201
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Chen R, Xu X, Huang L, Zhong W, Cui L. The Regulatory Role of Long Noncoding RNAs in Different Brain Cell Types Involved in Ischemic Stroke. Front Mol Neurosci 2019; 12:61. [PMID: 30967760 PMCID: PMC6440499 DOI: 10.3389/fnmol.2019.00061] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/22/2019] [Indexed: 01/01/2023] Open
Abstract
Stroke results in high morbidity and high mortality worldwide, with ischemic stroke accounting for 80% to 85%. As effective treatments for ischemic stroke remain limited because of the narrow therapeutic time window, a better understanding of the pathologic mechanism and new therapeutic intervention targets are needed. Due to the development of next-generation sequencing technologies and the genome-wide analysis of eukaryotic transcriptomes, a large amount of evidence to date demonstrates that long noncoding RNAs (lncRNAs) play a vital role in gene regulation and in ischemic stroke. In recent years, many studies have been focused on the clinical significance of lncRNAs in ischemic stroke, and data shows that the pathological processes underlying ischemic stroke are driven by interactions among different brain cell types, including neurons, glial cells, and vascular cells, which actively participate in the mechanisms of tissue injury and repair. In this mini review article, we provide an overview of the characteristics and underlying regulation mechanisms of lncRNAs relevant to different brain cell types during the course of ischemic stroke. Moreover, we reveal the roles of lncRNAs as potential biomarkers and treatment targets in ischemic stroke.
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Affiliation(s)
- Runsen Chen
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Xiangming Xu
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Lidan Huang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Wangtao Zhong
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Lili Cui
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
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202
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Volatile Evolution of Long Non-Coding RNA Repertoire in Retinal Pigment Epithelium: Insights from Comparison of Bovine and Human RNA Expression Profiles. Genes (Basel) 2019; 10:genes10030205. [PMID: 30857256 PMCID: PMC6471466 DOI: 10.3390/genes10030205] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 11/17/2022] Open
Abstract
Currently, several long non-coding RNAs (lncRNAs) (TUG1, MALAT1, MEG3 and others) have been discovered to regulate normal visual function and may potentially contribute to dysfunction of the retina. We decided to extend these analyses of lncRNA genes to the retinal pigment epithelium (RPE) to determine whether there is conservation of RPE-expressed lncRNA between human and bovine genomes. We reconstructed bovine RPE lncRNAs based on genome-guided assembly. Next, we predicted homologous human transcripts based on whole genome alignment. We found a small set of conserved lncRNAs that could be involved in signature RPE functions that are conserved across mammals. However, the fraction of conserved lncRNAs in the overall pool of lncRNA found in RPE appeared to be very small (less than 5%), perhaps reflecting a fast and flexible adaptation of the mammalian eye to various environmental conditions.
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203
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Zhang N, Shuai K, Cheng J, Yang W, Kan Z. LncRNA linc01116 prometes glioma cell migration and invasion by modulation of radixin targeted by miR-31. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:1078-1086. [PMID: 31933922 PMCID: PMC6945163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/21/2018] [Indexed: 06/10/2023]
Abstract
BACKGROUND Long non-coding RNA (lncRNA) linc01116 was found to be abnormally expressed in many malignant tumor tissues and involved in cancer progression, but its expression and role in glioma tissue is still unclear. This study was designed to investigate the expression of linc01116 in glioma tissues and the role of linc01116 in glioma cell migration and invasion. METHODS Linc01116 and miR-31 expression was measured in 135 cases of human glioma tissues and normal brain tissues using Real-time quantitative PCR (RT-qPCR). The function of linc01116 in glioma cells was determined by Transwell invasion assays and nude mice metastasis assay. Luciferase reporter system was used to confirm the connection between linc01116 and miR-31, or miR-31 and radixin. RESULTS Linc01116 is highly expressed in glioma tissue and cells, along with low expression of miR-31, and there was a negative correlation between the expression of linc01116 and miR-31 in glioma tissue. In addition, the expression of linc01116 in glioma patients with metastasis was significantly higher than that in patients without metastasis, while miR-31 was significantly lower. In vitro and in vivo studies shown that linc01116 promoted invasion and migration of glioma cells. The luciferase gene reporter system had confirmed that linc01116 targeted miR-31 and miR-31 targeted radixin in U251 cells. Moreover, radixin was downregulated and decreased E-cadherin protein expression, but increased MMP-9 and vimentin protein expression in U251 cells. CONCLUSION LncRNA linc01116 is highly expressed in glioma tissues, and it promotes glioma cell migration and invasion by modulation of radixin targeted by miR-31.
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Affiliation(s)
- Nan Zhang
- Department of Neurosurgery, Beijing Anzhen Hospital, Capital Medical UniversityBeijing, China
| | - Kegang Shuai
- Department of Neurosurgery, Drum Tower Hospital of Nanjing XianLinNanjing, China
| | - Junjun Cheng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Wei Yang
- Department of Neurosurgery, Beijing Anzhen Hospital, Capital Medical UniversityBeijing, China
| | - Zhisheng Kan
- Department of Neurosurgery, Beijing Anzhen Hospital, Capital Medical UniversityBeijing, China
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204
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Nozawa RS, Gilbert N. RNA: Nuclear Glue for Folding the Genome. Trends Cell Biol 2019; 29:201-211. [DOI: 10.1016/j.tcb.2018.12.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/10/2018] [Accepted: 12/14/2018] [Indexed: 12/20/2022]
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205
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Xiao H, Zhu Q, Zhou J. Long non-coding RNA MALAT1 interaction with miR-429 regulates the proliferation and EMT of lung adenocarcinoma cells through RhoA. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:419-430. [PMID: 31933847 PMCID: PMC6945089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/13/2018] [Indexed: 06/10/2023]
Abstract
Homo sapiens metastasis associated lung adenocarcinoma transcript 1 (LncRNA MALAT1) plays an important role in many types of cancer, but its role in human lung adenocarcinoma (LAC) is still unclear. In this paper, we found that LncRNA MALAT1 had high expression in human LAC tissues (vs. paracancerous normal tissue) and human lung adenocarcinoma cells (vs. human normal lung tissue cells). The expression of lncRNA MALAT1 was significantly associated with human lung adenocarcinoma tumor size, lymph node metastasis, and TNM staging, and was negatively correlated with miR-429 expression in lung adenocarcinoma tissues. In vitro, LncRNA MALAT1 could block human LAC cells in the G1 phase to inhibit proliferation by reducing the expression of cyclin D1 protein. LncRNA MALAT1 could inhibit the invasion and migration of human LAC cells by decreasing the expression of MMP-9 and vimentin and increasing the expression of E-cadherin. We also found that Malat1 functions as a competing endogenous RNA (ceRNA) for miR-429 and directly suppressed the expression of RhoA protein. RhoA knockout and transfection of miR-429-mimic could play the same function which is to decrease the expression of cyclin D1, MMP-9, and vimentin proteins and increased E-cadherin protein expression. These results suggested that LncRNA Malat1 could promote the proliferation and EMT of human lung adenocarcinoma cells by competing with RhoA for binding to miR-429.
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Affiliation(s)
- Haiping Xiao
- Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of PLAGuangzhou, Guangdong Province, China
| | - Qihang Zhu
- Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of PLAGuangzhou, Guangdong Province, China
| | - Jianlong Zhou
- Cancer Research Institute, Southern Medical UniversityGuangzhou, Guangdong Province, China
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206
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Carlevaro-Fita J, Polidori T, Das M, Navarro C, Zoller TI, Johnson R. Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs. Genome Res 2019. [PMID: 30587508 DOI: 10.1101/gr.229922.117.freely] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
Abstract
The sequence domains underlying long noncoding RNA (lncRNA) activities, including their characteristic nuclear enrichment, remain largely unknown. It has been proposed that these domains can originate from neofunctionalized fragments of transposable elements (TEs), otherwise known as RIDLs (repeat insertion domains of lncRNA), although just a handful have been identified. It is challenging to distinguish functional RIDL instances against a numerous genomic background of neutrally evolving TEs. We here show evidence that a subset of TE types experience evolutionary selection in the context of lncRNA exons. Together these comprise an enrichment group of 5374 TE fragments in 3566 loci. Their host lncRNAs tend to be functionally validated and associated with disease. This RIDL group was used to explore the relationship between TEs and lncRNA subcellular localization. By using global localization data from 10 human cell lines, we uncover a dose-dependent relationship between nuclear/cytoplasmic distribution and evolutionarily conserved L2b, MIRb, and MIRc elements. This is observed in multiple cell types and is unaffected by confounders of transcript length or expression. Experimental validation with engineered transgenes shows that these TEs drive nuclear enrichment in a natural sequence context. Together these data reveal a role for TEs in regulating the subcellular localization of lncRNAs.
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Affiliation(s)
- Joana Carlevaro-Fita
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Taisia Polidori
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Monalisa Das
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Carmen Navarro
- Department of Computer Science and Artificial Intelligence, University of Granada, 18071 Granada, Spain
| | - Tatjana I Zoller
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Rory Johnson
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
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207
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Zhang F, Ding L, Cui L, Barber R, Deng B. Identification of long non-coding RNA-related and -coexpressed mRNA biomarkers for hepatocellular carcinoma. BMC Med Genomics 2019; 12:25. [PMID: 30704465 PMCID: PMC6357343 DOI: 10.1186/s12920-019-0472-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND While changes in mRNA expression during tumorigenesis have been used widely as molecular biomarkers for the diagnosis of a number of cancers, the approach has limitations. For example, traditional methods do not consider the regulatory and positional relationship between mRNA and lncRNA. The latter has been largely shown to possess tumor suppressive or oncogenic properties. The combined analysis of mRNA and lncRNA is likely to facilitate the identification of biomarkers with higher confidence. RESULTS Therefore, we have developed an lncRNA-related method to identify traditional mRNA biomarkers. First we identified mRNAs that are differentially expressed in Hepatocellular Carcinoma (HCC) by comparing cancer and matched adjacent non-tumorous liver tissues. Then, we performed mRNA-lncRNA relationship and coexpression analysis and obtained 41 lncRNA-related and -coexpressed mRNA biomarkers. Next, we performed network analysis, gene ontology analysis and pathway analysis to unravel the functional roles and molecular mechanisms of these lncRNA-related and -coexpressed mRNA biomarkers. Finally, we validated the prediction and performance of the 41 lncRNA-related and -coexpressed mRNA biomarkers using Support Vector Machine model with five-fold cross-validation in an independent HCC dataset from RNA-seq. CONCLUSIONS Our results suggested that mRNAs expression profiles coexpressed with positionally related lncRNAs can provide important insights into early diagnosis and specific targeted gene therapy of HCC.
