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Morimoto K, Suzuki H, Kuno A, Daitoku Y, Tanimoto Y, Kato K, Murata K, Sugiyama F, Mizuno S. Regional random mutagenesis driven by multiple sgRNAs and diverse on-target genome editing events to identify functionally important elements in non-coding regions. Open Biol 2024; 14:240007. [PMID: 38565160 PMCID: PMC10987234 DOI: 10.1098/rsob.240007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/06/2024] [Indexed: 04/04/2024] Open
Abstract
Functional regions that regulate biological phenomena are interspersed throughout eukaryotic genomes. The most definitive approach for identifying such regions is to confirm the phenotype of cells or organisms in which specific regions have been mutated or removed from the genome. This approach is invaluable for the functional analysis of genes with a defined functional element, the protein-coding sequence. By contrast, no functional analysis platforms have been established for the study of cis-elements or microRNA cluster regions consisting of multiple microRNAs with functional overlap. Whole-genome mutagenesis approaches, such as via N-ethyl-N-nitrosourea and gene trapping, have greatly contributed to elucidating the function of coding genes. These methods almost never induce deletions of genomic regions or multiple mutations within a narrow region. In other words, cis-elements and microRNA clusters cannot be effectively targeted in such a manner. Herein, we established a novel region-specific random mutagenesis method named CRISPR- and transposase-based regional mutagenesis (CTRL-mutagenesis). We demonstrate that CTRL-mutagenesis randomly induces diverse mutations within target regions in murine embryonic stem cells. Comparative analysis of mutants harbouring subtly different mutations within the same region would facilitate the further study of cis-element and microRNA clusters.
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Affiliation(s)
- Kento Morimoto
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- Research Fellow of the Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Hayate Suzuki
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Akihiro Kuno
- Department of Anatomy and Embryology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Daitoku
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Tanimoto
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kanako Kato
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kazuya Murata
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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Desvignes T, Sydes J, Montfort J, Bobe J, Postlethwait JH. Evolution after Whole-Genome Duplication: Teleost MicroRNAs. Mol Biol Evol 2021; 38:3308-3331. [PMID: 33871629 PMCID: PMC8321539 DOI: 10.1093/molbev/msab105] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are important gene expression regulators implicated in many biological processes, but we lack a global understanding of how miRNA genes evolve and contribute to developmental canalization and phenotypic diversification. Whole-genome duplication events likely provide a substrate for species divergence and phenotypic change by increasing gene numbers and relaxing evolutionary pressures. To understand the consequences of genome duplication on miRNA evolution, we studied miRNA genes following the teleost genome duplication (TGD). Analysis of miRNA genes in four teleosts and in spotted gar, whose lineage diverged before the TGD, revealed that miRNA genes were retained in ohnologous pairs more frequently than protein-coding genes, and that gene losses occurred rapidly after the TGD. Genomic context influenced retention rates, with clustered miRNA genes retained more often than nonclustered miRNA genes and intergenic miRNA genes retained more frequently than intragenic miRNA genes, which often shared the evolutionary fate of their protein-coding host. Expression analyses revealed both conserved and divergent expression patterns across species in line with miRNA functions in phenotypic canalization and diversification, respectively. Finally, major strands of miRNA genes experienced stronger purifying selection, especially in their seeds and 3'-complementary regions, compared with minor strands, which nonetheless also displayed evolutionary features compatible with constrained function. This study provides the first genome-wide, multispecies analysis of the mechanisms influencing metazoan miRNA evolution after whole-genome duplication.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
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Fang LL, Wang XH, Sun BF, Zhang XD, Zhu XH, Yu ZJ, Luo H. Expression, regulation and mechanism of action of the miR-17-92 cluster in tumor cells (Review). Int J Mol Med 2017; 40:1624-1630. [PMID: 29039606 PMCID: PMC5716450 DOI: 10.3892/ijmm.2017.3164] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 09/11/2017] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs), a class of short, single-stranded non-coding RNAs, regulate and control gene expression in eukaryotes by degrading mRNA at the post-transcriptional level. Regulation by miRNAs involves a plethora of biological processes, such as cell differentiation, proliferation, metastasis, metabolism, apoptosis, tumorigenesis and others. miRNAs also represent a powerful tool in disease diagnosis and prognosis. The miR-17-92 cluster, one of the most extensively investigated microRNA clusters, comprises six mature miRNA members, including miR-17, miR-18a, miR-19a, miR-19b, miR-20a and miR-92a. Originally identified as being involved in tumorigenesis, it is currently evident that the expression of the miR-17-92 cluster is upregulated in a wide range of tumor cells and cancer types; thus, this cluster has been identified as a potential oncogene. Considering the growing interest in the field of miR-17-92 research, we herein review recent advances in the expression and regulation of this cluster in various cancer cells, discuss the proposed mechanism of action for tumorigenesis and tumor development, and propose clinical and therapeutic applications for miR-17-92 cluster members, such as potential cancer biomarkers.
