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Prabhakar B, Zhong XB, Rasmussen TP. Exploiting Long Noncoding RNAs as Pharmacological Targets to Modulate Epigenetic Diseases. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2017; 90:73-86. [PMID: 28356895 PMCID: PMC5369047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Long non-coding RNAs (lncRNAs) constitute the largest class of non-coding transcripts in the human genome. Results from next-generation sequencing and bioinformatics advances indicate that the human genome contains more non-coding RNA genes than protein-coding genes. Validated functions of lncRNAs suggest that they are master regulators of gene expression and often exert their influences via epigenetic mechanisms by modulating chromatin structure. Specific lncRNAs can regulate transcription in gene clusters. Since the functions of protein-coding genes in clusters are often tied to specific pathways, lncRNAs constitute attractive pharmacological targets. Here we review the current knowledge of lncRNA functions in human cells and their roles in disease processes. We also present forward-looking perspectives on how they might be manipulated pharmacologically for the treatment of a variety of human diseases, in which regulation of gene expression by epigenetic mechanisms plays a major role.
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Affiliation(s)
- Bindu Prabhakar
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT
| | - Xiao-bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT,Institute for Systems Genomics, University of Connecticut, Storrs/Farmington, CT
| | - Theodore P. Rasmussen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT,Institute for Systems Genomics, University of Connecticut, Storrs/Farmington, CT,To whom all correspondence should be addressed: Theodore P. Rasmussen, Ph.D., Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, CT 06269; Tel: (860) 486-8339; Fax: (860) 486-5792;
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Shi C, Zhang L, Qin C. Long non-coding RNAs in brain development, synaptic biology, and Alzheimer's disease. Brain Res Bull 2017; 132:160-169. [PMID: 28347717 DOI: 10.1016/j.brainresbull.2017.03.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/22/2017] [Indexed: 12/28/2022]
Abstract
Long non-coding RNAs (lncRNAs), which are long transcripts without apparent protein-coding roles, interfere with gene expression and signaling events at various stages. Increasing evidence has suggested that lncRNAs function in the regulation of tissue homeostasis and under pathophysiologic conditions. In the nervous system, the expression of lncRNAs has been detected and characterized under normal physiologic conditions and in disease states. Some lncRNAs regulate brain development and synaptic plasticity. In Alzheimer's disease (AD), several lncRNAs have been demonstrated to regulate β-amyloid production/generation, synaptic impairment, neurotrophin depletion, inflammation, mitochondrial dysfunction, and stress responses. This review summarizes data on lncRNA expression and focuses on neural lncRNAs that may function in AD. Although our understanding of lncRNAs remains in its infancy, this review provides insight into the contribution of lncRNAs to AD.
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Affiliation(s)
- Changhua Shi
- Comparative Medical Center, Peking Union Medical College (PUMC) and Institute of Laboratory Animal Science, Chinese Academy of Medical Science (CAMS), Beijing, China
| | - Ling Zhang
- Comparative Medical Center, Peking Union Medical College (PUMC) and Institute of Laboratory Animal Science, Chinese Academy of Medical Science (CAMS), Beijing, China
| | - Chuan Qin
- Comparative Medical Center, Peking Union Medical College (PUMC) and Institute of Laboratory Animal Science, Chinese Academy of Medical Science (CAMS), Beijing, China.
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Cao Y, Lin M, Bu Y, Ling H, He Y, Huang C, Shen Y, Song B, Cao D. p53-inducible long non-coding RNA PICART1 mediates cancer cell proliferation and migration. Int J Oncol 2017; 50:1671-1682. [PMID: 28339031 DOI: 10.3892/ijo.2017.3918] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 02/14/2017] [Indexed: 11/06/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) function in the development and progression of cancer, but only a small portion of lncRNAs have been characterized to date. A novel lncRNA transcript, 2.53 kb in length, was identified by transcriptome sequencing analysis, and was named p53-inducible cancer-associated RNA transcript 1 (PICART1). PICART1 was found to be upregulated by p53 through a p53-binding site at -1808 to -1783 bp. In breast and colorectal cancer cells and tissues, PICART1 expression was found to be decreased. Ectopic expression of PICART1 suppressed the growth, proliferation, migration, and invasion of MCF7, MDA-MB-231 and HCT116 cells whereas silencing of PICART1 stimulated cell growth and migration. In these cells, the expression of PICART1 suppressed levels of p-AKT (Thr308 and Ser473) and p-GSK3β (Ser9), and accordingly, β-catenin, cyclin D1 and c-Myc expression were decreased, while p21Waf/cip1 expression was increased. Together these data suggest that PICART1 is a novel p53-inducible tumor-suppressor lncRNA, functioning through the AKT/GSK3β/β-catenin signaling cascade.