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Affiliation(s)
- Fan Zhang
- Vermont Genetics Network, University of Vermont, Burlington, VT 05405 USA
- Department of Biology, University of Vermont, Burlington, VT 05405 USA
| | - Linda Ding
- School of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0606 USA
| | - Li Cui
- Department of Neurosciences, School of Medicine, University of California, San Diego, 9500 Gilman Drive #0949, La Jolla, CA 92093 USA
| | - Robert Barber
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX USA
| | - Bin Deng
- Vermont Genetics Network, University of Vermont, Burlington, VT 05405 USA
- Department of Biology, University of Vermont, Burlington, VT 05405 USA
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208
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Butova R, Vychytilova-Faltejskova P, Souckova A, Sevcikova S, Hajek R. Long Non-Coding RNAs in Multiple Myeloma. Noncoding RNA 2019; 5:E13. [PMID: 30682861 PMCID: PMC6468639 DOI: 10.3390/ncrna5010013] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Multiple myeloma (MM) is the second most common hematooncological disease of malignant plasma cells in the bone marrow. While new treatment brought unprecedented increase of survival of patients, MM pathogenesis is yet to be clarified. Increasing evidence of expression of long non-coding RNA molecules (lncRNA) linked to development and progression of many tumors suggested their important role in tumorigenesis. To date, over 15,000 lncRNA molecules characterized by diversity of function and specificity of cell distribution were identified in the human genome. Due to their involvement in proliferation, apoptosis, metabolism, and differentiation, they have a key role in the biological processes and pathogenesis of many diseases, including MM. This review summarizes current knowledge of non-coding RNAs (ncRNA), especially lncRNAs, and their role in MM pathogenesis. Undeniable involvement of lncRNAs in MM development suggests their potential as biomarkers.
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Affiliation(s)
- Romana Butova
- Babak Myeloma Group, Department of Pathological Physiology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic.
| | | | - Adela Souckova
- Babak Myeloma Group, Department of Pathological Physiology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic.
| | - Sabina Sevcikova
- Babak Myeloma Group, Department of Pathological Physiology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic.
| | - Roman Hajek
- Department of Hematooncology, University Hospital Ostrava and Faculty of Medicine, University Ostrava, 70852 Ostrava, Czech Republic.
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209
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Mauger F, Deleuze JF. Technological advances in studying epigenetics biomarkers of prognostic potential for clinical research. PROGNOSTIC EPIGENETICS 2019:45-83. [DOI: 10.1016/b978-0-12-814259-2.00003-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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210
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Parks MM. An exact test for comparing a fixed quantitative property between gene sets. Bioinformatics 2018; 34:971-977. [PMID: 29088314 DOI: 10.1093/bioinformatics/btx693] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/26/2017] [Indexed: 01/10/2023] Open
Abstract
Motivation A significant difference in the distribution of a feature between two gene sets can provide insight into function or regulation. This statistical setting differs from much of hypothesis testing theory because the genome is often considered to be effectively fixed, finite and entirely known in commonly studied organisms, such as human. The Mann-Whitney U test is commonly employed in this scenario despite the assumptions of the test not being met, leading to unreliable and generally underpowered results. Permutation tests are also commonly employed for this purpose, but are computationally burdensome and are not tractable for obtaining small P values or for multiple comparisons. Results We present an exact test for the null hypothesis that gene set membership is independent of the quantitative gene feature of interest. We derive an analytic expression for the randomization distribution of the median of the quantitative feature under the null hypothesis. Efficient implementation permits calculation of precise P values of arbitrary magnitude and makes thousands of simultaneous tests of transcriptome-sized gene sets computationally tractable. The flexibility of the hypothesis testing framework presented permits extension to a variety of related tests commonly found in genomics. The exact test is used to identify signatures of translation control and protein function in the human genome. Availability and implementation The exact test presented here is implemented in R in the package kpmt available on CRAN. Contact map2085@med.cornell.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthew M Parks
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
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211
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Carlevaro-Fita J, Polidori T, Das M, Navarro C, Zoller TI, Johnson R. Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs. Genome Res 2018; 29:208-222. [PMID: 30587508 PMCID: PMC6360812 DOI: 10.1101/gr.229922.117] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 12/18/2018] [Indexed: 01/02/2023]
Abstract
The sequence domains underlying long noncoding RNA (lncRNA) activities, including their characteristic nuclear enrichment, remain largely unknown. It has been proposed that these domains can originate from neofunctionalized fragments of transposable elements (TEs), otherwise known as RIDLs (repeat insertion domains of lncRNA), although just a handful have been identified. It is challenging to distinguish functional RIDL instances against a numerous genomic background of neutrally evolving TEs. We here show evidence that a subset of TE types experience evolutionary selection in the context of lncRNA exons. Together these comprise an enrichment group of 5374 TE fragments in 3566 loci. Their host lncRNAs tend to be functionally validated and associated with disease. This RIDL group was used to explore the relationship between TEs and lncRNA subcellular localization. By using global localization data from 10 human cell lines, we uncover a dose-dependent relationship between nuclear/cytoplasmic distribution and evolutionarily conserved L2b, MIRb, and MIRc elements. This is observed in multiple cell types and is unaffected by confounders of transcript length or expression. Experimental validation with engineered transgenes shows that these TEs drive nuclear enrichment in a natural sequence context. Together these data reveal a role for TEs in regulating the subcellular localization of lncRNAs.
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Affiliation(s)
- Joana Carlevaro-Fita
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.,Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Taisia Polidori
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.,Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Monalisa Das
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.,Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Carmen Navarro
- Department of Computer Science and Artificial Intelligence, University of Granada, 18071 Granada, Spain
| | - Tatjana I Zoller
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.,Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Rory Johnson
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.,Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
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212
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An H, Williams NG, Shelkovnikova TA. NEAT1 and paraspeckles in neurodegenerative diseases: A missing lnc found? Noncoding RNA Res 2018; 3:243-252. [PMID: 30533572 PMCID: PMC6257911 DOI: 10.1016/j.ncrna.2018.11.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/13/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative diseases are among the most common causes of disability worldwide. Although neurodegenerative diseases are heterogeneous in both their clinical features and the underlying physiology, they are all characterised by progressive loss of specific neuronal populations. Recent experimental evidence suggests that long non-coding RNAs (lncRNAs) play important roles in the CNS in health and disease. Nuclear Paraspeckle Assembly Transcript 1 (NEAT1) is an abundant, ubiquitously expressed lncRNA, which forms a scaffold for a specific RNA granule in the nucleus, or nuclear body, the paraspeckle. Paraspeckles act as molecular hubs for cellular processes commonly affected by neurodegeneration. Transcriptomic analyses of the diseased human tissue have revealed altered NEAT1 levels in the CNS in major neurodegenerative disorders as well as in some disease models. Although it is clear that changes in NEAT1 expression (and in some cases, paraspeckle assembly) accompany neuronal damage, our understanding of NEAT1 contribution to the disease pathogenesis is still rudimentary. In this review, we have summarised the available knowledge on NEAT1 involvement in the molecular processes linked to neurodegeneration and on NEAT1 dysregulation in this type of disease, with a special focus on amyotrophic lateral sclerosis. The goal of this review is to attract the attention of researchers in the field of neurodegeneration to NEAT1 and paraspeckles.
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Affiliation(s)
- Haiyan An
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Non G Williams
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Tatyana A Shelkovnikova
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
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213
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Behjati Ardakani F, Kattler K, Nordström K, Gasparoni N, Gasparoni G, Fuchs S, Sinha A, Barann M, Ebert P, Fischer J, Hutter B, Zipprich G, Imbusch CD, Felder B, Eils J, Brors B, Lengauer T, Manke T, Rosenstiel P, Walter J, Schulz MH. Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters. Epigenetics Chromatin 2018; 11:66. [PMID: 30414612 PMCID: PMC6230222 DOI: 10.1186/s13072-018-0236-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 10/26/2018] [Indexed: 01/12/2023] Open
Abstract
Background Bidirectional promoters (BPs) are prevalent in eukaryotic genomes. However, it is poorly understood how the cell integrates different epigenomic information, such as transcription factor (TF) binding and chromatin marks, to drive gene expression at BPs. Single-cell sequencing technologies are revolutionizing the field of genome biology. Therefore, this study focuses on the integration of single-cell RNA-seq data with bulk ChIP-seq and other epigenetics data, for which single-cell technologies are not yet established, in the context of BPs. Results We performed integrative analyses of novel human single-cell RNA-seq (scRNA-seq) data with bulk ChIP-seq and other epigenetics data. scRNA-seq data revealed distinct transcription states of BPs that were previously not recognized. We find associations between these transcription states to distinct patterns in structural gene features, DNA accessibility, histone modification, DNA methylation and TF binding profiles. Conclusions Our results suggest that a complex interplay of all of these elements is required to achieve BP-specific transcriptional output in this specialized promoter configuration. Further, our study implies that novel statistical methods can be developed to deconvolute masked subpopulations of cells measured with different bulk epigenomic assays using scRNA-seq data. Electronic supplementary material The online version of this article (10.1186/s13072-018-0236-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fatemeh Behjati Ardakani
- Excellence Cluster for Multimodal Computing and Interaction, Saarland Informatics Campus, Saarland University, Campus E1 7, Saarbrücken, 66123, Germany.,Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics, Campus E 4, Saarbrücken, 66123, Germany.,Graduate School of Computer Science, Saarland University, Campus E1 3, Saarbrücken, 66123, Germany
| | - Kathrin Kattler
- Department of Genetics, University of Saarland, Campus A2 4, Saarbrücken, 66123, Germany
| | - Karl Nordström
- Department of Genetics, University of Saarland, Campus A2 4, Saarbrücken, 66123, Germany
| | - Nina Gasparoni
- Department of Genetics, University of Saarland, Campus A2 4, Saarbrücken, 66123, Germany
| | - Gilles Gasparoni
- Department of Genetics, University of Saarland, Campus A2 4, Saarbrücken, 66123, Germany
| | - Sarah Fuchs
- Department of Genetics, University of Saarland, Campus A2 4, Saarbrücken, 66123, Germany
| | - Anupam Sinha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Rosalind-Franklin-Str. 12, Kiel, 24105, Germany
| | - Matthias Barann
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Rosalind-Franklin-Str. 12, Kiel, 24105, Germany
| | - Peter Ebert
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics, Campus E 4, Saarbrücken, 66123, Germany.,Graduate School of Computer Science, Saarland University, Campus E1 3, Saarbrücken, 66123, Germany
| | - Jonas Fischer
- Excellence Cluster for Multimodal Computing and Interaction, Saarland Informatics Campus, Saarland University, Campus E1 7, Saarbrücken, 66123, Germany.,Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics, Campus E 4, Saarbrücken, 66123, Germany.,Graduate School of Computer Science, Saarland University, Campus E1 3, Saarbrücken, 66123, Germany
| | - Barbara Hutter
- Applied Bioinformatics, Deutsches Krebsforschungszentrum, Berliner-Str. 41, Heidelberg, 69120, Germany
| | - Gideon Zipprich
- Data Management and Genomics IT, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Charles D Imbusch
- Applied Bioinformatics, Deutsches Krebsforschungszentrum, Berliner-Str. 41, Heidelberg, 69120, Germany
| | - Bärbel Felder
- Data Management and Genomics IT, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Jürgen Eils
- Data Management and Genomics IT, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Benedikt Brors
- Applied Bioinformatics, Deutsches Krebsforschungszentrum, Berliner-Str. 41, Heidelberg, 69120, Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics, Campus E 4, Saarbrücken, 66123, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg, 79108, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Rosalind-Franklin-Str. 12, Kiel, 24105, Germany
| | - Jörn Walter
- Department of Genetics, University of Saarland, Campus A2 4, Saarbrücken, 66123, Germany
| | - Marcel H Schulz
- Excellence Cluster for Multimodal Computing and Interaction, Saarland Informatics Campus, Saarland University, Campus E1 7, Saarbrücken, 66123, Germany. .,Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics, Campus E 4, Saarbrücken, 66123, Germany. .,Institute for Cardiovascular Regeneration, Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany. .,German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, 60590, Germany.