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Affiliation(s)
- Li-Li Fang
- Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Xing-Hui Wang
- Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, Guizhou 550004, P.R. China
| | - Bao-Fei Sun
- Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Xiao-Dong Zhang
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Xu-Hui Zhu
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Zi-Jiang Yu
- Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Heng Luo
- Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, Guizhou 550004, P.R. China
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Patel VD, Capra JA. Ancient human miRNAs are more likely to have broad functions and disease associations than young miRNAs. BMC Genomics 2017; 18:672. [PMID: 28859623 PMCID: PMC5579935 DOI: 10.1186/s12864-017-4073-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 08/16/2017] [Indexed: 12/16/2022] Open
Abstract
Background microRNAs (miRNAs) are essential to the regulation of gene expression in eukaryotes, and improper expression of miRNAs contributes to hundreds of diseases. Despite the essential functions of miRNAs, the evolutionary dynamics of how they are integrated into existing gene regulatory and functional networks is not well understood. Knowledge of the origin and evolutionary history a gene has proven informative about its functions and disease associations; we hypothesize that incorporating the evolutionary origins of miRNAs into analyses will help resolve differences in their functional dynamics and how they influence disease. Results We computed the phylogenetic age of miRNAs across 146 species and quantified the relationship between human miRNA age and several functional attributes. Older miRNAs are significantly more likely to be associated with disease than younger miRNAs, and the number of associated diseases increases with age. As has been observed for genes, the miRNAs associated with different diseases have different age profiles. For example, human miRNAs implicated in cancer are enriched for origins near the dawn of animal multicellularity. Consistent with the increasing contribution of miRNAs to disease with age, older miRNAs target more genes than younger miRNAs, and older miRNAs are expressed in significantly more tissues. Furthermore, miRNAs of all ages exhibit a strong preference to target older genes; 93% of validated miRNA gene targets were in existence at the origin of the targeting miRNA. Finally, we find that human miRNAs in evolutionarily related families are more similar in their targets and expression profiles than unrelated miRNAs. Conclusions Considering the evolutionary origin and history of a miRNA provides useful context for the analysis of its function. Consistent with recent work in Drosophila, our results support a model in which miRNAs increase their expression and functional regulatory interactions over evolutionary time, and thus older miRNAs have increased potential to cause disease. We anticipate that these patterns hold across mammalian species; however, comprehensively evaluating them will require refining miRNA annotations across species and collecting functional data in non-human systems. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4073-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vir D Patel
- Department of Biology, Duke University, Durham, NC, 27708, USA.,Department of Biology, Western Kentucky University, Bowling Green, KY, 42101, USA
| | - John A Capra
- Departments of Biological Sciences, Biomedical Informatics, and Computer Science, Vanderbilt Genetics Institute, Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA.
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Abstract
The discovery of the microRNAs, lin-4 and let-7 as critical mediators of normal development in Caenorhabditis elegans and their conservation throughout evolution has spearheaded research toward identifying novel roles of microRNAs in other cellular processes. To accurately elucidate these fundamental functions, especially in the context of an intact organism, various microRNA transgenic models have been generated and evaluated. Transgenic C. elegans (worms), Drosophila melanogaster (flies), Danio rerio (zebrafish), and Mus musculus (mouse) have contributed immensely toward uncovering the roles of multiple microRNAs in cellular processes such as proliferation, differentiation, and apoptosis, pathways that are severely altered in human diseases such as cancer. The simple model organisms, C. elegans, D. melanogaster, and D. rerio, do not develop cancers but have proved to be convenient systesm in microRNA research, especially in characterizing the microRNA biogenesis machinery which is often dysregulated during human tumorigenesis. The microRNA-dependent events delineated via these simple in vivo systems have been further verified in vitro, and in more complex models of cancers, such as M. musculus. The focus of this review is to provide an overview of the important contributions made in the microRNA field using model organisms. The simple model systems provided the basis for the importance of microRNAs in normal cellular physiology, while the more complex animal systems provided evidence for the role of microRNAs dysregulation in cancers. Highlights include an overview of the various strategies used to generate transgenic organisms and a review of the use of transgenic mice for evaluating preclinical efficacy of microRNA-based cancer therapeutics.