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Affiliation(s)
- Yu Cao
- Department of Medical Microbiology, Immunology and Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, Springfield, IL 62794, USA
| | - Minglin Lin
- Department of Medical Microbiology, Immunology and Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, Springfield, IL 62794, USA
| | - Yiwen Bu
- Department of Medical Microbiology, Immunology and Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, Springfield, IL 62794, USA
| | - Hongyan Ling
- Department of Medical Microbiology, Immunology and Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, Springfield, IL 62794, USA
| | - Yingchun He
- Department of Medical Microbiology, Immunology and Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, Springfield, IL 62794, USA
| | - Chenfei Huang
- Department of Medical Microbiology, Immunology and Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, Springfield, IL 62794, USA
| | - Yi Shen
- Department of Medical Microbiology, Immunology and Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, Springfield, IL 62794, USA
| | - Bob Song
- University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Deliang Cao
- Department of Medical Microbiology, Immunology and Cell Biology, Simmons Cancer Institute, Southern Illinois University School of Medicine, Springfield, IL 62794, USA
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HOTAIR functions as a competing endogenous RNA to regulate PTEN expression by inhibiting miR-19 in cardiac hypertrophy. Mol Cell Biochem 2017; 432:179-187. [PMID: 28316060 DOI: 10.1007/s11010-017-3008-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/07/2017] [Indexed: 01/18/2023]
Abstract
Sustained cardiac hypertrophy (CH) is related to a variety of physiological as well as pathological stimuli and eventually increases the risk of heart failure. HOTAIR has been identified as a competing endogenous RNA in multiple human biological processes. Whether lncRNA-HOTAIR is involved in the progress of CH and how it works still remain unknown. Herein, we found that HOTAIR was down-regulated, while miR-19 was up-regulated in both heart tissues from TAC-operated mice in vivo and cultural cardiomyocytes treated with Ang-II in vitro by real-time PCR. Meanwhile, HOTAIR expression was negatively correlated with miR-19 in TAC-operated mice. HOTAIR overexpression reduced cell surface area and the expression of hypertrophic markers ANP, BNP, and β-MHC in response to Ang-II stimulation as well as knockdown of miR-19. The further molecular mechanisms of HOTAIR action in CH demonstrated that HOTAIR may act as a competing endogenous RNA (ceRNA) for miR-19, thereby modulating the dis-inhibition of its endogenous target PTEN and playing an important role in inhibiting CH progress. These findings reveal a novel function of LncRNAs, which conduce to an extensive understanding of CH and provide novel research directions and therapeutic options for treating this disease.
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Abstract
Maintaining intestinal homeostasis is a key prerequisite for a healthy gut. Recent evidence points out that microRNAs (miRNAs) act at the epicenter of the signaling networks regulating this process. The fine balance in the interaction between gut microbiota, intestinal epithelial cells, and the host immune system is achieved by constant transmission of signals and their precise regulation. Gut microbes extensively communicate with the host immune system and modulate host gene expression. On the other hand, sensing of gut microbiota by the immune cells provides appropriate tolerant responses that facilitate the symbiotic relationships. While the role of many regulatory proteins, receptors and their signaling pathways in the regulation of the intestinal homeostasis is well documented, the involvement of non-coding RNA molecules in this process has just emerged. This review discusses the most recent knowledge about the contribution of miRNAs in the regulation of the intestinal homeostasis.
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Affiliation(s)
- Antoaneta Belcheva
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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Kazemzadeh M, Safaralizadeh R, Feizi MAH, Ravanbakhsh R, Somi MH, Hashemzadeh S. LOC100287225, novel long intergenic non-coding RNA, misregulates in colorectal cancer. Cancer Biomark 2016; 16:499-505. [PMID: 27062707 DOI: 10.3233/cbm-160589] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Colorectal cancer (CRC) is one of the most common cancers in the world; therefore, extensive research is needed to find new molecular therapeutic targets and biomarkers. LncRNA (long non-coding RNA), a new class of non-coding RNAs, has a crucial role in the onset and progression of various cancers including colorectal cancer. Research on lncRNA is still at initial stages and underlying molecular mechanisms of the vast majority of lncRNA have remained unclear. LOC100287225 is one of these novel lncRNAs (long intergenic non-coding RNA) located in the long arm of the chromosome 18. The purpose of this study was to determine the expression of LOC100287225 in colorectal tissue, and its misregulation in CRC patients. Quantitative real-time-PCR (qRT-PCR) was used to investigate the LOC100287225 expression in pairs of tumorous and adjacent tumor-free tissues of 39 colorectal cancer patients. Also, the relationship between the clinicopathology and expression of LOC100287225 was determined. QRT-PCR results revealed that not only is LOC100287225 expressed in the intestinal tissue, but has also been misregulated during tumorigenesis. Moreover, LOC100287225 RNA relative expression levels were significantly lower in tumor tissues compared with adjacent tumor-free tissues (P< 0.001). RNA expression level of LOC100287225 did not show significant correlation with clinical characteristics. In conclusion, our study demonstrated that LOC100287225 misregulation could be a potential target for gene therapy in colorectal cancer.