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214
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Nakagawa S, Yamazaki T, Hirose T. Molecular dissection of nuclear paraspeckles: towards understanding the emerging world of the RNP milieu. Open Biol 2018; 8:rsob.180150. [PMID: 30355755 PMCID: PMC6223218 DOI: 10.1098/rsob.180150] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/27/2018] [Indexed: 02/06/2023] Open
Abstract
Paraspeckles are nuclear bodies built on an architectural long noncoding RNA, NEAT1, and a series of studies have revealed their molecular components, fine internal structures and cellular and physiological functions. Emerging lines of evidence suggest that paraspeckle formation is elicited by phase separation of associating RNA-binding proteins containing intrinsically disordered regions, which induce ordered arrangement of paraspeckle components along NEAT1. In this review, we will summarize the history of paraspeckle research over the last couple of decades, especially focusing on the function and structure of the nuclear bodies. We also discuss the future directions of research on long noncoding RNAs that form ‘RNP milieux’, large and flexible phase-separated ribonucleoprotein complexes.
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Affiliation(s)
- Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Tomohiro Yamazaki
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
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215
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Zhou Y, Lutz PE, Wang YC, Ragoussis J, Turecki G. Global long non-coding RNA expression in the rostral anterior cingulate cortex of depressed suicides. Transl Psychiatry 2018; 8:224. [PMID: 30337518 PMCID: PMC6193959 DOI: 10.1038/s41398-018-0267-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 07/10/2018] [Accepted: 09/10/2018] [Indexed: 01/17/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are an emerging class of regulatory RNA that may be implicated in psychiatric disorders. Here we performed RNA-sequencing in the rostral anterior cingulate cortex of 26 depressed suicides and 24 matched controls. We first performed differential lncRNA expression analysis, and then conducted Weighted Gene Co-expression Network Analysis (WGCNA) to identify co-expression modules associating with depression and suicide. We identified 23 differentially expressed lncRNAs (FDR < 0.1) as well as their differentially expressed overlapping and antisense protein-coding genes. Several of these overlapping or antisense genes were associated with interferon signaling, which is a component of the innate immune response. Using WGCNA, we identified modules of highly co-expressed genes associated with depression and suicide and found protein-coding genes highly connected to differentially expressed lncRNAs within these modules. These protein-coding genes were located distal to their associated lncRNAs and were found to be part of several GO terms enriched in the significant modules, which include: cytoskeleton organization, plasma membrane, cell adhesion, nucleus, DNA-binding, and regulation of dendrite development and morphology. Altogether, we report that lncRNAs are differentially expressed in the brains of depressed individuals who died by suicide and may represent regulators of important molecular functions and biological processes.
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Grants
- R01 DA033684 NIDA NIH HHS
- Dr. G. Turecki holds a Canada Research Chair (Tier 1), FRQS Chercheur National salary award and a NARSAD Distinguished Investigator Award; he is supported by grants FDN148374, MOP93775, MOP11260, MOP119429, and MOP119430 from CIHR, by NIH grant 1R01DA033684, by the FRQS through the Quebec Network on Suicide, Mood Disorders, and Related Disorders, and through an investigator-initiated research grant from Pfizer
- Scholarships from the Fondation Fyssen, the Fondation Bettencourt-Schueller, the Canadian Institutes of Health Research, the American Foundation of Suicide Prevention, the Fondation Deniker and the Fondation pour la Recherche Médicale.
- CFI grant number 32557 and Genome Canada Genome Innovation Node awards.
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Affiliation(s)
- Yi Zhou
- McGill Group for Suicide Studies, McGill University, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada
| | - Pierre-Eric Lutz
- McGill Group for Suicide Studies, McGill University, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Yu Chang Wang
- McGill University and Génome Québec Innovation Centre, 740 Dr. Penfield Avenue, Room 7104, Montréal, QC, H3A 0G1, Canada
| | - Jiannis Ragoussis
- McGill University and Génome Québec Innovation Centre, 740 Dr. Penfield Avenue, Room 7104, Montréal, QC, H3A 0G1, Canada
| | - Gustavo Turecki
- McGill Group for Suicide Studies, McGill University, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada.
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216
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Sun W, Feng J. Differential lncRNA expression profiles reveal the potential roles of lncRNAs in antiviral immune response of Crassostrea gigas. FISH & SHELLFISH IMMUNOLOGY 2018; 81:233-241. [PMID: 30010017 DOI: 10.1016/j.fsi.2018.07.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
Long noncoding RNAs (lncRNAs) may play widespread roles in various biological processes. However, systematic profiles of lncRNAs in the biological responses of Pacific Oyster (Crassostrea gigas) to pathogen infection have not yet been demonstrated. Here, we have conducted an exhaustive comparative transcriptome analysis using a bioinformatics approach to exam the functions of lncRNAs response to Ostreid herpesvirus 1μVar (OsHV-1μVar) challenge. In total, 101 differentially expressed lncRNAs (DE-lncRNA) during OsHV-1μVar infections were identified. Compared with differentially expressed mRNAs (DE-mRNA), DE-lncRNAs are shorter in terms of overall length but longer in terms of exon length. These lncRNAs shared similar characteristics with previously reported invertebrate lncRNAs, such as relatively low GC content, low exon number and low sequence conservation, but low expression level were not observed. 20 DE-lncRNAs are typically co-expressed with their neighboring genes annotated as GO terms (GO: 0044237), indicating that these lncRNAs are involved in binding and cellular process functions in cis mode. The weighted gene co-expression network (WGCNA) analysis resulted in 15 modules. The highlighted blue module was specifically demonstrated a co-expression relationship between 14 DE-lncRNAs and 17 immune-related DE-mRNAs (IR-DE-mRNA). Three hub lncRNAs within this module were co-expressed with one hub IR-DE-mRNA involved in fibrinogen-related protein. It was speculated that lncRNAs is extensively involved in oyster antiviral innate immune system. The present study will facilitate subsequently experimental studies to unravel the function of lncRNAs in marine invertebrate response to pathogen infection.
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Affiliation(s)
- Weiming Sun
- Ocean School, Yantai University, Yantai 264005, China.
| | - Jixing Feng
- Ocean School, Yantai University, Yantai 264005, China
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217
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Kathuria H, Millien G, McNally L, Gower AC, Tagne JB, Cao Y, Ramirez MI. NKX2-1-AS1 negatively regulates CD274/PD-L1, cell-cell interaction genes, and limits human lung carcinoma cell migration. Sci Rep 2018; 8:14418. [PMID: 30258080 PMCID: PMC6158174 DOI: 10.1038/s41598-018-32793-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 09/13/2018] [Indexed: 12/20/2022] Open
Abstract
The function of most long noncoding RNAs (lncRNAs) is unknown. However, recent studies reveal important roles of lncRNAs in regulating cancer-related pathways. Human antisense lncRNA-NKX2-1-AS1 partially overlaps the NKX2-1/TTF1 gene within chromosomal region 14q13.3. Amplification of this region and/or differential expression of genes therein are associated with cancer progression. Herein we show higher levels of NKX2-AS1 and NKX2-1 in lung adenocarcinomas relative to non-tumor controls but no correlation between NKX2-1-AS1 and NKX2-1 levels across specimens, or with amplification of the 14q13.3 region, suggesting that NKX2-1-AS1 and NKX2-1 are independently regulated. Loss-and-gain of function experiments showed that NKX2-1-AS1 does not regulate NKX2-1 expression, or nearby genes, but controls genes in trans. Genes up-regulated by NKX2-1-AS1-knockdown belong to cell adhesion and PD-L1/PD-1 checkpoint pathways. NKX2-1-AS1 negatively regulates endogenous CD274/PD-L1, a known target of NKX2-1, and the transcriptional activity of -1kb-CD274 promoter-reporter construct. Furthermore, NKX2-1-AS1 interferes with NKX2-1 protein binding to the CD274-promoter, likely by NKX2-1 protein-NKX2-1-AS1 interactions. Finally, NKX2-1-AS1 negatively regulates cell migration and wound healing, but not proliferation or apoptosis. These findings support potential roles of NKX2-1-AS1 in limiting motility and immune system evasion of lung carcinoma cells, highlighting a novel mechanism that may influence tumorigenic capabilities of lung epithelial cells.
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Affiliation(s)
- Hasmeena Kathuria
- The Pulmonary Center, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Guetchyn Millien
- The Pulmonary Center, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Liam McNally
- The Pulmonary Center, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Adam C Gower
- Clinical and Translational Science Institute, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Jean-Bosco Tagne
- The Pulmonary Center, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Yuxia Cao
- The Pulmonary Center, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Maria I Ramirez
- The Pulmonary Center, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA.
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA.
- Center for Translational Medicine, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA.
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218
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He J, Tu C, Liu Y. Role of lncRNAs in aging and age-related diseases. Aging Med (Milton) 2018; 1:158-175. [PMID: 31942494 PMCID: PMC6880696 DOI: 10.1002/agm2.12030] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 01/10/2023] Open
Abstract
Aging is progressive physiological degeneration and consequently declined function, which is linked to senescence on both cellular and organ levels. Accumulating studies indicate that long noncoding RNAs (lncRNAs) play important roles in cellular senescence at all levels-transcriptional, post-transcriptional, translational, and post-translational. Understanding the molecular mechanism of lncRNAs underlying senescence could facilitate interpretation and intervention of aging and age-related diseases. In this review, we describe categories of known and novel lncRNAs that have been involved in the progression of senescence. We also identify the lncRNAs implicated in diseases arising from age-driven degeneration or dysfunction in some representative organs and systems (brains, liver, muscle, cardiovascular system, bone pancreatic islets, and immune system). Improved comprehension of lncRNAs in the aging process on all levels, from cell to organismal, may provide new insights into the amelioration of age-related pathologies and prolonged healthspan.
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Affiliation(s)
- Jieyu He
- Department of GeriatricsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Chao Tu
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Youshuo Liu
- Department of GeriatricsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
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219
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Dousti F, Shahrisa A, Ansari H, Hajjari M, Tahmasebi Birgani Y, Mohammadiasl J, Tahmasebi Birgani M. Long non-coding RNAs expression levels in diffuse large B-cell lymphoma: An in silico analysis. Pathol Res Pract 2018; 214:1462-1466. [PMID: 30104077 DOI: 10.1016/j.prp.2018.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/28/2018] [Accepted: 08/06/2018] [Indexed: 01/03/2023]
Abstract
Long non-coding RNAs (lncRNAs), are lengthy noncoding transcripts with pivotal roles in biological pathways including cell cycle, apoptosis and chromatin remodeling. Aberrant expression of lncRNAs has been strongly connected with tumor progression and metastasis. However, the prognostic significance of lncRNAs in diffuse large-B-cell lymphoma (DLBCL) remains unclear. In this study, the expression levels of 189 approved lncRNAs were considered in DLBCL patients using several different genomic and transcriptome datasets. The analyses showed that the lncRNA GAS5 allocated the maximum score of RNA dysregulation and can be considered as good choice in DLBCLs' researches.
