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Hiers NM, Li T, Traugot CM, Xie M. Target-directed microRNA degradation: Mechanisms, significance, and functional implications. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1832. [PMID: 38448799 PMCID: PMC11098282 DOI: 10.1002/wrna.1832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 03/08/2024]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play a fundamental role in enabling miRNA-mediated target repression, a post-transcriptional gene regulatory mechanism preserved across metazoans. Loss of certain animal miRNA genes can lead to developmental abnormalities, disease, and various degrees of embryonic lethality. These short RNAs normally guide Argonaute (AGO) proteins to target RNAs, which are in turn translationally repressed and destabilized, silencing the target to fine-tune gene expression and maintain cellular homeostasis. Delineating miRNA-mediated target decay has been thoroughly examined in thousands of studies, yet despite these exhaustive studies, comparatively less is known about how and why miRNAs are directed for decay. Several key observations over the years have noted instances of rapid miRNA turnover, suggesting endogenous means for animals to induce miRNA degradation. Recently, it was revealed that certain targets, so-called target-directed miRNA degradation (TDMD) triggers, can "trigger" miRNA decay through inducing proteolysis of AGO and thereby the bound miRNA. This process is mediated in animals via the ZSWIM8 ubiquitin ligase complex, which is recruited to AGO during engagement with triggers. Since its discovery, several studies have identified that ZSWIM8 and TDMD are indispensable for proper animal development. Given the rapid expansion of this field of study, here, we summarize the key findings that have led to and followed the discovery of ZSWIM8-dependent TDMD. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Nicholas M Hiers
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Conner M Traugot
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
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2
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Jones BT, Han J, Zhang H, Hammer RE, Evers BM, Rakheja D, Acharya A, Mendell JT. Target-directed microRNA degradation regulates developmental microRNA expression and embryonic growth in mammals. Genes Dev 2023; 37:661-674. [PMID: 37553261 PMCID: PMC10499020 DOI: 10.1101/gad.350906.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that play critical roles in development and disease. Target-directed miRNA degradation (TDMD), a pathway in which miRNAs that bind to specialized targets with extensive complementarity are rapidly decayed, has emerged as a potent mechanism of controlling miRNA levels. Nevertheless, the biological role and scope of miRNA regulation by TDMD in mammals remains poorly understood. To address these questions, we generated mice with constitutive or conditional deletion of Zswim8, which encodes an essential TDMD factor. Loss of Zswim8 resulted in developmental defects in the heart and lungs, growth restriction, and perinatal lethality. Small RNA sequencing of embryonic tissues revealed widespread miRNA regulation by TDMD and greatly expanded the known catalog of miRNAs regulated by this pathway. These experiments also uncovered novel features of TDMD-regulated miRNAs, including their enrichment in cotranscribed clusters and examples in which TDMD underlies "arm switching," a phenomenon wherein the dominant strand of a miRNA precursor changes in different tissues or conditions. Importantly, deletion of two miRNAs, miR-322 and miR-503, rescued growth of Zswim8-null embryos, directly implicating the TDMD pathway as a regulator of mammalian body size. These data illuminate the broad landscape and developmental role of TDMD in mammals.
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Affiliation(s)
- Benjamin T Jones
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jaeil Han
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Robert E Hammer
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Bret M Evers
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Asha Acharya
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA;
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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3
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Jones BT, Han J, Zhang H, Hammer RE, Evers BM, Rakheja D, Acharya A, Mendell JT. Target-directed microRNA degradation regulates developmental microRNA expression and embryonic growth in mammals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546601. [PMID: 37425885 PMCID: PMC10327180 DOI: 10.1101/2023.06.26.546601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that play critical roles in development and disease. Target-directed miRNA degradation (TDMD), a pathway in which miRNAs that bind to specialized targets with extensive complementarity are rapidly decayed, has emerged as a potent mechanism of controlling miRNA levels. Nevertheless, the biological role and scope of miRNA regulation by TDMD in mammals remains poorly understood. To address these questions, we generated mice with constitutive or conditional deletion of Zswim8 , which encodes an essential TDMD factor. Loss of Zswim8 resulted in developmental defects in heart and lung, growth restriction, and perinatal lethality. Small RNA sequencing of embryonic tissues revealed widespread miRNA regulation by TDMD and greatly expanded the known catalog of miRNAs regulated by this pathway. These experiments also uncovered novel features of TDMD-regulated miRNAs, including their enrichment in co-transcribed clusters and examples in which TDMD underlies 'arm switching', a phenomenon wherein the dominant strand of a miRNA precursor changes in different tissues or conditions. Importantly, deletion of two miRNAs, miR-322 and miR-503, rescued growth of Zswim8 null embryos, directly implicating the TDMD pathway as a regulator of mammalian body size. These data illuminate the broad landscape and developmental role of TDMD in mammals.