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Affiliation(s)
- Mina Kazemzadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | | | - Reyhaneh Ravanbakhsh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mohammad Hossein Somi
- Liver and Gastroenterology Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahryar Hashemzadeh
- Liver and Gastrointestinal Disease Research Center and Department of General and Thoracic Surgery, Tabriz University of Medical Sciences, Tabriz, Iran
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Abstract
The advent of next-generation sequencing has demonstrated that eukaryotic genomes are extremely complex than what were previously thought. Recent studies revealed that in addition to protein-coding genes, nonprotein-coding genes have allocated a large fraction of the genome. Long noncoding RNA (lncRNA) genes are classified as nonprotein-coding genes, serving as a molecular signal, decoy, guide and scaffold. They were suggested to play important roles in chromatin states, epigenetic and posttranscriptional regulation of genes. Aberrant expression of lncRNAs and changes in their structure are associated with a wide spectrum of diseases ranging from different types of cancer and neurodegeneration to ?-thalassaemia. The purpose of this study was to summarize the current progress in understanding the genomic bases and origin of lncRNAs. Moreover, this study focusses on the diverse functions of lncRNAs in normal cells as well as various types of disease to illustrate the potential impacts of lncRNAs on diverse biological processes and their therapeutic significance.
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58
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Ferreira D, Meles S, Escudeiro A, Mendes-da-Silva A, Adega F, Chaves R. Satellite non-coding RNAs: the emerging players in cells, cellular pathways and cancer. Chromosome Res 2016; 23:479-93. [PMID: 26293605 DOI: 10.1007/s10577-015-9482-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
For several decades, transcriptional inactivity was considered as one of the particular features of constitutive heterochromatin and, therefore, of its major component, satellite DNA sequences. However, more recently, succeeding evidences have demonstrated that these sequences can indeed be transcribed, yielding satellite non-coding RNAs with important roles in the organization and regulation of genomes. Since then, several studies have been conducted, trying to understand the function(s) of these sequences not only in the normal but also in cancer genomes. It is thought that the association between cancer and satncRNAs is mostly due to the influence of these transcripts in the genome instability, a hallmark of cancer. The few reports on satellite DNA transcription in cancer contexts point to its overexpression; however, this scenario may be far more complex, variable, and influenced by a number of factors and the exact role of satncRNAs in the oncogenic process remains poorly understood. The greater is the knowledge on the association of satncRNAs with cancer, the greater would be the opportunity to assist cancer treatment, either by the design of effective therapies targeting these molecules or by using them as biomarkers in cancer diagnosis, prognosis, and with predictive value.
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Affiliation(s)
- Daniela Ferreira
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Lisboa, Portugal
| | - Susana Meles
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Lisboa, Portugal
| | - Ana Escudeiro
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Lisboa, Portugal
| | - Ana Mendes-da-Silva
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Lisboa, Portugal
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Lisboa, Portugal
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.
- Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Lisboa, Portugal.
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Tripathi R, Patel S, Kumari V, Chakraborty P, Varadwaj PK. DeepLNC, a long non-coding RNA prediction tool using deep neural network. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s13721-016-0129-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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60
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How Our Other Genome Controls Our Epi-Genome. Trends Microbiol 2016; 24:777-787. [PMID: 27289569 DOI: 10.1016/j.tim.2016.05.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/03/2016] [Accepted: 05/18/2016] [Indexed: 12/12/2022]
Abstract
Eukaryotes and prokaryotes produce extracellular nanovescicles that contain RNAs and other molecules that they exploit to communicate. Recently, inter-kingdom crosstalk was demonstrated between humans and bacteria through fecal microRNAs. We suggest here how bacteria interact with humans via RNAs within membrane vesicles to alter our epigenome, thus filling the gap and closing the circle. At the same time, there are indications that there could be a wider inter-kingdom communication network that might encompass all known kingdoms. Now that the connection with our other genome has been established, we also should begin to explore the 'social' network that we have around us.
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61
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Hu R, Sun X. lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics. J Bioinform Comput Biol 2016; 14:1650016. [PMID: 27306075 DOI: 10.1142/s0219720016500165] [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: 02/06/2023]
Abstract
Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. We provided lncRNATargets, which is a web-based platform for lncRNA target prediction based on nucleic acid thermodynamics. The nearest-neighbor (NN) model was used to calculate binging-free energy. The main principle of NN model for nucleic acid assumes that identity and orientation of neighbor base pairs determine stability of a given base pair. lncRNATargets features the following options: setting of a specific temperature that allow use not only for human but also for other animals or plants; processing all lncRNAs in high throughput without RNA size limitation that is superior to any other existing tool; and web-based, user-friendly interface, and colored result displays that allow easy access for nonskilled computer operators and provide better understanding of results. This technique could provide accurate calculation on the binding-free energy of lncRNA-target dimers to predict if these structures are well targeted together. lncRNATargets provides high accuracy calculations, and this user-friendly program is available for free at http://www.herbbol.org:8001/lrt/ .