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Affiliation(s)
- Fatemeh Dousti
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Arman Shahrisa
- Department of Molecular Genetics, Faculty of Biosciences, Tarbiat Modares University, Tehran, Iran
| | - Hossein Ansari
- Departments of Biotechnology, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran.
| | - Mohammadreza Hajjari
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Yaser Tahmasebi Birgani
- Department of Environmental Health Engineering, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Javad Mohammadiasl
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Tahmasebi Birgani
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Cellular and Molecular Research Center, Ahvaz Jundishapur University of Medical Sciences, Iran.
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220
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Poller W, Dimmeler S, Heymans S, Zeller T, Haas J, Karakas M, Leistner DM, Jakob P, Nakagawa S, Blankenberg S, Engelhardt S, Thum T, Weber C, Meder B, Hajjar R, Landmesser U. Non-coding RNAs in cardiovascular diseases: diagnostic and therapeutic perspectives. Eur Heart J 2018; 39:2704-2716. [PMID: 28430919 PMCID: PMC6454570 DOI: 10.1093/eurheartj/ehx165] [Citation(s) in RCA: 304] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/14/2017] [Accepted: 03/15/2017] [Indexed: 02/06/2023] Open
Abstract
Recent research has demonstrated that the non-coding genome plays a key role in genetic programming and gene regulation during development as well as in health and cardiovascular disease. About 99% of the human genome do not encode proteins, but are transcriptionally active representing a broad spectrum of non-coding RNAs (ncRNAs) with important regulatory and structural functions. Non-coding RNAs have been identified as critical novel regulators of cardiovascular risk factors and cell functions and are thus important candidates to improve diagnostics and prognosis assessment. Beyond this, ncRNAs are rapidly emgerging as fundamentally novel therapeutics. On a first level, ncRNAs provide novel therapeutic targets some of which are entering assessment in clinical trials. On a second level, new therapeutic tools were developed from endogenous ncRNAs serving as blueprints. Particularly advanced is the development of RNA interference (RNAi) drugs which use recently discovered pathways of endogenous short interfering RNAs and are becoming versatile tools for efficient silencing of protein expression. Pioneering clinical studies include RNAi drugs targeting liver synthesis of PCSK9 resulting in highly significant lowering of LDL cholesterol or targeting liver transthyretin (TTR) synthesis for treatment of cardiac TTR amyloidosis. Further novel drugs mimicking actions of endogenous ncRNAs may arise from exploitation of molecular interactions not accessible to conventional pharmacology. We provide an update on recent developments and perspectives for diagnostic and therapeutic use of ncRNAs in cardiovascular diseases, including atherosclerosis/coronary disease, post-myocardial infarction remodelling, and heart failure.
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Affiliation(s)
- Wolfgang Poller
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Center of Molecular Medicine, Johann Wolfgang Goethe Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany
- DZHK, Site Rhein-Main, Frankfurt, Germany
| | - Stephane Heymans
- Center for Heart Failure Research, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Jan Haas
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Mahir Karakas
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - David-Manuel Leistner
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Philipp Jakob
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama, Japan
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo, Japan
| | - Stefan Blankenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Stefan Engelhardt
- Institute for Pharmacology and Toxikology, Technische Universität München, Biedersteiner Strasse 29, München, Germany
- DZHK, Site Munich, Munich, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Christian Weber
- DZHK, Site Munich, Munich, Germany
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität, Pettenkoferstrasse 8a/9, Munich, Germany
| | - Benjamin Meder
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Roger Hajjar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ulf Landmesser
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
- Berlin Institute of Health, Kapelle-Ufer 2, Berlin, Germany
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221
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Yan F, Wang X, Zeng Y. 3D genomic regulation of lncRNA and Xist in X chromosome. Semin Cell Dev Biol 2018; 90:174-180. [PMID: 30017906 DOI: 10.1016/j.semcdb.2018.07.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 01/19/2023]
Abstract
Long noncoding RNAs (lncRNAs) act as important regulators in cardiovascular diseases, neural degenerative disease, or cancers, by localizing and spreading across chromatins. lncRNA can regulate the 3D architecture of the enhancer cluster at the target gene locus, relevant to analogous lncRNA-protein coding gene pairs. X inactive specific transcript (Xist) plays a critical role in the process and biological function of lncRNAs. The lncRNA Jpx, Xist activator, is a nonprotein-coding RNA transcribed from a gene within the X-inactivation center and acts as a numerator element to control X-chromosome number and activate Xist transcription by interacting with CCCTC-binding factor. Up-regulated lncRNA Xist initiates X chromosome inactivation process and attracts specific chromatin modifiers. A number of chromatin-modified factors interact with lncRNAs modify 3D genome architecture and mediate Xist function in embryo development. Thus, the regulation of lncRNAs in 3D genome progresses is the key mechanism of Xist, as a therapeutic potential for Xist associated diseases.
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Affiliation(s)
- Furong Yan
- Center for Molecular Diagnosis and Therapy, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Xiangdong Wang
- Center for Molecular Diagnosis and Therapy, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Fujian Medical University, Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian Province, China.
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222
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Birth, coming of age and death: The intriguing life of long noncoding RNAs. Semin Cell Dev Biol 2018; 79:143-152. [DOI: 10.1016/j.semcdb.2017.11.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/06/2017] [Accepted: 11/09/2017] [Indexed: 01/27/2023]
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223
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Li Y, Liu Y, Liu S, Wu F, Li S, Yang F, Gu Y, Xu Z, Wang G. Differential expression profile of long non-coding RNAs in human thoracic aortic aneurysm. J Cell Biochem 2018; 119:7991-7997. [PMID: 29323743 DOI: 10.1002/jcb.26670] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 01/09/2018] [Indexed: 11/09/2022]
Abstract
Thoracic aortic aneurysm (TAA) is progressive fatal aortic pathological dilation, which is characterized by increased proteoglycans and loss of elastic fibers. Recent advances in long non-coding RNAs (lncRNAs), an important regulator in many biological processes, suggested the close correlation between expression patterns and disease progression. In the present study, the ascending aortic tissues were collected from ascending TAA patients (n = 33) and organ donors (n = 16). Microarray analysis and real-time PCR were then applied to detect the lncRNA expression profiles. A total of 147 differentially expressed lncRNAs were determined, including 104 upregulated and 43 downregulated lncRNAs. Bioinformatics analysis showed 51.7% of differentially expressed lncRNAs were sense-overlapping, and most of the down-regulated lncRNAs were located on chromosome 1, 7, and 12. Subgroup analysis of TAA patients indicated that the expression of lnc-HLTF-5 was significantly higher in hypertension group than non-hypertension group (P < 0.05). Spearman correlation analysis further confirmed that the lnc-HLTF-5 level was positively correlated with the expanded ascending aortic diameter (rs = 0.483, P = 0.004) and MMP9 level (rs = 0.465, P = 0.006). Our results expanded the lncRNA expression patterns in aortic disease, and provided experimental basis for future investigation on TAA pathogenesis.
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Affiliation(s)
- Yang Li
- Department of Cardiovascular Surgery, Institution of Cardiac Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Yang Liu
- Department of Cardiovascular Surgery, Institution of Cardiac Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Suxuan Liu
- Department of Cardiology, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Feng Wu
- Department of Cardiology, 98th Military Hospital, Huzhou, Zhejiang, China
| | - Songhua Li
- Department of Cardiology, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Fan Yang
- Department of Cardiovascular Surgery, Institution of Cardiac Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Ying Gu
- Department of Cardiology, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Zhiyun Xu
- Department of Cardiovascular Surgery, Institution of Cardiac Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Guokun Wang
- Department of Cardiovascular Surgery, Institution of Cardiac Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, China
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224
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Capra E, Lazzari B, Frattini S, Chessa S, Coizet B, Talenti A, Castiglioni B, Marsan PA, Crepaldi P, Pagnacco G, Williams JL, Stella A. Distribution of ncRNAs expression across hypothalamic-pituitary-gonadal axis in Capra hircus. BMC Genomics 2018; 19:417. [PMID: 29848285 PMCID: PMC5977473 DOI: 10.1186/s12864-018-4767-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 05/09/2018] [Indexed: 11/10/2022] Open
Abstract
Background Molecular regulation of the hypothalamic-pituitary-gonadal (HPG) axis plays an essential role in the fine tuning of seasonal estrus in Capra hircus. Noncoding RNAs (ncRNAs) are emerging as key regulators in sexual development and mammalian reproduction. In order to identify ncRNAs and to assess their expression patterns, along the HPG axis, we sequenced ncRNA libraries from hypothalamus, pituitary and ovary of three goats. Results Among the medium length noncoding RNAs (mncRNAs) identified, small nucleolar RNAs (snoRNAs) and transfer RNAs (tRNAs) were found to be more abundant in ovary and hypothalamus, respectively. The observed GC content was representative for different classes of ncRNAs, allowing the identification of a tRNA-derived RNA fragments (tRFs) subclass, which had a peak distribution around 32–38% GC content in the hypothalamus. Differences observed among organs confirmed the specificity of microRNA (miRNA) profiles for each organ system. Conclusions Data on ncRNAs in organs constituting the HPG axis will contribute to understanding their role in the physiological regulation of reproduction in goats. Electronic supplementary material The online version of this article (10.1186/s12864-018-4767-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emanuele Capra
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - Barbara Lazzari
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy.,Parco Tecnologico Padano, Lodi, Italy
| | - Stefano Frattini
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - Stefania Chessa
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - Beatrice Coizet
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - Andrea Talenti
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - Bianca Castiglioni
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - Paolo Ajmone Marsan
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - Giulio Pagnacco
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy.,Parco Tecnologico Padano, Lodi, Italy.,Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Australia
| | - Alessandra Stella
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy. .,Parco Tecnologico Padano, Lodi, Italy.
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225
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Chen W, Moore J, Ozadam H, Shulha HP, Rhind N, Weng Z, Moore MJ. Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling. Cell 2018; 173:1031-1044.e13. [PMID: 29727662 PMCID: PMC6090549 DOI: 10.1016/j.cell.2018.03.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/09/2018] [Accepted: 03/23/2018] [Indexed: 12/31/2022]
Abstract
Full understanding of eukaryotic transcriptomes and how they respond to different conditions requires deep knowledge of all sites of intron excision. Although RNA sequencing (RNA-seq) provides much of this information, the low abundance of many spliced transcripts (often due to their rapid cytoplasmic decay) limits the ability of RNA-seq alone to reveal the full repertoire of spliced species. Here, we present "spliceosome profiling," a strategy based on deep sequencing of RNAs co-purifying with late-stage spliceosomes. Spliceosome profiling allows for unambiguous mapping of intron ends to single-nucleotide resolution and branchpoint identification at unprecedented depths. Our data reveal hundreds of new introns in S. pombe and numerous others that were previously misannotated. By providing a means to directly interrogate sites of spliceosome assembly and catalysis genome-wide, spliceosome profiling promises to transform our understanding of RNA processing in the nucleus, much as ribosome profiling has transformed our understanding mRNA translation in the cytoplasm.