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Affiliation(s)
- Arpita S Pal
- PULSe Graduate Program, Purdue University, West Lafayette, IN, United States
| | - Andrea L Kasinski
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, United States.
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Gong W, Huang Y, Xie J, Wang G, Yu D, Sun X. Genome-wide identification of novel microRNAs from genome sequences using computational approach in the mudskipper (Boleophthalmus pectinirostris). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017040161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Dambal S, Giangreco AA, Acosta AM, Fairchild A, Richards Z, Deaton R, Wagner D, Vieth R, Gann PH, Kajdacsy-Balla A, Van der Kwast T, Nonn L. microRNAs and DICER1 are regulated by 1,25-dihydroxyvitamin D in prostate stroma. J Steroid Biochem Mol Biol 2017; 167:192-202. [PMID: 28089917 PMCID: PMC5304339 DOI: 10.1016/j.jsbmb.2017.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 12/31/2022]
Abstract
Vitamin D deficiency increases the risk of lethal prostate adenocarcinomas (PCa) and the majority of older men are deficient. Although PCa arises from the epithelium, the surrounding stroma has hormonal regulatory control over the epithelium and contributes to carcinogenesis. Herein, we describe regulation of microRNAs (miRs) by the active hormone dihydroxyvitamin D (1,25(OH)2D) in human prostate stroma. 1,25(OH)2D binds the vitamin D receptor (VDR) transcription factor to regulate gene expression, including miRs, which have emerged as potent regulators of protein expression. 1,25(OH)2D-regulated miRs were identified by profiling in primary human prostatic stromal cells (PrS) and three miRs, miR-126-3p, miR 154-5p and miR-21-5p were subsequently validated in laser-capture micro-dissected prostate stromal tissue from a vitamin D3 clinical trial (N=45). Regulation of these miRs by 1,25(OH)2D was VDR-dependent. Network analysis of known and putative mRNA targets of these miRs was enriched with cancer and inflammation pathways, consistent with known roles of stroma and of vitamin D in carcinogenesis. Expression of the miR processing ribonuclease, DICER1, positively correlated with vitamin D metabolite levels in the clinical trial specimens. High epithelial/stromal ratios of DICER1 were significantly associated biochemical recurrence (OR 3.1, p=0.03) in a tissue microarray of 170 matched PCa patients. In summary, these results underscore the role of the prostate stroma in regulating responses to the hormone 1,25(OH)2D and identified miRs and DICER1 as being regulated in human prostate stroma. Regulation of stromal DICER1 by 1,25(OH)2D may also have clinical relevance in protection against aggressive PCa.
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Affiliation(s)
- Shweta Dambal
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, United States
| | - Angeline A Giangreco
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, United States
| | - Andres M Acosta
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, United States
| | - Andrew Fairchild
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, United States
| | - Zachary Richards
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, United States
| | - Ryan Deaton
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, United States
| | - Dennis Wagner
- Department of Nutritional Sciences, Laboratory Medicine and Pathobiology, University of Toronto, ON, Canada
| | - Reinhold Vieth
- Department of Nutritional Sciences, Laboratory Medicine and Pathobiology, University of Toronto, ON, Canada
| | - Peter H Gann
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, United States; University of Illinois Cancer Center, Chicago, IL, United States
| | - Andre Kajdacsy-Balla
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, United States; University of Illinois Cancer Center, Chicago, IL, United States
| | | | - Larisa Nonn
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, United States; University of Illinois Cancer Center, Chicago, IL, United States.
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8
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Ren H, Tao C, Li K, Bi Y, Zheng X. Generation of a Floxed Allele of the Mouse MicroRNA-200 Clusters. Appl Biochem Biotechnol 2017; 182:1218-1228. [PMID: 28078648 DOI: 10.1007/s12010-016-2394-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 12/29/2016] [Indexed: 11/29/2022]
Abstract
MicroRNA-8 and its target gene, u-shaped (ush), regulate body size in Drosophila. As the mouse homolog of the Drosophila miR-8, whether the miR-200 family has similar functions and how they perform their regulatory roles in body size control is unknown. In order to discover the biological function of the miR-200s in vivo, we generated mice lacking the miR-200b/200a/429 gene cluster using the Cre/loxp system. miR-200b/200a/429 null mutant mice were viable, fertile, and showed normal development.