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Affiliation(s)
- Benjamin T Jones
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jaeil Han
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert E. Hammer
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bret M. Evers
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Asha Acharya
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshua T. Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Orbán TI. One locus, several functional RNAs-emerging roles of the mechanisms responsible for the sequence variability of microRNAs. Biol Futur 2023:10.1007/s42977-023-00154-7. [PMID: 36847925 DOI: 10.1007/s42977-023-00154-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/08/2023] [Indexed: 03/01/2023]
Abstract
With the development of modern molecular genetics, the original "one gene-one enzyme" hypothesis has been outdated. For protein coding genes, the discovery of alternative splicing and RNA editing provided the biochemical background for the RNA repertoire of a single locus, which also serves as an important pillar for the enormous protein variability of the genomes. Non-protein coding RNA genes were also revealed to produce several RNA species with distinct functions. The loci of microRNAs (miRNAs), encoding for small endogenous regulatory RNAs, were also found to produce a population of small RNAs, rather than a single defined product. This review aims to present the mechanisms contributing to the astonishing variability of miRNAs revealed by the new sequencing technologies. One important source is the careful balance of arm selection, producing sequentially different 5p- or 3p-miRNAs from the same pre-miRNA, thereby broadening the number of regulated target RNAs and the phenotypic response. In addition, the formation of 5', 3' and polymorphic isomiRs, with variable end and internal sequences also leads to a higher number of targeted sequences, and increases the regulatory output. These miRNA maturation processes, together with other known mechanisms such as RNA editing, further increase the potential outcome of this small RNA pathway. By discussing the subtle mechanisms behind the sequence diversity of miRNAs, this review intends to reveal this engaging aspect of the inherited "RNA world", how it contributes to the almost infinite molecular variability among living organisms, and how this variability can be exploited to treat human diseases.
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Affiliation(s)
- Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar Tudósok Körútja 2, Budapest, 1117, Hungary.
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Circulating miRNAs Act as Diagnostic Biomarkers for Bladder Cancer in Urine. Int J Mol Sci 2021; 22:ijms22084278. [PMID: 33924142 PMCID: PMC8074331 DOI: 10.3390/ijms22084278] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) can be secreted into body fluids and have thus been reported as a new type of cancer biomarker. This study aimed to determine whether urinary miRNAs act as noninvasive biomarkers for diagnosing bladder cancer. Small RNA profiles from urine were generated for 10 patients with bladder cancer and 10 healthy controls by using next-generation sequencing. We identified 50 urinary miRNAs that were differentially expressed in bladder cancer compared with controls, comprising 44 upregulated and six downregulated miRNAs. Pathway enrichment analysis revealed that the biological role of these differentially expressed miRNAs might be involved in cancer-associated signaling pathways. Further analysis of the public database revealed that let-7b-5p, miR-149-5p, miR-146a-5p, miR-193a-5p, and miR-423-5p were significantly increased in bladder cancer compared with corresponding adjacent normal tissues. Furthermore, high miR-149-5p and miR-193a-5p expression was significantly correlated with poor overall survival in patients with bladder cancer. The qRT-PCR approach revealed that the expression levels of let-7b-5p, miR-149-5p, miR-146a-5p and miR-423-5p were significantly increased in the urine of patients with bladder cancer compared with those of controls. Although our results indicated that urinary miRNAs are promising biomarkers for diagnosing bladder cancer, this must be validated in larger cohorts in the future.