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Affiliation(s)
- Weijun Chen
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jill Moore
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Hakan Ozadam
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Hennady P Shulha
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Zhiping Weng
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Melissa J Moore
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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226
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Biswas S, Thomas AA, Chen S, Aref-Eshghi E, Feng B, Gonder J, Sadikovic B, Chakrabarti S. MALAT1: An Epigenetic Regulator of Inflammation in Diabetic Retinopathy. Sci Rep 2018; 8:6526. [PMID: 29695738 PMCID: PMC5916949 DOI: 10.1038/s41598-018-24907-w] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/12/2018] [Indexed: 12/16/2022] Open
Abstract
Despite possessing limited protein-coding potential, long non-coding RNAs (lncRNAs) have been implicated in a myriad of pathologic conditions. Most well documented in cancer, one prominent intergenic lncRNA known as MALAT1 is notorious for its role in impacting epigenetic mechanisms. In this study, we established a novel epigenetic paradigm for MALAT in diabetic retinopathy (DR) by employing siRNA-mediated MALAT1 knockdown in human retinal endothelial cells (HRECs), a Malat1 knockout animal model, vitreous humor from diabetic patients, pharmacological inhibitors for histone and DNA methylation, RNA immunoprecipitation, western blotting, and a unique DNA methylation array to determine glucose-related alterations in MALAT1. Our findings indicated that MALAT1 is capable of impacting the expressions of inflammatory transcripts through its association with components of the PRC2 complex in diabetes. Furthermore, the vitreous humors from diabetic patients revealed increased expressions of MALAT1, TNF-α, and IL-6. Intriguingly, our DNA methylation array demonstrated that transient high glucose exposure in HRECs does not contribute to significant methylation alterations at CpG sites across the MALAT1 gene. However, global inhibition of DNA methyltransferases induced significant increases in MALAT1 and associated inflammatory transcripts in HRECs. Our findings collectively demonstrate the importance of MALAT1 in inflammation and epigenetic regulation in DR.
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Affiliation(s)
- Saumik Biswas
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Anu Alice Thomas
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Shali Chen
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Biao Feng
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - John Gonder
- Department of Ophthalmology, Western University, London, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Subrata Chakrabarti
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
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227
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Epigenetics of Circadian Rhythms in Imprinted Neurodevelopmental Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:67-92. [PMID: 29933957 DOI: 10.1016/bs.pmbts.2017.11.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
DNA sequence information alone cannot account for the immense variability between chromosomal alleles within diverse cell types in the brain, whether these differences are observed across time, cell type, or parental origin. The complex control and maintenance of gene expression and modulation are regulated by a multitude of molecular and cellular mechanisms that layer on top of the genetic code. The integration of genetic and environmental signals required for regulating brain development and function is achieved in part by a dynamic epigenetic landscape that includes DNA methylation, histone modifications, and noncoding RNAs. These epigenetic mechanisms establish and maintain core biological processes, including genomic imprinting and entrainment of circadian rhythms. This chapter will focus on how the epigenetic layers of DNA methylation and long, noncoding RNAs interact with circadian rhythms at specific imprinted chromosomal loci associated with the human neurodevelopmental disorders Prader-Willi, Angelman, Kagami-Ogata, and Temple syndromes.
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228
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Expression pattern of genome-scale long noncoding RNA following acute myocardial infarction in Chinese Uyghur patients. Oncotarget 2018; 8:31449-31464. [PMID: 28418905 PMCID: PMC5458221 DOI: 10.18632/oncotarget.16355] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 02/13/2017] [Indexed: 11/30/2022] Open
Abstract
In this study, we examined the long noncoding RNA (lncRNA) expression pattern in Uyghur patients (a minority of China) with acute myocardial infarction (AMI) on a genome-wide scale. Total RNAs were extracted from the peripheral blood of 55 Uyghur AMI patients and 55 healthy volunteers. The expression levels of genome-wide scale lncRNAs and mRNAs were determined by microarray in 10 samples (5 AMI and 5 controls). qRT-PCR was used to validate lncRNA expression levels in 100 samples (50 AMI and 50 controls). Data analyses were performed using R and Bioconductor. A total of 3624 up- and 1637 down-regulated lncRNAs were identified to be significantly and differentially expressed between these two groups. The annotation result of their co-expressed mRNAs showed that the most significantly related category of GO analysis was regulation of biological processes, and the most significantly related pathway was apoptosis and its corresponding p53. The microarray identified ENST00000416860.2, ENST00000421157.1 and TCONS_00025701 lncRNAs were confirmed by qRT-PCR. Our study indicated that clusters of lncRNAs were significantly and differentially expressed in the peripheral blood of AMI patients when compared with healthy controls within the Uyghur population. These newly identified lncRNAs may have a potential role in the development of AMI.
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229
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de Oliveira da Silva B, Alberici LC, Ramos LF, Silva CM, da Silveira MB, Dechant CRP, Friedman SL, Sakane KK, Gonçalves LR, Moraes KCM. Altered global microRNA expression in hepatic stellate cells LX-2 by angiotensin-(1-7) and miRNA-1914-5p identification as regulator of pro-fibrogenic elements and lipid metabolism. Int J Biochem Cell Biol 2018. [PMID: 29524604 DOI: 10.1016/j.biocel.2018.02.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of new therapeutic strategies to control or reverse hepatic fibrosis requires thorough knowledge about its molecular and cellular basis. It is known that the heptapeptide angiotensin-(1-7) [ang-(1-7)] can reduce hepatic fibrosis and steatosis in vivo; therefore, it is important to uncover the mechanisms regulating its activity and cellular model of investigation. Ang-(1-7) is a peptide of the renin-angiotensin system (RAS), and here we investigated its modulatory effect on the expression pattern of microRNAs (miRNAs) in hepatic stellate cells (HSCs) LX-2, which transdifferentiate into fibrogenic and proliferative cells. We compared the miRNA profiles between quiesced, activated and ang-(1-7)-treated activated HSCs to identify miRNAs that may regulate their transdifferentiation. Thirteen miRNAs were pointed, and cellular and molecular analyses identified miRNA-1914-5p as a molecule that contributes to the effects of ang-(1-7) on lipid metabolism and on the pro-fibrotic environment control. In our cellular model, we also analyzed the regulators of fatty acid metabolism. Specifically, miRNA-1914-5p regulates the expression of malonyl-CoA decarboxylase (MLYCD) and phosphatidic acid phosphohydrolase (PAP or Lipin-1). Additionally, Lipin-1 was closely correlated with mRNA expression of peroxisome proliferator-activated receptors (PPAR)-α and -γ, which also contribute to lipid homeostasis and to the reduction of TGF-β1 expression. These findings provide a novel link between RAS and lipid metabolism in controlling HSCs activation.
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Affiliation(s)
- Brenda de Oliveira da Silva
- Núcleo de Pesquisa em Biologia, Universidade Federal de Ouro Preto, UFOP, Ouro Preto, MG, Brazil; Molecular Biology Laboratory, Department of Biology, Bioscience Institute, Universidade Estadual Paulista "Júlio de Mesquita Filho", UNESP, Rio Claro, SP, Brazil
| | - Luciane Carla Alberici
- Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, Universidade de São Paulo, USP, Ribeirão Preto, SP, Brazil
| | - Letícia Ferreira Ramos
- Molecular Biology Laboratory, Department of Biology, Bioscience Institute, Universidade Estadual Paulista "Júlio de Mesquita Filho", UNESP, Rio Claro, SP, Brazil
| | - Caio Mateus Silva
- Molecular Biology Laboratory, Department of Biology, Bioscience Institute, Universidade Estadual Paulista "Júlio de Mesquita Filho", UNESP, Rio Claro, SP, Brazil
| | - Marina Bonfogo da Silveira
- Molecular Biology Laboratory, Department of Biology, Bioscience Institute, Universidade Estadual Paulista "Júlio de Mesquita Filho", UNESP, Rio Claro, SP, Brazil
| | - Carlos R P Dechant
- Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, Universidade de São Paulo, USP, Ribeirão Preto, SP, Brazil
| | - Scott L Friedman
- Division of Liver Diseases, Department of Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - Kumiko Koibuchi Sakane
- Institute of Research and Development of Universidade do Vale do Paraíba, UNIVAP, São José dos Campos, SP, Brazil
| | - Letícia Rocha Gonçalves
- Molecular Biology Laboratory, Department of Biology, Bioscience Institute, Universidade Estadual Paulista "Júlio de Mesquita Filho", UNESP, Rio Claro, SP, Brazil
| | - Karen C M Moraes
- Molecular Biology Laboratory, Department of Biology, Bioscience Institute, Universidade Estadual Paulista "Júlio de Mesquita Filho", UNESP, Rio Claro, SP, Brazil.
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230
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Yavropoulou MP, Yovos JG. The "dark matter" of DNA and the regulation of bone metabolism: The role of non-coding RNAs. JOURNAL OF MUSCULOSKELETAL & NEURONAL INTERACTIONS 2018; 18:18-31. [PMID: 29504575 PMCID: PMC5881125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Epigenetics, present a new discipline that attempts to explain significant differences in phenotypes among patients with the same disease. In contrast to the other epigenetic mechanisms that modulate gene transcription, non-coding RNAs act at the post-transcriptional level. They directly modulate the gene expression of mRNA genes leading to mRNA target cleavage and degradation and translation repression. Bioinformatic predictions indicate that non coding RNAs may be involved in the regulation of 60% of the coding genes and each non-coding RNA can have multiple target genes, and each gene may be regulated by more than one non-coding RNAs. In the last decade several studies have shown a significant role of non-coding RNAs in the regulation of bone metabolism and function of bone cells opening a new era in the understanding of bone biology in health and disease.
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Affiliation(s)
- Maria P. Yavropoulou
- Laboratory of Clinical and Molecular Endocrinology, 1st Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece,Corresponding author: Maria P. Yavropoulou, MD, MSc, PhD, Endocrinologist Consultant, 1st Department of Internal Medicine, AHEPA Univ. Hospital, 1 S. Kyriakidi street 54636, Thessaloniki, Greece E-mail:
| | - John G. Yovos
- Laboratory of Clinical and Molecular Endocrinology, 1st Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
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231
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Faiq MA, Kumar A, Singh HN, Pareek V, Kumar P. Commentary: A Possible Mechanism of Zika Virus Associated Microcephaly: Imperative Role of Retinoic Acid Response Element (RARE) Consensus Sequence Repeats in the Viral Genome. Front Microbiol 2018. [PMID: 29515529 PMCID: PMC5826298 DOI: 10.3389/fmicb.2018.00190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Muneeb A Faiq
- Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India.,Laboratory for Molecular Reproduction and Genetics, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India.,Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, New Delhi, India.,Etiologically Elusive Disorders Research Network, New Delhi, India
| | - Ashutosh Kumar
- Etiologically Elusive Disorders Research Network, New Delhi, India.,Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
| | - Himanshu N Singh
- Etiologically Elusive Disorders Research Network, New Delhi, India.,Functional Genomics Unit, Institute of Genomics and Integrative Biology, New Delhi, India.,Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Vikas Pareek
- Etiologically Elusive Disorders Research Network, New Delhi, India.,Computational Neuroscience and Neuroimaging Division, National Brain Research Centre, Manesar, India
| | - Pavan Kumar
- Etiologically Elusive Disorders Research Network, New Delhi, India.,Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
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232
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Das M, Renganathan A, Dighe SN, Bhaduri U, Shettar A, Mukherjee G, Kondaiah P, Satyanarayana Rao MR. DDX5/p68 associated lncRNA LOC284454 is differentially expressed in human cancers and modulates gene expression. RNA Biol 2018; 15:214-230. [PMID: 29227193 PMCID: PMC5798960 DOI: 10.1080/15476286.2017.1397261] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/04/2017] [Accepted: 10/22/2017] [Indexed: 12/21/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as important players in regulation of gene expression in higher eukaryotes. DDX5/p68 RNA helicase protein which is involved in splicing of precursor mRNAs also interacts with lncRNAs like, SRA and mrhl, to modulate gene expression. We performed RIP-seq analysis in HEK293T cells to identify the complete repertoire of DDX5/p68 interacting transcripts including 73 single exonic (SE) lncRNAs. The LOC284454 lncRNA is the second top hit of the list of SE lncRNAs which we have characterized in detail for its molecular features and cellular functions. The RNA is located in the same primary transcript harboring miR-23a∼27a∼24-2 cluster. LOC284454 is a stable, nuclear restricted and chromatin associated lncRNA. The sequence is conserved only in primates among 26 different species and is expressed in multiple human tissues. Expression of LOC284454 is significantly reduced in breast, prostate, uterus and kidney cancer and also in breast cancer cell lines (MCF7 and T47D). Global gene expression studies upon loss and gain of function of LOC284454 revealed perturbation of genes related to cancer-related pathways. Focal adhesion and cell migration pathway genes are downregulated under overexpression condition, and these genes are significantly upregulated in breast cancer cell lines as well as breast cancer tissue samples suggesting a functional role of LOC284454 lncRNA in breast cancer pathobiology.