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Affiliation(s)
- Ruifeng Hu
- 1 Beijing Key Laboratory of Innovative, Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, P. R. China.,2 Key Laboratory of Bioactive Substances and Resource, Utilization of Chinese Herbal Medicine, Ministry of Education, P. R. China.,3 Zhongguancun Open Laboratory of the Research and Development of Natural Medicine and Health Products, P. R. China
| | - Xiaobo Sun
- 1 Beijing Key Laboratory of Innovative, Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, P. R. China.,2 Key Laboratory of Bioactive Substances and Resource, Utilization of Chinese Herbal Medicine, Ministry of Education, P. R. China.,3 Zhongguancun Open Laboratory of the Research and Development of Natural Medicine and Health Products, P. R. China
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Wang X, Ai G, Zhang C, Cui L, Wang J, Li H, Zhang J, Ye Z. Expression and diversification analysis reveals transposable elements play important roles in the origin of Lycopersicon-specific lncRNAs in tomato. THE NEW PHYTOLOGIST 2016; 209:1442-55. [PMID: 26494192 DOI: 10.1111/nph.13718] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/20/2015] [Indexed: 05/20/2023]
Abstract
Long noncoding RNAs (lncRNAs) regulate gene expression and biological processes. With the development of high-throughput RNA sequencing technology, lncRNAs have been extensively studied in recent years. Nevertheless, the expression and evolution of lncRNAs in plants remain poorly understood. Here, we identified 413 and 709 multi-exon noncoding transcripts from 353 and 595 loci of the cultivar tomato Heinz1706 and its wild relative LA1589, respectively. Systematic comparison of the sequence and expression of lncRNAs showed that they are poorly conserved in Solanaceae, with only < 0.4% lncRNAs present in all sequenced genomes of tomato and potato. Sequence analysis of Lycopersicon-specific lncRNA loci in Solanum lycopersicum and S. pennellii showed that the origins of these molecules are associated with transposable elements (TEs). LncRNA-314, a fruit-specific lncRNA expressed in S. lycopersicum and S. pimpinellifolium, but not in S. pennellii, originated through two evolutionary events: speciation of S. pennellii resulted in insertion of a long terminal repeat (LTR) retrotransposon into chromosome 10 and contributed to most of the transcribed region of lncRNA-314; and a large deletion in Lycopersicon generated the promoter region and part of the transcribed region of lncRNA-314. These results provide novel insights into the evolution of lncRNAs in plants.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Guo Ai
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chunli Zhang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Long Cui
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jiafa Wang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hanxia Li
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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63
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Ge M, Li A, Wang M. A Bipartite Network-based Method for Prediction of Long Non-coding RNA-protein Interactions. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:62-71. [PMID: 26917505 PMCID: PMC4792848 DOI: 10.1016/j.gpb.2016.01.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/04/2016] [Accepted: 01/06/2016] [Indexed: 01/08/2023]
Abstract
As one large class of non-coding RNAs (ncRNAs), long ncRNAs (lncRNAs) have gained considerable attention in recent years. Mutations and dysfunction of lncRNAs have been implicated in human disorders. Many lncRNAs exert their effects through interactions with the corresponding RNA-binding proteins. Several computational approaches have been developed, but only few are able to perform the prediction of these interactions from a network-based point of view. Here, we introduce a computational method named lncRNA–protein bipartite network inference (LPBNI). LPBNI aims to identify potential lncRNA–interacting proteins, by making full use of the known lncRNA–protein interactions. Leave-one-out cross validation (LOOCV) test shows that LPBNI significantly outperforms other network-based methods, including random walk (RWR) and protein-based collaborative filtering (ProCF). Furthermore, a case study was performed to demonstrate the performance of LPBNI using real data in predicting potential lncRNA–interacting proteins.
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Affiliation(s)
- Mengqu Ge
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China
| | - Ao Li
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China; Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China.
| | - Minghui Wang
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China; Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China
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64
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Predicting Long Noncoding RNA and Protein Interactions Using Heterogeneous Network Model. BIOMED RESEARCH INTERNATIONAL 2015; 2015:671950. [PMID: 26839884 PMCID: PMC4709602 DOI: 10.1155/2015/671950] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 11/16/2015] [Accepted: 12/01/2015] [Indexed: 12/11/2022]
Abstract
Recent study shows that long noncoding RNAs (lncRNAs) are participating in diverse biological processes and complex diseases. However, at present the functions of lncRNAs are still rarely known. In this study, we propose a network-based computational method, which is called lncRNA-protein interaction prediction based on Heterogeneous Network Model (LPIHN), to predict the potential lncRNA-protein interactions. First, we construct a heterogeneous network by integrating the lncRNA-lncRNA similarity network, lncRNA-protein interaction network, and protein-protein interaction (PPI) network. Then, a random walk with restart is implemented on the heterogeneous network to infer novel lncRNA-protein interactions. The leave-one-out cross validation test shows that our approach can achieve an AUC value of 96.0%. Some lncRNA-protein interactions predicted by our method have been confirmed in recent research or database, indicating the efficiency of LPIHN to predict novel lncRNA-protein interactions.