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Hong X, Chen R, Yuan L, Zha J. Global microRNA and isomiR expression associated with liver metabolism is induced by organophosphorus flame retardant exposure in male Chinese rare minnow (Gobiocypris rarus). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 649:829-838. [PMID: 30176492 DOI: 10.1016/j.scitotenv.2018.08.305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/31/2018] [Accepted: 08/22/2018] [Indexed: 06/08/2023]
Abstract
To reveal the adverse effects of organophosphorus flame retardants (OPFRs) on aquatic organisms at the epigenetic level, male Chinese rare minnows were exposed to 0.24 mg/L tris(2‑butoxyethyl) phosphate (TBOEP), 0.04 mg/L tris(1,3‑dichloro‑2‑propyl) phosphate (TDCIPP), or 0.012 mg/L triphenyl phosphate (TPHP) for 14 days. The effects of sub-acute OPFR exposure on liver miRNA and the 3' isomiR expression profiles of Chinese rare minnows were investigated. Through small RNA sequencing and bioinformatics analysis, a total of 32, 84, and 19 differentially expressed miRNAs were detected for TBOEP, TDCIPP, and TPHP exposure, respectively (p < 0.05). Target prediction of the differentially expressed miRNAs and pathway enrichment analysis indicated that predicted altered mRNAs for all three OPFRs were associated with metabolic pathways, whereas base excision repair was only predicted to be perturbed by the TPHP treatment. In addition, 3' isomiR-Us were unexpectedly abundant in all groups (e.g., miR-143), and TDCIPP strongly increased the ratio of 3' isomiR-U expression. Finally, histological examination and metabolic enzyme activity analyses werein agreement with the predicted metabolic pathways. As such, our study indicates that the investigation of epigenetics changes in miRNA gene transcription is a considerable method for the assessment of aquatic toxicity.
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Affiliation(s)
- Xiangsheng Hong
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100085, China
| | - Rui Chen
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lilai Yuan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jinmiao Zha
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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Chen Y, Zhao B, Liu M, Wang J, Qiu X, Zhu C, Wu X. MicroRNAs Profiling Identifies miR-125a and Its Target Gene Wnt2 in Skins of Different Haired Rabbits. Front Genet 2018; 9:628. [PMID: 30619457 PMCID: PMC6295454 DOI: 10.3389/fgene.2018.00628] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/23/2018] [Indexed: 11/21/2022] Open
Abstract
MicroRNAs (miRNAs) play critical roles in the control of skin and hair follicle development, epidermal homeostasis and pigmentation. However, the roles of miRNAs in the skins of rabbits with different hair types are unclear. In this study, we profiled miRNAs in the skins of long and short haired rabbits by Illumina deep sequencing. The dataset was compared with known mammalian miRNAs in miRBase 21.0. In total, 118 miRNAs were found to be differentially expressed between the two different rabbit types, of which 94 were upregulated, and 24 were downregulated in the skin of short haired vs. long haired rabbits. The expression levels of five randomly selected miRNAs detected by quantitative real-time PCR indicated that the expression patterns were consistent with Illumina sequencing results. What's more, bioinformatics analysis showed that miR-125a might target Wnt2, an important modulator for hair follicle development. To test whether Wnt2 is a target of miR-125a, luciferase reporter vector (pMir-report-Wnt2-3'-UTR-WT) and its substitution mutant (pMir-report-Wnt2-3'-UTR-MUT) were constructed. Co-transfection and reporter enzyme assays showed that compared with control (miR-125a NC transfection), miR-125a mimics transfection significantly inhibited the reporter luciferase activities expressed by pMir-report-Wnt2-3'-UTR-WT, while transfection of miR-125a inhibitors increased reporter enzyme activities. RT-PCR and Simple Western analysis found that Wnt2 mRNA and protein levels were induced or repressed by miR-125a overexpression or inhibition, respectively. Moreover, the mRNA expression levels of genes in Wnt signaling pathway, such as CTNNB1, LEF-1, PPARD and TGFB1, were also significantly changed (P < 0.05), consistent with Wnt2. It indicated that the regulation of Wnt2 expression by miRNAs may depend on the transcriptional degradation. The results will help to further understand the role of miRNAs in hair follicle development and the genetic mechanism underlying hair length phenotype.