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Affiliation(s)
- Monalisa Das
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advance Scientific Research, Bangalore, Karnataka, India
| | - Arun Renganathan
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advance Scientific Research, Bangalore, Karnataka, India
| | - Shrinivas Nivrutti Dighe
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advance Scientific Research, Bangalore, Karnataka, India
| | - Utsa Bhaduri
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advance Scientific Research, Bangalore, Karnataka, India
| | - Abhijith Shettar
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, Karnataka, India
| | | | - Paturu Kondaiah
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, Karnataka, India
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233
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Paraspeckles: Where Long Noncoding RNA Meets Phase Separation. Trends Biochem Sci 2018; 43:124-135. [DOI: 10.1016/j.tibs.2017.12.001] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/30/2017] [Accepted: 12/04/2017] [Indexed: 12/26/2022]
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234
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Sun Q, Hao Q, Prasanth KV. Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression. Trends Genet 2018; 34:142-157. [PMID: 29249332 PMCID: PMC6002860 DOI: 10.1016/j.tig.2017.11.005] [Citation(s) in RCA: 435] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 02/06/2023]
Abstract
A significant portion of the human genome encodes genes that transcribe long nonprotein-coding RNAs (lncRNAs). A large number of lncRNAs localize in the nucleus, either enriched on the chromatin or localized to specific subnuclear compartments. Nuclear lncRNAs participate in several biological processes, including chromatin organization, and transcriptional and post-transcriptional gene expression, and also act as structural scaffolds of nuclear domains. Here, we highlight recent studies demonstrating the role of lncRNAs in regulating gene expression and nuclear organization in mammalian cells. In addition, we update current knowledge about the involvement of the most-abundant and conserved lncRNA, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), in gene expression control.
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Affiliation(s)
- Qinyu Sun
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA; These authors contributing equally
| | - Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA; These authors contributing equally
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA.
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235
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Zhao F, Lee EY, Shin Y. Improved Reversible Cross-Linking-Based Solid-Phase RNA Extraction for Pathogen Diagnostics. Anal Chem 2018; 90:1725-1733. [DOI: 10.1021/acs.analchem.7b03493] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Fei Zhao
- Department of Convergence Medicine, Asan Medical Center,
University of Ulsan College of Medicine, and Biomedical Engineering
Research Center, Asan Institute of Life Sciences, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Center,
University of Ulsan College of Medicine, and Biomedical Engineering
Research Center, Asan Institute of Life Sciences, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center,
University of Ulsan College of Medicine, and Biomedical Engineering
Research Center, Asan Institute of Life Sciences, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
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236
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Lee KT, Nam JW. Post-transcriptional and translational regulation of mRNA-like long non-coding RNAs by microRNAs in early developmental stages of zebrafish embryos. BMB Rep 2018; 50:226-231. [PMID: 28320503 PMCID: PMC5437968 DOI: 10.5483/bmbrep.2017.50.4.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Indexed: 01/16/2023] Open
Abstract
At the post-transcriptional and translational levels, microRNA (miRNA) represses protein-coding genes via seed pairing to the 3′ untranslated regions (UTRs) of mRNA. Although working models of miRNA-mediated gene silencing are successfully established using miRNA transfections and knockouts, the regulatory interaction between miRNA and long non-coding RNA (lncRNA) remain unknown. In particular, how the mRNA-resembling lncRNAs with 5′ cap, 3′ poly(A)-tail, or coding features, are regulated by miRNA is yet to be examined. We therefore investigated the functional interaction between miRNAs and lncRNAs with/without those features, in miRNA-transfected early zebrafish embryos. We observed that the greatest determinants of the miRNA-mediated silencing of lncRNAs were the 5′ cap and 3′ poly(A)-tails in lncRNAs, at both the post-transcriptional and translational levels. The lncRNAs confirmed to contain 5′ cap, 3′ poly(A)-tail, and the canonical miRNA target sites, were observed to be repressed in the level of both RNA and ribosome-protected fragment, while those with the miRNA target sites and without 5′ cap and 3′ poly(A)-tail, were not robustly repressed by miRNA introduction, thus suggesting a role as a miRNA-decoy.
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Affiliation(s)
- Kyung-Tae Lee
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University; Research Institute for Natural Sciences, Hanyang University; Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 133791, Korea
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237
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Hershkovitz-Rokah O, Geva P, Salmon-Divon M, Shpilberg O, Liberman-Aronov S. Network analysis of microRNAs, genes and their regulation in diffuse and follicular B-cell lymphomas. Oncotarget 2018; 9:7928-7941. [PMID: 29487703 PMCID: PMC5814270 DOI: 10.18632/oncotarget.23974] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/21/2017] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRs) are short non-coding regulatory RNAs that control gene expression at the post-transcriptional level and play an important role in cancer development and progression, acting either as oncogenes or as tumor suppressors. Identification of aberrantly expressed miRs in patients with hematological malignancies as compared to healthy individuals has suggested that these molecules may serve as novel clinical diagnostic and prognostic biomarkers. We conducted a systematic literature review of articles published between 2007 and 2017 and re-analyzed experimentally-validated human miR expression signatures in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) from various biological sources (tumor tissue, peripheral blood, bone marrow and cell lines). A unique miR expression pattern was observed for each disease. Compared to healthy individuals, 61 miRs were aberrantly expressed in DLBCL and 85 in FL; 20-30% of aberrantly expressed miRs overlapped between the two lymphoma subtypes. Analysis of integrative positive and negative miRNA-mRNA relationships using the Ingenuity Pathway Analysis (IPA) system revealed 970 miR-mRNA pairs for DLBCL and 90 for FL. Through gene ontology analysis, we found potential regulatory pathways that are deregulated in DLBCL and FL due to improper expression of miR target genes. By comparing the expression level of the aberrantly expressed miRs in DLBCL to their expression levels in other malignancies, we identified seven miRs that are aberrantly expressed in DLBCL tumor tissues (miR-15a, miR-16, miR-17, miR-106, miR-21, miR-155 and miR-34a-5p). This specific expression pattern may be a potential diagnostic tool for DLBCL.
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Affiliation(s)
- Oshrat Hershkovitz-Rokah
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel, Israel.,Translational Research Laboratory, Assuta Medical Centers, Tel Aviv, Israel.,Institude of Hematology, Assuta Medical Centers, Tel Aviv, Israel
| | - Polina Geva
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel, Israel
| | - Mali Salmon-Divon
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel, Israel
| | - Ofer Shpilberg
- Translational Research Laboratory, Assuta Medical Centers, Tel Aviv, Israel.,Institude of Hematology, Assuta Medical Centers, Tel Aviv, Israel.,Pre-Medicine Department, School of Health Sciences, Ariel University, Ariel, Israel
| | - Stella Liberman-Aronov
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel, Israel
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238
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Wen X, Gao L, Guo X, Li X, Huang X, Wang Y, Xu H, He R, Jia C, Liang F. lncSLdb: a resource for long non-coding RNA subcellular localization. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:1-6. [PMID: 30219837 PMCID: PMC6146130 DOI: 10.1093/database/bay085] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 07/23/2018] [Indexed: 01/18/2023]
Abstract
While long non-coding RNAs (lncRNAs) may play important roles in cellular function and biological process, we still know little about them. Growing evidences indicate that subcellular localization of lncRNAs may provide clues to their functionality. To facilitate researchers functionally characterize thousands of lncRNAs, we developed a database-driven application, lncSLdb, which stores and manages user-collected qualitative and quantitative subcellular localization information of lncRNAs from literature mining. The current release contains >11 000 transcripts from three species. Based on the accumulated region of lncRNAs, we classify transcripts into three basic localization types (nucleus, cytoplasm and nucleus/cytoplasm). In some conditions, the nucleus and cytoplasm types can be divided into three more accurate subtypes (chromosome, nucleoplasm and ribosome). Besides browsing and downloading data in lncSLdb, our system provides a set of comprehensive tools to search by gene symbols, genome coordinates or sequence similarity. We hope that lncSLdb will provide a convenient platform for researchers to investigate the functions and the molecular mechanisms of lncRNAs in the view of subcellular localization.
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Affiliation(s)
- Xiao Wen
- School of Computer Science and Technology, Xidian University, Xi'an Shaanxi, PR China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi'an Shaanxi, PR China
| | - Xingli Guo
- School of Computer Science and Technology, Xidian University, Xi'an Shaanxi, PR China
| | - Xing Li
- School of Computer Science and Technology, Xidian University, Xi'an Shaanxi, PR China
| | - Xiaotai Huang
- School of Computer Science and Technology, Xidian University, Xi'an Shaanxi, PR China
| | - Ying Wang
- School of Computer Science and Technology, Xidian University, Xi'an Shaanxi, PR China
| | - Haifu Xu
- School of Computer Science and Technology, Xidian University, Xi'an Shaanxi, PR China
| | - Ruijie He
- School of Computer Science and Technology, Xidian University, Xi'an Shaanxi, PR China
| | - Chenglong Jia
- School of Computer Science and Technology, Xidian University, Xi'an Shaanxi, PR China
| | - Feixiang Liang
- School of Computer Science and Technology, Xidian University, Xi'an Shaanxi, PR China
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Guglas K, Bogaczyńska M, Kolenda T, Ryś M, Teresiak A, Bliźniak R, Łasińska I, Mackiewicz J, Lamperska K. lncRNA in HNSCC: challenges and potential. Contemp Oncol (Pozn) 2017; 21:259-266. [PMID: 29416430 PMCID: PMC5798417 DOI: 10.5114/wo.2017.72382] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 10/27/2017] [Indexed: 01/17/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cause of cancer mortality in the world. Some progress has been made in the therapy of HNSCC, however treatment remains unsatisfactory. Recent studies have shown that different types of long non-coding RNAs (lncRNAs) are dysregulated in HNSCC and correlate with tumor progression, lymph node metastasis, clinical stage and poor prognosis. lncRNAs are a class of functional RNA molecules that can not be translated into proteins but can modulate the activity of transcription factors or regulate changes in chromatin structure. The lncRNAs might have potential of biomarker in HNSCC diagnosis, prognosis, prediction and targeted treatment. In this review we describe the potential role of lncRNAs as new biomarkers and discuss their features including source of origin, extraction methods, stability, detection methods and data normalization and potential function as biomarkers in HNSCC.