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Affiliation(s)
- Hongyan Ren
- Key Laboratory of Animal Embryo & Molecular Breeding of Hubei Province, Institute of Veterinary and Animal Science, Hubei Academy of Agricultural Science, Wuhan, 430064, China
| | - Cong Tao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Kui Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yanzhen Bi
- Key Laboratory of Animal Embryo & Molecular Breeding of Hubei Province, Institute of Veterinary and Animal Science, Hubei Academy of Agricultural Science, Wuhan, 430064, China
| | - Xinmin Zheng
- Key Laboratory of Animal Embryo & Molecular Breeding of Hubei Province, Institute of Veterinary and Animal Science, Hubei Academy of Agricultural Science, Wuhan, 430064, China.
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Guo L, Zhang Q, Ma X, Wang J, Liang T. miRNA and mRNA expression analysis reveals potential sex-biased miRNA expression. Sci Rep 2017; 7:39812. [PMID: 28045090 PMCID: PMC5206641 DOI: 10.1038/srep39812] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/25/2016] [Indexed: 12/22/2022] Open
Abstract
Recent studies suggest that mRNAs may be differentially expressed between males and females. This study aimed to perform expression analysis of mRNA and its main regulatory molecule, microRNA (miRNA), to discuss the potential sex-specific expression patterns using abnormal expression profiles from The Cancer Genome Atlas database. Generally, deregulated miRNAs and mRNAs had consistent expression between males and females, but some miRNAs may be oppositely expressed in specific diseases: up-regulated in one group and down-regulated in another. Studies of miRNA gene families and clusters further confirmed that these sequence or location related miRNAs might have opposing expression between sexes. The specific miRNA might have greater expression divergence across different groups, suggesting flexible expression across different individuals, especially in tumor samples. The typical analysis regardless of the sex will ignore or balance these sex-specific deregulated miRNAs. Compared with flexible miRNAs, their targets of mRNAs showed relative stable expression between males and females. These relevant results provide new insights into miRNA-mRNA interaction and sex difference.
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Affiliation(s)
- Li Guo
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Qiang Zhang
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xiao Ma
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Jun Wang
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, China
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10
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Guo L, Liang T. MicroRNAs and their variants in an RNA world: implications for complex interactions and diverse roles in an RNA regulatory network. Brief Bioinform 2016; 19:245-253. [DOI: 10.1093/bib/bbw124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Indexed: 01/09/2023] Open
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11
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Khuu C, Utheim TP, Sehic A. The Three Paralogous MicroRNA Clusters in Development and Disease, miR-17-92, miR-106a-363, and miR-106b-25. SCIENTIFICA 2016; 2016:1379643. [PMID: 27127675 PMCID: PMC4834410 DOI: 10.1155/2016/1379643] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 05/06/2023]
Abstract
MicroRNAs (miRNAs) form a class of noncoding RNA genes whose products are small single-stranded RNAs that are involved in the regulation of translation and degradation of mRNAs. There is a fine balance between deregulation of normal developmental programs and tumor genesis. An increasing body of evidence suggests that altered expression of miRNAs is entailed in the pathogenesis of human cancers. Studies in mouse and human cells have identified the miR-17-92 cluster as a potential oncogene. The miR-17-92 cluster is often amplified or overexpressed in human cancers and has recently emerged as the prototypical oncogenic polycistron miRNA. The functional analysis of miR-17-92 is intricate by the existence of two paralogues: miR-106a-363 and miR-106b-25. During early evolution of vertebrates, it is likely that the three clusters commenced via a series of duplication and deletion occurrences. As miR-106a-363 and miR-106b-25 contain miRNAs that are very similar, and in some cases identical, to those encoded by miR-17-92, it is feasible that they regulate a similar set of genes and have overlapping functions. Further understanding of these three clusters and their functions will increase our knowledge about cancer progression. The present review discusses the characteristics and functions of these three miRNA clusters.