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Affiliation(s)
- Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ming Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingyi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiaoqing Qiu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | | | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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Lin MH, Chen YZ, Lee MY, Weng KP, Chang HT, Yu SY, Dong BJ, Kuo FR, Hung LT, Liu LF, Chen WS, Tsai KW. Comprehensive identification of microRNA arm selection preference in lung cancer: miR-324-5p and -3p serve oncogenic functions in lung cancer. Oncol Lett 2018; 15:9818-9826. [PMID: 29844840 PMCID: PMC5958786 DOI: 10.3892/ol.2018.8557] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 11/16/2017] [Indexed: 12/31/2022] Open
Abstract
MicroRNA (miRNA/miR) dysfunction is a hallmark of lung cancer, and results in the dysregulation of tumor suppressors and oncogenes during lung cancer progression. Selection of the 5p and 3p arms of miRNA is a mechanism that improves the modulation of miRNA biological functions and complicates the regulatory network in human types of cancer. However, the involvement of arm selection preference of miRNA in lung cancer remains unclear. In the present study, changes in miRNA arm selection preference were comprehensively identified in lung cancer and corresponding adjacent normal tissues by analyzing The Cancer Genome Atlas. Arm selection was revealed to be consistent in the majority of miRNAs in lung cancer. Only a few miRNAs had significantly altered arm selection preference in lung cancer. Among these, the biological functions of the individual arms of miR-324 were investigated further. The data revealed that miR-324-5p and -3p were significantly overexpressed in lung cancer cells. Ectopic expression of miR-324-5p significantly promoted cell proliferation and invasion in lung cancer cells, while miR-324-3p overexpression significantly increased cell proliferation but did not alter the invasion of lung cancer cells. In conclusion, the arm selection preference of miRNA may be an additional mechanism through which biological functions are modulated. The results of the present study provide a novel insight into the underlying mechanisms of lung cancer and may direct research into future therapies.
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Affiliation(s)
- Min-Hsi Lin
- Division of Chest Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,School of Medicine, National Yang-Ming University, Taipei 112, Taiwan, R.O.C
| | - You-Zuo Chen
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C
| | - Mei-Yu Lee
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,Department of Biological Science and Technology, I-Shou University, Kaohsiung 813, Taiwan, R.O.C
| | - Ken-Pen Weng
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan, R.O.C.,Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,Department of Physical Therapy, Shu-Zen College of Medicine and Management, Kaohsiung 813, Taiwan, R.O.C
| | - Hong-Tai Chang
- Center for Geriatrics and Gerontology, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C
| | - Shou-Yu Yu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C
| | - Bo-Jhu Dong
- Department of Chemical Biology, National Pingtung University of Education, Pingtung 900, Taiwan, R.O.C
| | - Fan-Rong Kuo
- Department of Chemical Biology, National Pingtung University of Education, Pingtung 900, Taiwan, R.O.C
| | - Li-Tzu Hung
- Department of Chemical Biology, National Pingtung University of Education, Pingtung 900, Taiwan, R.O.C
| | - Li-Feng Liu
- Department of Biological Science and Technology, I-Shou University, Kaohsiung 813, Taiwan, R.O.C
| | - Wei-Shone Chen
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan, R.O.C.,Department of Surgery, Veterans General Hospital, Taipei 112, Taiwan, R.O.C
| | - Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,Department of Chemical Biology, National Pingtung University of Education, Pingtung 900, Taiwan, R.O.C.,Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 813, Taiwan, R.O.C
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Zhang X, Li L, Jiang H, Ma JE, Li J, Chen J. Identification and differential expression of microRNAs in testis and ovary of Amur sturgeon (Acipenser schrenckii). Gene 2018. [PMID: 29524574 DOI: 10.1016/j.gene.2018.03.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) cooperate with sex-related genes in post-transcriptional regulation and play extremely important roles in the establishment of sexually dimorphic traits in animals. However, the gonad miRNAs and expression patterns of miRNAs in sturgeon have not been investigated. METHODS In the present study, we used high-throughput small RNA sequencing (RNA-Seq) to discover gonad miRNAs from the ovaries and testes of Amur sturgeons (Acipenser schrenckii). Further, microarray and real-time PCR assays were performed to identify the expression patterns of gonad miRNAs. RESULTS As a result, a total of 679 conserved and 51 novel miRNAs were successfully discovered in the gonads of A. schrenckii. Moreover, we found wide sequence variations (isomiRs) in gonad miRNAs, including 5' and 3' isomiRs. Our microarray analysis further characterized the 730 miRNAs expression profiles, which indicated that 117 differentially expressed miRNAs were detected with sex-biased patterns: 71 testis-biased and 46 ovary-biased miRNAs. Based on bioinformatics prediction, we found that there were functional differences between the testis-biased and ovary-biased miRNA targets involved in reproductive-related GO and KEGG pathways. Further, the association of the differentially expressed miRNAs and sex-related target mRNAs was uncovered. Finally, the expression patterns of 11 sex-biased miRNAs and 7 sex-related targets were validated in testes and ovaries using real-time PCR. Putative, negatively expressed miRNA-mRNA relationships were confirmed, such as Dmrt1 and asc-miR-2779, AR and asc-miR-203b-3p, foxl2 and asc-miR-30d. CONCLUSION This study provides information regarding the gonad miRNAs in sturgeon. The differential expression miRNAs in the gonads will help us to further understand the role of miRNA-mediated post-transcriptional regulation in the ovary and testis of sturgeon.
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Affiliation(s)
- Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jing E Ma
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Juan Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China..
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10
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Jia X, Liao Q, Chen S, Wang J, Lai S. Investigation of significant microRNA-mRNA pairs associated with nonspecific digestive disorder in rabbits. WORLD RABBIT SCIENCE 2017. [DOI: 10.4995/wrs.2017.6839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Nonspecific digestive disorders (NSDD) are one of the major intestinal problems in rabbit, with considerable economic losses in industrial rabbit farms. MicroRNAs (miRNAs), as small non-coding RNAs, have significant biological involvement in intestinal disorders. In this study, we investigated the expression levels of 25 genes and 25 miRNAs in ileum, rabbit sacculus rotundus (RSR) and colon tissues from 9 rabbits with different severity of NSDD. These molecules have been found to be related to NSDD or inflammatory bowel disease, which will help recognise the miRNA-mRNA pairs. Finally, 108 possible pairs of miRNA-mRNA pairs with an anti-correlation were identified by Pearson’s correlation analysis between differentially expressed 25 miRNAs and 23 mRNAs. Ninety-five of these miRNA-mRNA pairs were hitherto unexplored, and their roles in NSDD biology require further elucidation. Our results give a clue to the potential miRNA-mRNA pairs for the NSDD that can further improve the understanding of the pathogenesis of NSDD in rabbit.