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Affiliation(s)
- Kacper Guglas
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marta Bogaczyńska
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- HAN University of Applied Sciences, Nijmegen, Netherlands
| | - Tomasz Kolenda
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Poland
| | - Marcel Ryś
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
| | - Izabela Łasińska
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, Poland
| | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, Poland
- Department of Biology and Environmental Sciences, Poznan University of Medical Sciences, Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland
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240
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Shi JY, Huang H, Zhang YN, Long YX, Yiu SM. Predicting binary, discrete and continued lncRNA-disease associations via a unified framework based on graph regression. BMC Med Genomics 2017; 10:65. [PMID: 29322937 PMCID: PMC5763297 DOI: 10.1186/s12920-017-0305-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND In human genomes, long non-coding RNAs (lncRNAs) have attracted more and more attention because their dysfunctions are involved in many diseases. However, the associations between lncRNAs and diseases (LDA) still remain unknown in most cases. While identifying disease-related lncRNAs in vivo is costly, computational approaches are promising to not only accelerate the possible identification of associations but also provide clues on the underlying mechanism of various lncRNA-caused diseases. Former computational approaches usually only focus on predicting new associations between lncRNAs having known associations with diseases and other lncRNA-associated diseases. They also only work on binary lncRNA-disease associations (whether the pair has an association or not), which cannot reflect and reveal other biological facts, such as the number of proteins involved in LDA or how strong the association is (i.e., the intensity of LDA). RESULTS To address abovementioned issues, we propose a graph regression-based unified framework (GRUF). In particular, our method can work on lncRNAs, which have no previously known disease association and diseases that have no known association with any lncRNAs. Also, instead of only a binary answer for the association, our method tries to uncover more biological relationship between a pair of lncRNA and disease, which may provide better clues for researchers. We compared GRUF with three state-of-the-art approaches and demonstrated the superiority of GRUF, which achieves 5%~16% improvement in terms of the area under the receiver operating characteristic curve (AUC). GRUF also provides a predicted confidence score for the predicted LDA, which reveals the significant correlation between the score and the number of RNA-Binding Proteins involved in LDAs. Lastly, three out of top-5 LDA candidates generated by GRUF in novel prediction are verified indirectly by medical literature and known biological facts. CONCLUSIONS The proposed GRUF has two advantages over existing approaches. Firstly, it can be used to work on lncRNAs that have no known disease association and diseases that have no known association with any lncRNAs. Secondly, instead of providing a binary answer (with or without association), GRUF works for both discrete and continued LDA, which help revealing the pathological implications between lncRNAs and diseases.
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Affiliation(s)
- Jian-Yu Shi
- School of Life Sciences, Northwestern Polytechnical University, Xi’an, 710072 China
| | - Hua Huang
- School of Software and Microelectronics, Northwestern Polytechnical University, Xi’an, 710072 China
| | - Yan-Ning Zhang
- School of Computer Science, Northwestern Polytechnical University, Xi’an, 710072 China
| | - Yu-Xi Long
- School of Computer Science, Northwestern Polytechnical University, Xi’an, 710072 China
| | - Siu-Ming Yiu
- Department of Computer Science, the University of Hong Kong, Hong Kong, 999077 China
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Ong MS, Cai W, Yuan Y, Leong HC, Tan TZ, Mohammad A, You ML, Arfuso F, Goh BC, Warrier S, Sethi G, Tolwinski NS, Lobie PE, Yap CT, Hooi SC, Huang RY, Kumar AP. 'Lnc'-ing Wnt in female reproductive cancers: therapeutic potential of long non-coding RNAs in Wnt signalling. Br J Pharmacol 2017; 174:4684-4700. [PMID: 28736855 PMCID: PMC5727316 DOI: 10.1111/bph.13958] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/30/2017] [Accepted: 07/17/2017] [Indexed: 02/06/2023] Open
Abstract
Recent discoveries in the non-coding genome have challenged the original central dogma of molecular biology, as non-coding RNAs and related processes have been found to be important in regulating gene expression. MicroRNAs and long non-coding RNAs (lncRNAs) are among those that have gained attention recently in human diseases, including cancer, with the involvement of many more non-coding RNAs (ncRNAs) waiting to be discovered. ncRNAs are a group of ribonucleic acids transcribed from regions of the human genome, which do not become translated into proteins, despite having essential roles in cellular physiology. Deregulation of ncRNA expression and function has been observed in cancer pathogenesis. Recently, the roles of a group of ncRNA known as lncRNA have gained attention in cancer, with increasing reports of their oncogenic involvement. Female reproductive cancers remain a leading cause of death in the female population, accounting for almost a third of all female cancer deaths in 2016. The Wnt signalling pathway is one of the most important oncogenic signalling pathways which is hyperactivated in cancers, including female reproductive cancers. The extension of ncRNA research into their mechanistic roles in human cancers has also led to novel reported roles of ncRNAs in the Wnt pathway and Wnt-mediated oncogenesis. This review aims to provide a critical summary of the respective roles and cellular functions of Wnt-associated lncRNAs in female reproductive cancers and explores the potential of circulating cell-free lncRNAs as diagnostic markers and lncRNAs as therapeutic targets. LINKED ARTICLES This article is part of a themed section on WNT Signalling: Mechanisms and Therapeutic Opportunities. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.24/issuetoc.
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Affiliation(s)
- Mei S Ong
- Departments of Physiology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Wanpei Cai
- Departments of Pharmacology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Yi Yuan
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Hin C Leong
- Departments of Pharmacology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Tuan Z Tan
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Asad Mohammad
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Ming L You
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
| | - Frank Arfuso
- Stem Cell and Cancer Biology Laboratory, School of Biomedical Sciences, Curtin Health Innovation Research InstituteCurtin UniversityPerthWAAustralia
| | - Boon C Goh
- Departments of Pharmacology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
- National University Cancer InstituteNational University Health SystemSingapore
- Department of Haematology‐OncologyNational University Health SystemSingapore
| | - Sudha Warrier
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative MedicineManipal UniversityBangaloreIndia
- School of Biomedical Sciences, Curtin Health Innovation Research InstituteCurtin UniversityPerthWAAustralia
| | - Gautam Sethi
- Departments of Pharmacology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
- School of Biomedical Sciences, Curtin Health Innovation Research InstituteCurtin UniversityPerthWAAustralia
| | - Nicholas S Tolwinski
- Division of ScienceYale‐NUS CollegeSingapore
- Department of Biological ScienceNational University of SingaporeSingapore
| | - Peter E Lobie
- Departments of Pharmacology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
- Departments of Anatomy, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
- Tsinghua Berkeley Shenzhen Institute and Division of Life Science and HealthTsinghua University Graduate SchoolShenzhenChina
| | - Celestial T Yap
- Departments of Physiology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
- National University Cancer InstituteNational University Health SystemSingapore
| | - Shing C Hooi
- Departments of Physiology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Ruby Y Huang
- Departments of Anatomy, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
- National University Cancer InstituteNational University Health SystemSingapore
- Department of Obstetrics and GynaecologyNational University HospitalSingapore
| | - Alan P Kumar
- Departments of Pharmacology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
- Cancer Science Institute of SingaporeNational University of SingaporeSingapore
- National University Cancer InstituteNational University Health SystemSingapore
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative MedicineManipal UniversityBangaloreIndia
- Curtin Medical School, Faculty of Health ScienceCurtin UniversityPerthWAAustralia
- Department of Biological SciencesUniversity of North TexasDentonTXUSA
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242
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Ransohoff JD, Wei Y, Khavari PA. The functions and unique features of long intergenic non-coding RNA. Nat Rev Mol Cell Biol 2017; 19:143-157. [PMID: 29138516 DOI: 10.1038/nrm.2017.104] [Citation(s) in RCA: 964] [Impact Index Per Article: 120.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Long intergenic non-coding RNA (lincRNA) genes have diverse features that distinguish them from mRNA-encoding genes and exercise functions such as remodelling chromatin and genome architecture, RNA stabilization and transcription regulation, including enhancer-associated activity. Some genes currently annotated as encoding lincRNAs include small open reading frames (smORFs) and encode functional peptides and thus may be more properly classified as coding RNAs. lincRNAs may broadly serve to fine-tune the expression of neighbouring genes with remarkable tissue specificity through a diversity of mechanisms, highlighting our rapidly evolving understanding of the non-coding genome.
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Affiliation(s)
- Julia D Ransohoff
- Program in Epithelial Biology, Stanford University School of Medicine, California 94305, USA
| | - Yuning Wei
- Program in Epithelial Biology, Stanford University School of Medicine, California 94305, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, California 94305, USA.,Veterans Affairs Palo Alto Healthcare System, Palo Alto, California 94304, USA
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243
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Qiu JJ, Liu YN, Ren ZR, Yan JB. Dysfunctions of mitochondria in close association with strong perturbation of long noncoding RNAs expression in down syndrome. Int J Biochem Cell Biol 2017; 92:115-120. [DOI: 10.1016/j.biocel.2017.09.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 08/23/2017] [Accepted: 09/23/2017] [Indexed: 01/07/2023]
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244
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Wu H, Wu R, Chen M, Li D, Dai J, Zhang Y, Gao K, Yu J, Hu G, Guo Y, Lin C, Li X. Comprehensive analysis of differentially expressed profiles of lncRNAs and construction of miR-133b mediated ceRNA network in colorectal cancer. Oncotarget 2017; 8:21095-21105. [PMID: 28177879 PMCID: PMC5400568 DOI: 10.18632/oncotarget.15045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/09/2017] [Indexed: 01/15/2023] Open
Abstract
Background Growing evidence suggests that long non-coding RNAs (lncRNAs) play a key role in tumorigenesis. However, the mechanism remains largely unknown. Results Thousands of significantly dysregulated lncRNAs and mRNAs were identified by microarray. Furthermore, a miR-133b-meditated lncRNA-mRNA ceRNA network was revealed, a subset of which was validated in 14 paired CRC patient tumor/non-tumor samples. Gene set enrichment analysis (GSEA) results demonstrated that lncRNAs ENST00000520055 and ENST00000535511 shared KEGG pathways with miR-133b target genes. Materials and Methods We used microarrays to survey the lncRNA and mRNA expression profiles of colorectal cancer and para-cancer tissues. Gene Ontology (GO) and KEGG pathway enrichment analyses were performed to explore the functions of the significantly dysregulated genes. An innovate method was employed that combined analyses of two microarray data sets to construct a miR-133b-mediated lncRNA-mRNA competing endogenous RNAs (ceRNA) network. Quantitative RT-PCR analysis was used to validate part of this network. GSEA was used to predict the potential functions of these lncRNAs. Conclusions This study identifies and validates a new method to investigate the miR-133b-mediated lncRNA-mRNA ceRNA network and lays the foundation for future investigation into the role of lncRNAs in colorectal cancer.