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65
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Wang P, Fu H, Cui J, Chen X. Differential lncRNA‑mRNA co‑expression network analysis revealing the potential regulatory roles of lncRNAs in myocardial infarction. Mol Med Rep 2015; 13:1195-203. [PMID: 26676325 PMCID: PMC4732855 DOI: 10.3892/mmr.2015.4669] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 11/05/2015] [Indexed: 11/06/2022] Open
Abstract
Previous studies have reported that long, non-coding RNAs (lncRNAs) are important in cardiovascular disease. However, the lncRNAs involved in myocardial infarction and their detailed mechanism have not been well characterized. In the present study, an affymetrix microarray associated with myocardial infarction was re-annotated, following which a myocardial infarction-related differential lncRNA-mRNA co-expression network (MILMN) was constructed. Subsequently, pathway enrichment analysis was used for all the mRNAs in the MILMN, and an lncRNA-pathway network was constructed. It was found that the mRNAs were predominantly involved in certain cardiovascular disease-associated pathway, for example the dilated cardiomyopathy and mitogen-activated protein kinase signaling pathway. Finally, a total of 39 key lncRNAs were identified, which regulate crucial pathways in myocardial infarction. Through pathway analysis of these 39 key lncRNAs, the novel function of an annotated lncRNAs-H19 was predicted, which may regulate apoptosis signal-regulating kinase, which is a protein that promotes pathological cardiac remodeling following myocardial infarction. The results of the present study not only provide potential non-coding RNA biomarkers, but also provide further insights into understanding the molecular mechanism of lncRNAs.
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Affiliation(s)
- Ping Wang
- Department of Otolaryngology‑Head and Neck Surgery, First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Haiying Fu
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130000, P.R. China
| | - Jiayue Cui
- Department of Histology and Embryology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130000, P.R. China
| | - Xia Chen
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130000, P.R. China
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66
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Exploration of Deregulated Long Non-Coding RNAs in Association with Hepatocarcinogenesis and Survival. Cancers (Basel) 2015; 7:1847-62. [PMID: 26378581 PMCID: PMC4586798 DOI: 10.3390/cancers7030865] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are larger than 200 nucleotides in length and pervasively expressed across the genome. An increasing number of studies indicate that lncRNA transcripts play integral regulatory roles in cellular growth, division, differentiation and apoptosis. Deregulated lncRNAs have been observed in a variety of human cancers, including hepatocellular carcinoma (HCC). We determined the expression profiles of 90 lncRNAs for 65 paired HCC tumor and adjacent non-tumor tissues, and 55 lncRNAs were expressed in over 90% of samples. Eight lncRNAs were significantly down-regulated in HCC tumor compared to non-tumor tissues (p < 0.05), but no lncRNA achieved statistical significance after Bonferroni correction for multiple comparisons. Within tumor tissues, carrying more aberrant lncRNAs (6–7) was associated with a borderline significant reduction in survival (HR = 8.5, 95% CI: 1.0–72.5). The predictive accuracy depicted by the AUC was 0.93 for HCC survival when using seven deregulated lncRNAs (likelihood ratio test p = 0.001), which was similar to that combining the seven lncRNAs with tumor size and treatment (AUC = 0.96, sensitivity = 87%, specificity = 87%). These data suggest the potential association of deregulated lncRNAs with hepatocarcinogenesis and HCC survival.
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67
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Biswas AK, Kang M, Kim DC, Ding CHQ, Zhang B, Wu X, Gao JX. Inferring disease associations of the long non-coding RNAs through non-negative matrix factorization. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s13721-015-0081-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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68
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Predicting the functions of long noncoding RNAs using RNA-seq based on Bayesian network. BIOMED RESEARCH INTERNATIONAL 2015; 2015:839590. [PMID: 25815337 PMCID: PMC4359839 DOI: 10.1155/2015/839590] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 02/01/2023]
Abstract
Long noncoding RNAs (lncRNAs) have been shown to play key roles in various biological processes. However, functions of most lncRNAs are poorly characterized. Here, we represent a framework to predict functions of lncRNAs through construction of a regulatory network between lncRNAs and protein-coding genes. Using RNA-seq data, the transcript profiles of lncRNAs and protein-coding genes are constructed. Using the Bayesian network method, a regulatory network, which implies dependency relations between lncRNAs and protein-coding genes, was built. In combining protein interaction network, highly connected coding genes linked by a given lncRNA were subsequently used to predict functions of the lncRNA through functional enrichment. Application of our method to prostate RNA-seq data showed that 762 lncRNAs in the constructed regulatory network were assigned functions. We found that lncRNAs are involved in diverse biological processes, such as tissue development or embryo development (e.g., nervous system development and mesoderm development). By comparison with functions inferred using the neighboring gene-based method and functions determined using lncRNA knockdown experiments, our method can provide comparable predicted functions of lncRNAs. Overall, our method can be applied to emerging RNA-seq data, which will help researchers identify complex relations between lncRNAs and coding genes and reveal important functions of lncRNAs.