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Affiliation(s)
- Cuong Khuu
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
- *Cuong Khuu:
| | - Tor Paaske Utheim
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital, 0407 Oslo, Norway
- Department of Ophthalmology, Drammen Hospital, Vestre Viken Hospital Trust, 3004 Drammen, Norway
- Faculty of Health Sciences, University College of South East Norway, 3614 Kongsberg, Norway
| | - Amer Sehic
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
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12
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Fan L, Qi H, Teng J, Su B, Chen H, Wang C, Xia Q. Identification of serum miRNAs by nano-quantum dots microarray as diagnostic biomarkers for early detection of non-small cell lung cancer. Tumour Biol 2015; 37:7777-84. [DOI: 10.1007/s13277-015-4608-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/07/2015] [Indexed: 02/06/2023] Open
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13
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Huang Y, Cheng JH, Luo FN, Pan H, Sun XJ, Diao LY, Qin XJ. Genome-wide identification and characterization of microRNA genes and their targets in large yellow croaker (Larimichthys crocea). Gene 2015; 576:261-7. [PMID: 26523500 DOI: 10.1016/j.gene.2015.10.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/04/2015] [Accepted: 10/13/2015] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs or miRs) are a class of non-coding RNAs of 20-25 nucleotides (nt) in length, which regulates the expression of gene in eukaryotic organism. Studies has been confirmed that miRNA plays an important role in various biological and metabolic processes in both animals and plants. Predicting new miRNAs by computer based homology search analysis is an effective way to discover novel miRNAs. Though a large number of miRNAs have been reported in many fish species, reports of miRNAs in large yellow croaker (L. crocea) are limited especially via the computational-based approaches. In this paper, a method of comparative genomic approach by computational genomic homology based on the conservation of miRNA sequences and the stem-loop hairpin secondary structures of miRNAs was adopted. A total of 199 potential miRNAs were predicted representing 81 families. 12 of them were chose to be validated by real time RT-PCR, apart from miR-7132b-5p which was not detected. Results indicated that the prediction method that we used to identify the miRNAs was effective. Furthermore, 948 potential target genes were predicted. Gene ontology (GO) analysis revealed that 175, 287, and 486 target genes were involved in cellular components, biological processes and molecular functions, respectively. Overall, our findings provide a first computational identification and characterization of L. crocea miRNAs and their potential targets in functional analysis, and will be useful in laying the foundation for further characterization of their role in the regulation of diversity of physiological processes.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China.
| | - Jia-Heng Cheng
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Fu-Nong Luo
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Hao Pan
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xiao-Juan Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Lan-Yu Diao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xiao-Juan Qin
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
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14
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L'Hernault A, Dölken L. Small RNAs growing tall: miRNAs as drug targets in herpesvirus infections. Curr Opin Virol 2015; 15:41-7. [PMID: 26256575 DOI: 10.1016/j.coviro.2015.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 12/27/2022]
Abstract
Herpesviruses establish life-long latent infections. They can cause severe morbidity and significant mortality particularly in immunocompromised hosts. Several are associated with cancers. Most express large amounts of microRNAs during latent or lytic infection. There is increasing evidence that these small RNA molecules play important roles in many aspects of pathogenesis, including lytic and latent infections, immune evasion and tumorigenesis. Therapies targeting microRNAs have already successfully made it into clinics, for example, to treat hepatitis C virus (HCV) infection. In this review, we will focus on regulatory functions of herpesvirus miRNAs that may be suitable for antiviral intervention.
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Affiliation(s)
| | - Lars Dölken
- Department of Medicine, University of Cambridge, UK; Institute of Virology and Immunobiology, University of Würzburg, Germany.
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15
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Dambal S, Shah M, Mihelich B, Nonn L. The microRNA-183 cluster: the family that plays together stays together. Nucleic Acids Res 2015; 43:7173-88. [PMID: 26170234 PMCID: PMC4551935 DOI: 10.1093/nar/gkv703] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/25/2015] [Indexed: 12/28/2022] Open
Abstract
The microRNA (miR)183 cluster, which is comprised of miRs-183, -96 and -182, is also a miR family with sequence homology. Despite the strong similarity in the sequences of these miRs, minute differences in their seed sequences result in both overlapping and distinct messenger RNA targets, which are often within the same pathway. These miRs have tightly synchronized expression during development and are required for maturation of sensory organs. In comparison to their defined role in normal development, the miR-183 family is frequently highly expressed in a variety of non-sensory diseases, including cancer, neurological and auto-immune disorders. Here, we discuss the conservation of the miR-183 cluster and the functional role of this miR family in normal development and diseases. We also describe the regulation of vital cellular pathways by coordinated expression of these miR siblings. This comprehensive review sheds light on the likely reasons why the genomic organization and seeming redundancy of the miR-183 family cluster was conserved through 600 million years of evolution.
