08/29/2018] [Indexed: 12/24/2022]
Abstract
Alternative polyadenylation generates numerous 3' mRNA isoforms that can vary in biological properties, such as stability and localization. We developed methods to obtain transcriptome-scale structural information and protein binding on individual 3' mRNA isoforms in vivo. Strikingly, near-identical mRNA isoforms can possess dramatically different structures throughout the 3' UTR. Analyses of identical mRNAs in different species or refolded in vitro indicate that structural differences in vivo are often due to trans-acting factors. The level of Pab1 binding to poly(A)-containing isoforms is surprisingly variable, and differences in Pab1 binding correlate with the extent of structural variation for closely spaced isoforms. A pattern encompassing single-strandedness near the 3' terminus, double-strandedness of the poly(A) tail, and low Pab1 binding is associated with mRNA stability. Thus, individual 3' mRNA isoforms can be remarkably different physical entities in vivo. Sequences responsible for isoform-specific structures, differential Pab1 binding, and mRNA stability are evolutionarily conserved, indicating biological function.
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Affiliation(s)
- Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph V Geisberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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48
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Qian X, Zhao J, Yeung PY, Zhang QC, Kwok CK. Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches. Trends Biochem Sci 2018; 44:33-52. [PMID: 30459069 DOI: 10.1016/j.tibs.2018.09.012] [Citation(s) in RCA: 290] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/11/2018] [Accepted: 09/19/2018] [Indexed: 11/28/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as significant players in almost every level of gene function and regulation. Thus, characterizing the structures and interactions of lncRNAs is essential for understanding their mechanistic roles in cells. Through a combination of (bio)chemical approaches and automated capillary and high-throughput sequencing (HTS), the complexity and diversity of RNA structures and interactions has been revealed in the transcriptomes of multiple species. These methods have uncovered important biological insights into the mechanistic and functional roles of lncRNA in gene expression and RNA metabolism, as well as in development and disease. In this review, we summarize the latest sequencing strategies to reveal RNA structure, RNA-RNA, RNA-DNA, and RNA-protein interactions, and highlight the recent applications of these approaches to map functional lncRNAs. We discuss the advantages and limitations of these strategies, and provide recommendations to further advance methodologies capable of mapping RNA structure and interactions in order to discover new biology of lncRNAs and decipher their molecular mechanisms and implication in diseases.
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Affiliation(s)
- Xingyang Qian
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; These authors contributed equally to this work
| | - Jieyu Zhao
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China; These authors contributed equally to this work
| | - Pui Yan Yeung
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China; These authors contributed equally to this work
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
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Dhanoa JK, Sethi RS, Verma R, Arora JS, Mukhopadhyay CS. Long non-coding RNA: its evolutionary relics and biological implications in mammals: a review. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2018; 60:25. [PMID: 30386629 PMCID: PMC6201556 DOI: 10.1186/s40781-018-0183-7] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/05/2018] [Indexed: 02/08/2023]
Abstract
The central dogma of gene expression propounds that DNA is transcribed to mRNA and finally gets translated into protein. Only 2–3% of the genomic DNA is transcribed to protein-coding mRNA. Interestingly, only a further minuscule part of genomic DNA encodes for long non-coding RNAs (lncRNAs) which are characteristically more than 200 nucleotides long and can be transcribed from both protein-coding (e.g. H19 and TUG1) as well as non-coding DNA by RNA polymerase II. The lncRNAs do not have open reading frames (with some exceptions), 3`-untranslated regions (3’-UTRs) and necessarily these RNAs lack any translation-termination regions, however, these can be spliced, capped and polyadenylated as mRNA molecules. The flexibility of lncRNAs confers them specific 3D-conformations that eventually enable the lncRNAs to interact with proteins, DNA or other RNA molecules via base pairing or by forming networks. The lncRNAs play a major role in gene regulation, cell differentiation, cancer cell invasion and metastasis and chromatin remodeling. Deregulation of lncRNA is also responsible for numerous diseases in mammals. Various studies have revealed their significance as biomarkers for prognosis and diagnosis of cancer. The aim of this review is to overview the salient features, evolution, biogenesis and biological importance of these molecules in the mammalian system.
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Affiliation(s)
- Jasdeep Kaur Dhanoa
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
| | - Ram Saran Sethi
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
| | - Ramneek Verma
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
| | - Jaspreet Singh Arora
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
| | - Chandra Sekhar Mukhopadhyay
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab India
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Long noncoding RNA SYISL regulates myogenesis by interacting with polycomb repressive complex 2. Proc Natl Acad Sci U S A 2018; 115:E9802-E9811. [PMID: 30279181 DOI: 10.1073/pnas.1801471115] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Although many long noncoding RNAs (lncRNAs) have been identified in muscle, their physiological function and regulatory mechanisms remain largely unexplored. In this study, we systematically characterized the expression profiles of lncRNAs during C2C12 myoblast differentiation and identified an intronic lncRNA, SYISL (SYNPO2 intron sense-overlapping lncRNA), that is highly expressed in muscle. Functionally, SYISL promotes myoblast proliferation and fusion but inhibits myogenic differentiation. SYISL knockout in mice results in significantly increased muscle fiber density and muscle mass. Mechanistically, SYISL recruits the enhancer of zeste homolog 2 (EZH2) protein, the core component of polycomb repressive complex 2 (PRC2), to the promoters of the cell-cycle inhibitor gene p21 and muscle-specific genes such as myogenin (MyoG), muscle creatine kinase (MCK), and myosin heavy chain 4 (Myh4), leading to H3K27 trimethylation and epigenetic silencing of target genes. Taken together, our results reveal that SYISL is a repressor of muscle development and plays a vital role in PRC2-mediated myogenesis.
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