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69
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Li JH, Liu S, Zheng LL, Wu J, Sun WJ, Wang ZL, Zhou H, Qu LH, Yang JH. Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets. Front Bioeng Biotechnol 2015; 2:88. [PMID: 25642422 PMCID: PMC4294205 DOI: 10.3389/fbioe.2014.00088] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 12/22/2014] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as important regulatory molecules in developmental, physiological, and pathological processes. However, the precise mechanism and functions of most of lncRNAs remain largely unknown. Recent advances in high-throughput sequencing of immunoprecipitated RNAs after cross-linking (CLIP-Seq) provide powerful ways to identify biologically relevant protein–lncRNA interactions. In this study, by analyzing millions of RNA-binding protein (RBP) binding sites from 117 CLIP-Seq datasets generated by 50 independent studies, we identified 22,735 RBP–lncRNA regulatory relationships. We found that one single lncRNA will generally be bound and regulated by one or multiple RBPs, the combination of which may coordinately regulate gene expression. We also revealed the expression correlation of these interaction networks by mining expression profiles of over 6000 normal and tumor samples from 14 cancer types. Our combined analysis of CLIP-Seq data and genome-wide association studies data discovered hundreds of disease-related single nucleotide polymorphisms resided in the RBP binding sites of lncRNAs. Finally, we developed interactive web implementations to provide visualization, analysis, and downloading of the aforementioned large-scale datasets. Our study represented an important step in identification and analysis of RBP–lncRNA interactions and showed that these interactions may play crucial roles in cancer and genetic diseases.
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Affiliation(s)
- Jun-Hao Li
- RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University , Guangzhou , China
| | - Shun Liu
- RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University , Guangzhou , China
| | - Ling-Ling Zheng
- RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University , Guangzhou , China
| | - Jie Wu
- RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University , Guangzhou , China
| | - Wen-Ju Sun
- RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University , Guangzhou , China
| | - Ze-Lin Wang
- RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University , Guangzhou , China
| | - Hui Zhou
- RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University , Guangzhou , China
| | - Liang-Hu Qu
- RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University , Guangzhou , China
| | - Jian-Hua Yang
- RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University , Guangzhou , China
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70
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Shang D, Yang H, Xu Y, Yao Q, Zhou W, Shi X, Han J, Su F, Su B, Zhang C, Li C, Li X. A global view of network of lncRNAs and their binding proteins. MOLECULAR BIOSYSTEMS 2014; 11:656-63. [PMID: 25483728 DOI: 10.1039/c4mb00409d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recently, the long non-coding RNAs (lncRNAs) have obtained wide attention because they have broad and crucial functions in regulating complex biological processes. Many lncRNAs functioned by interfacing with corresponding RNA binding proteins and the complexity of lncRNAs' function was attributed to multiple lncRNA-protein interactions. To gain insights into the global relationship between lncRNAs and their binding proteins, here we constructed a lncRNA-protein network (LPN) based on experimentally determined functional interactions between them. This network included 177 lncRNAs, 92 proteins and 683 relationships between them. Cluster analysis of LPN revealed that some proteins (such as AGO and IGFBP families) and lncRNA (such as XIST and MALAT1) were densely connected, suggesting the potential co-regulated mechanism and functional cross-talk of different lncRNAs. We then characterized the lncRNA functions and found that lncRNA binding proteins (LBPs) enriched in many cancer or cancer-related pathways. Finally, we investigated the different topological properties of LBPs in PPIs network. Compared with disease proteins and average ones, LBPs tend to have significantly higher degree, betweenness, and closeness but a relatively lower clustering coefficient, indicating their centrality and essentiality in the context of a biological network.
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Affiliation(s)
- Desi Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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71
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Ushakov K, Rudnicki A, Avraham KB. MicroRNAs in sensorineural diseases of the ear. Front Mol Neurosci 2013; 6:52. [PMID: 24391537 PMCID: PMC3870287 DOI: 10.3389/fnmol.2013.00052] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/04/2013] [Indexed: 12/30/2022] Open
Abstract
Non-coding microRNAs (miRNAs) have a fundamental role in gene regulation and expression in almost every multicellular organism. Only discovered in the last decade, miRNAs are already known to play a leading role in many aspects of disease. In the vertebrate inner ear, miRNAs are essential for controlling development and survival of hair cells. Moreover, dysregulation of miRNAs has been implicated in sensorineural hearing impairment, as well as in other ear diseases such as cholesteatomas, vestibular schwannomas, and otitis media. Due to the inaccessibility of the ear in humans, animal models have provided the optimal tools to study miRNA expression and function, in particular mice and zebrafish. A major focus of current research has been to discover the targets of the miRNAs expressed in the inner ear, in order to determine the regulatory pathways of the auditory and vestibular systems. The potential for miRNAs manipulation in development of therapeutic tools for hearing impairment is as yet unexplored, paving the way for future work in the field.