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Affiliation(s)
- Shweta Dambal
- Department of Pathology, University of Illinois at Chicago, 840 S. Wood Street, Room 130 CSN, MC 847, Chicago, IL 60612, USA
| | - Mit Shah
- Department of Pathology, University of Illinois at Chicago, 840 S. Wood Street, Room 130 CSN, MC 847, Chicago, IL 60612, USA
| | - Brittany Mihelich
- Department of Pathology, University of Illinois at Chicago, 840 S. Wood Street, Room 130 CSN, MC 847, Chicago, IL 60612, USA
| | - Larisa Nonn
- Department of Pathology, University of Illinois at Chicago, 840 S. Wood Street, Room 130 CSN, MC 847, Chicago, IL 60612, USA University of Illinois Cancer Center, Chicago, IL 60612, USA
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16
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Guo L, Zhao Y, Zhang H, Yang S, Chen F. Integrated evolutionary analysis of human miRNA gene clusters and families implicates evolutionary relationships. Gene 2014; 534:24-32. [DOI: 10.1016/j.gene.2013.10.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 10/10/2013] [Accepted: 10/15/2013] [Indexed: 12/01/2022]
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Abstract
Understanding of the roles of noncoding RNAs (ncRNAs) within complex organisms has fundamentally changed. It is increasingly possible to use ncRNAs as diagnostic and therapeutic tools in medicine. Regarding disease pathogenesis, it has become evident that confinement to the analysis of protein-coding regions of the human genome is insufficient because ncRNA variants have been associated with important human diseases. Thus, inclusion of noncoding genomic elements in pathogenetic studies and their consideration as therapeutic targets is warranted. We consider aspects of the evolutionary and discovery history of ncRNAs, as far as they are relevant for the identification and selection of ncRNAs with likely therapeutic potential. Novel therapeutic strategies are based on ncRNAs, and we discuss here RNA interference as a highly versatile tool for gene silencing. RNA interference-mediating RNAs are small, but only parts of a far larger spectrum encompassing ncRNAs up to many kilobasepairs in size. We discuss therapeutic options in cardiovascular medicine offered by ncRNAs and key issues to be solved before clinical translation. Convergence of multiple technical advances is highlighted as a prerequisite for the translational progress achieved in recent years. Regarding safety, we review properties of RNA therapeutics, which may immunologically distinguish them from their endogenous counterparts, all of which underwent sophisticated evolutionary adaptation to specific biological contexts. Although our understanding of the noncoding human genome is only fragmentary to date, it is already feasible to develop RNA interference against a rapidly broadening spectrum of therapeutic targets and to translate this to the clinical setting under certain restrictions.
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Affiliation(s)
- Wolfgang Poller
- From the Department of Cardiology and Pneumology, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Juliane Tank
- From the Department of Cardiology and Pneumology, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Carsten Skurk
- From the Department of Cardiology and Pneumology, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Martina Gast
- From the Department of Cardiology and Pneumology, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Berlin, Germany
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18
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19
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Philippe L, Alsaleh G, Bahram S, Pfeffer S, Georgel P. The miR-17 ∼ 92 Cluster: A Key Player in the Control of Inflammation during Rheumatoid Arthritis. Front Immunol 2013; 4:70. [PMID: 23516027 PMCID: PMC3601326 DOI: 10.3389/fimmu.2013.00070] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/04/2013] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are now recognized as essential regulators of gene expression in plants and animals. They potentially modulate the expression of multiple genes thereby enabling homeostatic settings in physiological conditions. Their role is also increasingly considered in many diseases in which deregulated epigenetic mechanisms induce aberrant gene expression. Work conducted in our laboratory has recently led to the identification of miRNAs essential for the control of inflammatory reactions that occur during rheumatoid arthritis (RA). In this review, we describe two such miRNAs, members of the miR-17 ∼ 92 cluster, which has been previously implicated in cancer. Based on our data and on predicted miRNA:mRNA interactions, we will extrapolate a model whereby the miR-17 ∼ 92 cluster appears as a global regulator of the Apoptosis Signal-Regulating Kinase 1 signalosome, a central actor in the inflammatory pathways activated during RA. We will also discuss the potential therapeutic outcomes emerging from this model.
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Affiliation(s)
- Lucas Philippe
- ImmunoRhumatologie Moléculaire, INSERM UMR_S 1109, Centre de Recherche d'Immunologie et d'Hématologie, Université de Strasbourg Strasbourg Cedex, France
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