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Affiliation(s)
- Hao Wu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Runliu Wu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Miao Chen
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Daojiang Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Jing Dai
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Yi Zhang
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Kai Gao
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Jun Yu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Gui Hu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Yihang Guo
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Changwei Lin
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Xiaorong Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
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Zhang X, Hamblin MH, Yin KJ. The long noncoding RNA Malat1: Its physiological and pathophysiological functions. RNA Biol 2017; 14:1705-1714. [PMID: 28837398 DOI: 10.1080/15476286.2017.1358347] [Citation(s) in RCA: 361] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Recent studies suggest that in humans, DNA sequences responsible for protein coding regions comprise only 2% of the total genome. The rest of the transcripts result in RNA transcripts without protein-coding ability, including long noncoding RNAs (lncRNAs). Different from most members in the lncRNA family, the metastasis-associated lung adenocarcinoma transcript 1 (Malat1) is abundantly expressed and evolutionarily conserved throughout various mammalian species. Malat1 is one of the first identified lncRNAs associated with human disease, and cumulative studies have indicated that Malat1 plays critical roles in the development and progression of various cancers. Malat1 is also actively involved in various physiologic processes, including alternative splicing, epigenetic modification of gene expression, synapse formation, and myogenesis. Furthermore, extensive evidences show that Malat1 plays pivotal roles in multiple pathological conditions as well. In this review, we will summarize latest findings related to the physiologic and pathophysiological processes of Malat1 and discuss its therapeutic potentials.
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Affiliation(s)
- Xuejing Zhang
- a Pittsburgh Institute of Brain Disorders & Recovery , Department of Neurology , University of Pittsburgh School of Medicine , Pittsburgh , PA USA
| | - Milton H Hamblin
- b Department of Pharmacology , Tulane University School of Medicine , New Orleans , LA , USA
| | - Ke-Jie Yin
- a Pittsburgh Institute of Brain Disorders & Recovery , Department of Neurology , University of Pittsburgh School of Medicine , Pittsburgh , PA USA
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246
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Gudde AEEG, van Heeringen SJ, de Oude AI, van Kessel IDG, Estabrook J, Wang ET, Wieringa B, Wansink DG. Antisense transcription of the myotonic dystrophy locus yields low-abundant RNAs with and without (CAG)n repeat. RNA Biol 2017; 14:1374-1388. [PMID: 28102759 PMCID: PMC5711456 DOI: 10.1080/15476286.2017.1279787] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 12/21/2016] [Accepted: 12/30/2016] [Indexed: 12/20/2022] Open
Abstract
The unstable (CTG·CAG)n trinucleotide repeat in the myotonic dystrophy type 1 (DM1) locus is bidirectionally transcribed from genes with terminal overlap. By transcription in the sense direction, the DMPK gene produces various alternatively spliced mRNAs with a (CUG)n repeat in their 3' UTR. Expression in opposite orientation reportedly yields (CAG)n-repeat containing RNA, but both structure and biologic significance of this antisense gene (DM1-AS) are largely unknown. Via a combinatorial approach of computational and experimental analyses of RNA from unaffected individuals and DM1 patients we discovered that DM1-AS spans >6 kb, contains alternative transcription start sites and uses alternative polyadenylation sites up- and downstream of the (CAG)n repeat. Moreover, its primary transcripts undergo alternative splicing, whereby the (CAG)n segment is removed as part of an intron. Thus, in patients a mixture of DM1-AS RNAs with and without expanded (CAG)n repeat are produced. DM1-AS expression appears upregulated in patients, but transcript abundance remains very low in all tissues analyzed. Our data suggest that DM1-AS transcripts belong to the class of long non-coding RNAs. These and other biologically relevant implications for how (CAG)n-expanded transcripts may contribute to DM1 pathology can now be explored experimentally.
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Affiliation(s)
- Anke E. E. G. Gudde
- Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | - Simon J. van Heeringen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Amanda I. de Oude
- Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | | | - Joseph Estabrook
- Department of Molecular Genetics and Microbiology, Center for Neurogenetics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Eric T. Wang
- Department of Molecular Genetics and Microbiology, Center for Neurogenetics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Bé Wieringa
- Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | - Derick G. Wansink
- Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
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247
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Shen P, Pichler M, Chen M, Calin GA, Ling H. To Wnt or Lose: The Missing Non-Coding Linc in Colorectal Cancer. Int J Mol Sci 2017; 18:ijms18092003. [PMID: 28930145 PMCID: PMC5618652 DOI: 10.3390/ijms18092003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/09/2017] [Accepted: 09/13/2017] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third most frequent cancer and one of the leading causes for cancer-related mortality. Aberrant activation of the Wnt signaling is an essential initiating factor in colon carcinogenesis, and a driving force of CRC progression. Recently, long non-coding RNAs (lncRNAs) have emerged as significant players in CRC pathogenesis through diversified mechanisms. Although both Wnt signaling and lncRNAs represent interesting research areas for CRC, an effort of directly connecting these two areas is lacking. To fill in the knowledge gap, we focus on the reported findings of lncRNAs that regulate Wnt signaling or essential Wnt signaling targets. These include several newly discovered lncRNAs originated from the amplified cancer-associated chromosome 8q24 region that surrounds the essential Wnt target MYC gene, lncRNAs reported to be involved in CRC stem cells, and several individual lncRNAs connected to Wnt signaling through other mechanisms. This review will provide essential information that assists in understanding the missing link of lncRNAs to the classical Wnt signaling in CRC.
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Affiliation(s)
- Peng Shen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Nanfang Hospital, Southern Medical University/The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Research Unit of Non-Coding RNA and Genome Editing in Cancer, Division of Oncology, Medical University of Graz, Graz 8010, Austria.
| | - Meng Chen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- The Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Bai WL, Zhao SJ, Wang ZY, Zhu YB, Dang YL, Cong YY, Xue HL, Wang W, Deng L, Guo D, Wang SQ, Zhu YX, Yin RH. LncRNAs in Secondary Hair Follicle of Cashmere Goat: Identification, Expression, and Their Regulatory Network in Wnt Signaling Pathway. Anim Biotechnol 2017; 29:199-211. [PMID: 28846493 DOI: 10.1080/10495398.2017.1356731] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Long noncoding RNAs (lncRNAs) are a novel class of eukaryotic transcripts. They are thought to act as a critical regulator of protein-coding gene expression. Herein, we identified and characterized 13 putative lncRNAs from the expressed sequence tags from secondary hair follicle of Cashmere goat. Furthermore, we investigated their transcriptional pattern in secondary hair follicle of Liaoning Cashmere goat during telogen and anagen phases. Also, we generated intracellular regulatory networks of upregulated lncRNAs at anagen in Wnt signaling pathway based on bioinformatics analysis. The relative expression of six putative lncRNAs (lncRNA-599618, -599556, -599554, -599547, -599531, and -599509) at the anagen phase is significantly higher than that at telogen. Compared with anagen, the relative expression of four putative lncRNAs (lncRNA-599528, -599518, -599511, and -599497) was found to be significantly upregulated at telogen phase. The network generated showed that a rich and complex regulatory relationship of the putative lncRNAs and related miRNAs with their target genes in Wnt signaling pathway. Our results from the present study provided a foundation for further elucidating the functional and regulatory mechanisms of these putative lncRNAs in the development of secondary hair follicle and cashmere fiber growth of Cashmere goat.
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Affiliation(s)
- Wen L Bai
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Su J Zhao
- b Institute of Biotechnology , Sichuan Animal Science Academy , Chengdu , P. R. China
| | - Ze Y Wang
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Yu B Zhu
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Yun L Dang
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Yu Y Cong
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Hui L Xue
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Wei Wang
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Liang Deng
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
| | - Dan Guo
- c Academy of Animal Husbandry Science of Liaoning Province , Liaoyang , P. R. China
| | - Shi Q Wang
- c Academy of Animal Husbandry Science of Liaoning Province , Liaoyang , P. R. China
| | - Yan X Zhu
- c Academy of Animal Husbandry Science of Liaoning Province , Liaoyang , P. R. China
| | - Rong H Yin
- a College of Animal Science and Veterinary Medicine , Shenyang Agricultural University , Shenyang , P. R. China
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249
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Peng B, Liu A, Yu X, Xu E, Dai J, Li M, Yang Q. Silencing of lncRNA AFAP1-AS1 suppressed lung cancer development by regulatory mechanism in cis and trans. Oncotarget 2017; 8:93608-93623. [PMID: 29212176 PMCID: PMC5706822 DOI: 10.18632/oncotarget.20549] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/04/2017] [Indexed: 12/18/2022] Open
Abstract
Although the long noncoding RNA AFAP1-AS1 has been shown to be involved in various types of cancer, its involvement in lung cancer remains poorly understood. In the current study, we found that AFAP1-AS1 was substantially over expressed in lung cancer tissues and cell lines. In addition, AFAP1-AS1 expression level was proven to be associated with the malignant features of lung cancer. Knockdown of AFAP1-AS1 significantly suppressed cell proliferation by increasing cell apoptosis and G0/G1 phase retardation of cell cycle in lung cancer cells. Furthermore, AFAP1-AS1 knockdown could suppress tumor growth of lung cancer in BALB/c nude mice. We also identified that AFAP1-AS1 silencing could influence the expression of AFAP1 and KRT1 on mRNA and protein level by cis and trans regulatory mechanism. Moreover, the oncogenic activities of AFAP1-AS1 on cell proliferation are partially mediated by KRT1. In summary, these findings demonstrate that AFAP1-AS1 plays an essential role in promoting lung cancer development in vitro and vivo. It indicated that AFAP1-AS1 is a promising prognostic predictor for patients with lung cancer.
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Affiliation(s)
- Baoying Peng
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Yuexiu District, Guangzhou 510120, PR China.,The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Anfei Liu
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Xuanwei Yu
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Enwu Xu
- Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of Chinese People's Liberation Army, Guangzhou 510010, China
| | - Jiabin Dai
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Mengcheng Li
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Qiaoyuan Yang
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Yuexiu District, Guangzhou 510120, PR China.,The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
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250
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Chen YG, Satpathy AT, Chang HY. Gene regulation in the immune system by long noncoding RNAs. Nat Immunol 2017; 18:962-972. [PMID: 28829444 PMCID: PMC9830650 DOI: 10.1038/ni.3771] [Citation(s) in RCA: 520] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/16/2017] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression in the immune system. Studies have shown that lncRNAs are expressed in a highly lineage-specific manner and control the differentiation and function of innate and adaptive cell types. In this Review, we focus on mechanisms used by lncRNAs to regulate genes encoding products involved in the immune response, including direct interactions with chromatin, RNA and proteins. In addition, we address new areas of lncRNA biology, such as the functions of enhancer RNAs, circular RNAs and chemical modifications to RNA in cellular processes. We emphasize critical gaps in knowledge and future prospects for the roles of lncRNAs in the immune system and autoimmune disease.
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Affiliation(s)
- Y Grace Chen
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.,These authors contributed equally to this work
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,These authors contributed equally to this work
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
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