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Affiliation(s)
- Kathy Ushakov
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
| | - Anya Rudnicki
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
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72
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Lv J, Cui W, Liu H, He H, Xiu Y, Guo J, Liu H, Liu Q, Zeng T, Chen Y, Zhang Y, Wu Q. Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data. PLoS One 2013; 8:e71152. [PMID: 23967161 PMCID: PMC3743905 DOI: 10.1371/journal.pone.0071152] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 06/21/2013] [Indexed: 11/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) as a key group of non-coding RNAs have gained widely attention. Though lncRNAs have been functionally annotated and systematic explored in higher mammals, few are under systematical identification and annotation. Owing to the expression specificity, known lncRNAs expressed in embryonic brain tissues remain still limited. Considering a large number of lncRNAs are only transcribed in brain tissues, studies of lncRNAs in developmental brain are therefore of special interest. Here, publicly available RNA-sequencing (RNA-seq) data in embryonic brain are integrated to identify thousands of embryonic brain lncRNAs by a customized pipeline. A significant proportion of novel transcripts have not been annotated by available genomic resources. The putative embryonic brain lncRNAs are shorter in length, less spliced and show less conservation than known genes. The expression of putative lncRNAs is in one tenth on average of known coding genes, while comparable with known lncRNAs. From chromatin data, putative embryonic brain lncRNAs are associated with active chromatin marks, comparable with known lncRNAs. Embryonic brain expressed lncRNAs are also indicated to have expression though not evident in adult brain. Gene Ontology analysis of putative embryonic brain lncRNAs suggests that they are associated with brain development. The putative lncRNAs are shown to be related to possible cis-regulatory roles in imprinting even themselves are deemed to be imprinted lncRNAs. Re-analysis of one knockdown data suggests that four regulators are associated with lncRNAs. Taken together, the identification and systematic analysis of putative lncRNAs would provide novel insights into uncharacterized mouse non-coding regions and the relationships with mammalian embryonic brain development.
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Affiliation(s)
- Jie Lv
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Wei Cui
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Hongbo Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Hongjuan He
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Youcheng Xiu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Jing Guo
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Hui Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Qi Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Tiebo Zeng
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Yan Chen
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
- * E-mail:
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73
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Long and short non-coding RNAs as regulators of hematopoietic differentiation. Int J Mol Sci 2013; 14:14744-70. [PMID: 23860209 PMCID: PMC3742271 DOI: 10.3390/ijms140714744] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/05/2013] [Accepted: 07/09/2013] [Indexed: 02/06/2023] Open
Abstract
Genomic analyses estimated that the proportion of the genome encoding proteins corresponds to approximately 1.5%, while at least 66% are transcribed, suggesting that many non-coding DNA-regions generate non-coding RNAs (ncRNAs). The relevance of these ncRNAs in biological, physiological as well as in pathological processes increased over the last two decades with the understanding of their implication in complex regulatory networks. This review particularly focuses on the involvement of two large families of ncRNAs, namely microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the regulation of hematopoiesis. To date, miRNAs have been widely studied, leading to a wealth of data about processing, regulation and mechanisms of action and more specifically, their involvement in hematopoietic differentiation. Notably, the interaction of miRNAs with the regulatory network of transcription factors is well documented whereas roles, regulation and mechanisms of lncRNAs remain largely unexplored in hematopoiesis; this review gathers current data about lncRNAs as well as both potential and confirmed roles in normal and pathological hematopoiesis.
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74
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McGraw S, Shojaei Saadi HA, Robert C. Meeting the methodological challenges in molecular mapping of the embryonic epigenome. Mol Hum Reprod 2013; 19:809-27. [PMID: 23783346 DOI: 10.1093/molehr/gat046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The past decade of life sciences research has been driven by progress in genomics. Many voices are already proclaiming the post-genomics era, in which phenomena other than sequence polymorphism influence gene expression and also explain complex phenotypes. One of these burgeoning fields is the study of the epigenome. Although the mechanisms by which chromatin structure and reorganization as well as cytosine methylation influence gene expression are not fully understood, they are being invoked to explain the now-accepted long-term impact of the environment on gene expression, which appears to be a factor in the development of numerous diseases. Such studies are particularly relevant in early embryonic development, during which waves of epigenetic reprogramming are known to have profound impacts. Since gametes and zygotes are in the process of resetting the genome in order to create embryonic stem cells that will each differentiate to create one of many specific tissue types, this phase of life is now viewed as a window of susceptibility to epigenetic reprogramming errors. Epigenetics could explain the influence of factors such as the nutritional/metabolic status of the mother or the artificial environment of assisted reproductive technologies. However, the peculiar nature of early embryos in addition to their scarcity poses numerous technological challenges that are slowly being overcome. The principal subject of this article is to review the suitability of various current and emerging technological platforms to study oocytes and early embryonic epigenome with more emphasis on studying DNA methylation. Furthermore, the constraint of samples size, inherent to the study of preimplantation embryo development, was put in perspective with the various molecular platforms described.
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Affiliation(s)
- Serge McGraw
- Department of Human Genetics, Montreal Children's Hospital Research Institute, McGill University, Montréal, QC H3Z 2Z3, Canada
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75
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Tang JY, Lee JC, Chang YT, Hou MF, Huang HW, Liaw CC, Chang HW. Long noncoding RNAs-related diseases, cancers, and drugs. ScientificWorldJournal 2013; 2013:943539. [PMID: 23843741 PMCID: PMC3690748 DOI: 10.1155/2013/943539] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 05/20/2013] [Indexed: 12/20/2022] Open
Abstract
Long noncoding RNA (lncRNA) function is described in terms of related gene expressions, diseases, and cancers as well as their polymorphisms. Potential modulators of lncRNA function, including clinical drugs, natural products, and derivatives, are discussed, and bioinformatic resources are summarized. The improving knowledge of the lncRNA regulatory network has implications not only in gene expression, diseases, and cancers, but also in the development of lncRNA-based pharmacology.
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Affiliation(s)
- Jen-Yang Tang
- Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jin-Ching Lee
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yung-Ting Chang
- Doctor Degree Program in Marine Biotechnology, National Sun Yat-sen University/Academia Sinica, Kaohsiung, Taiwan
| | - Ming-Feng Hou
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
| | - Hurng-Wern Huang
- Institute of Biomedical Science, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Chih-Chuang Liaw
- Doctor Degree Program in Marine Biotechnology, National Sun Yat-sen University/Academia Sinica, Kaohsiung, Taiwan
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Hsueh-Wei Chang
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
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76
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Regulatory Roles for Long ncRNA and mRNA. Cancers (Basel) 2013; 5:462-90. [PMID: 24216986 PMCID: PMC3730338 DOI: 10.3390/cancers5020462] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/05/2013] [Accepted: 04/19/2013] [Indexed: 01/31/2023] Open
Abstract
Recent advances in high-throughput sequencing technology have identified the transcription of a much larger portion of the genome than previously anticipated. Especially in the context of cancer it has become clear that aberrant transcription of both protein-coding and long non-coding RNAs (lncRNAs) are frequent events. The current dogma of RNA function describes mRNA to be responsible for the synthesis of proteins, whereas non-coding RNA can have regulatory or epigenetic functions. However, this distinction between protein coding and regulatory ability of transcripts may not be that strict. Here, we review the increasing body of evidence for the existence of multifunctional RNAs that have both protein-coding and trans-regulatory roles. Moreover, we demonstrate that coding transcripts bind to components of the Polycomb Repressor Complex 2 (PRC2) with similar affinities as non-coding transcripts, revealing potential epigenetic regulation by mRNAs. We hypothesize that studies on the regulatory ability of disease-associated mRNAs will form an important new field of research.
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77
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Recent insights and novel bioinformatics tools to understand the role of microRNAs binding to 5' untranslated region. Int J Mol Sci 2012; 14:480-95. [PMID: 23271365 PMCID: PMC3565276 DOI: 10.3390/ijms14010480] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/06/2012] [Accepted: 12/06/2012] [Indexed: 02/02/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression through the binding of the 3′ untranslated region (3′UTR) of specific mRNAs. MiRNAs are post-transcriptional regulators and determine the repression of translation processes or the degradation of mRNA targets. Recently, another kind of miRNA-mediated regulation of translation (repression or activation) involving the binding of miRNA to the 5′UTR of target gene has been reported. The possible interactions and the mechanism of action have been reported in many works that we reviewed here. Moreover, we discussed also the available bioinformatics tools for predicting the miRNA binding sites in the 5′UTR and public databases collecting this information.
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78
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Long non-coding RNAs and p53 regulation. Int J Mol Sci 2012; 13:16708-17. [PMID: 23222637 PMCID: PMC3546715 DOI: 10.3390/ijms131216708] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/03/2012] [Accepted: 12/03/2012] [Indexed: 12/20/2022] Open
Abstract
The advent of novel and high-throughput sequencing (next generation) technologies allowed for the sequencing of the genome at an unprecedented depth. The majority of transcribed RNAs have been classified as non-coding RNAs. Among them, long non-coding RNAs (lncRNAs) are emerging as important regulators in many biological processes. Here, we discuss the role of those lncRNAs which are under the control of p53 or that are able to regulate its activity, due to the central role of p53 pathway in many conditions. We also briefly discussed the emerging need of having novel strategies and computational tools to completely unravel the multifaceted roles of lncRNAs and to pave the way to the development of novel diagnostic and therapeutic applications based on these peculiar molecules.
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79
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Computational prediction of polycomb-associated long non-coding RNAs. PLoS One 2012; 7:e44878. [PMID: 23028655 PMCID: PMC3441527 DOI: 10.1371/journal.pone.0044878] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 08/09/2012] [Indexed: 11/19/2022] Open
Abstract
Among thousands of long non-coding RNAs (lncRNAs) only a small subset is functionally characterized and the functional annotation of lncRNAs on the genomic scale remains inadequate. In this study we computationally characterized two functionally different parts of human lncRNAs transcriptome based on their ability to bind the polycomb repressive complex, PRC2. This classification is enabled by the fact that while all lncRNAs constitute a diverse set of sequences, the classes of PRC2-binding and PRC2 non-binding lncRNAs possess characteristic combinations of sequence-structure patterns and, therefore, can be separated within the feature space. Based on the specific combination of features, we built several machine-learning classifiers and identified the SVM-based classifier as the best performing. We further showed that the SVM-based classifier is able to generalize on the independent data sets. We observed that this classifier, trained on the human lncRNAs, can predict up to 59.4% of PRC2-binding lncRNAs in mice. This suggests that, despite the low degree of sequence conservation, many lncRNAs play functionally conserved biological roles.
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