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11
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Tsai KW, Leung CM, Lo YH, Chen TW, Chan WC, Yu SY, Tu YT, Lam HC, Li SC, Ger LP, Liu WS, Chang HT. Arm Selection Preference of MicroRNA-193a Varies in Breast Cancer. Sci Rep 2016; 6:28176. [PMID: 27307030 PMCID: PMC4910092 DOI: 10.1038/srep28176] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/31/2016] [Indexed: 01/28/2023] Open
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs derived from the 3′ and 5′ ends of the same precursor. However, the biological function and mechanism of miRNA arm expression preference remain unclear in breast cancer. We found significant decreases in the expression levels of miR-193a-5p but no significant differences in those of miR-193a-3p in breast cancer. MiR-193a-3p suppressed breast cancer cell growth and migration and invasion abilities, whereas miR-193a-5p suppressed cell growth but did not influence cell motility. Furthermore, NLN and CCND1, PLAU, and SEPN1 were directly targeted by miR-193a-5p and miR-193a-3p, respectively, in breast cancer cells. The endogenous levels of miR-193a-5p and miR-193a-3p were significantly increased by transfecting breast cancer cells with the 3′UTR of their direct targets. Comprehensive analysis of The Cancer Genome Atlas database revealed significant differences in the arm expression preferences of several miRNAs between breast cancer and adjacent normal tissues. Our results collectively indicate that the arm expression preference phenomenon may be attributable to the target gene amount during breast cancer progression. The miRNA arm expression preference may be a means of modulating miRNA function, further complicating the mRNA regulatory network. Our findings provide a new insight into miRNA regulation and an application for breast cancer therapy.
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Affiliation(s)
- Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Chemical Biology, National Pingtung University of Education, Pingtung, Taiwan
| | - Chung-Man Leung
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yi-Hao Lo
- Department of Family Medicine, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung, Taiwan
| | - Ting-Wen Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan
| | - Wen-Ching Chan
- Genomics &Proteomics Core Laboratory, Department of medical research, Kaohsiung, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shou-Yu Yu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Ya-Ting Tu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Hing-Chung Lam
- Center For Geriatrics and Gerontology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Genomics &Proteomics Core Laboratory, Department of medical research, Kaohsiung, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Luo-Ping Ger
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Wen-Shan Liu
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Radiation Oncology, Tri-Service General Hospital, Taipei, Twiwan
| | - Hong-Tai Chang
- Center For Geriatrics and Gerontology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
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12
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Hong X, Qin J, Chen R, Yuan L, Zha J, Wang Z. Identification and characterization of novel and conserved microRNAs in several tissues of the Chinese rare minnow (Gobiocypris rarus) based on illumina deep sequencing technology. BMC Genomics 2016; 17:283. [PMID: 27066897 PMCID: PMC4828758 DOI: 10.1186/s12864-016-2606-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/28/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs), which comprise a large family of endogenous small non-coding RNA molecules, play important roles in the regulation of gene expression in various biological processes. The Chinese rare minnow (Gobiocypris rarus) is a Chinese native fish species and is used extensively as an experimental fish in China; however, relevant biological data, especially miRNA transcriptome data, have not been well documented. To discover conserved and potential novel miRNAs in Chinese rare minnows, a pool of equal amounts of RNA obtained from 6 different adult rare minnow tissues (brain, eye, gill, liver, muscle and heart) was sequenced using illumina deep sequencing technology. RESULTS In the present study, 26,930,553 raw reads, representing 2,118,439 unique high-quality reads, were obtained from the pooled small RNA library. Using bioinformatics analysis, 352 conserved and 112 novel Chinese rare minnow miRNAs were first discovered and characterized in this study. Moreover, we found extensive sequence variations (isomiRs) in rare minnow miRNAs, including internal miRNA isomiRs and terminal isomiRs at both the 5' and 3' ends and nucleotide variants. Six conserved and 4 novel miRNAs were selected and validated in 6 different adult rare minnow tissues using quantitative real-time PCR (qPCR). The results showed that miR-30a, miR-30b, and Novel-37 are ubiquitously expressed in a variety of tissues. miR-16a, miR-9, miR-125b, miR-34a, and Novel-69 were predominantly expressed in the brain. Novel-115 and Novel-7 were highly expressed in gills, but were relatively weakly expressed in other tissues. These results provided the expression patterns of miRNA genes in Chinese rare minnow. Finally, based on bioinformatics predictions, we mainly found that Novel-94 and Novel-1b-5p were simultaneously targeted to the 3'UTR of Dmrt1, which controls sex determination and/or sexual differentiation in a variety of metazoans at different sites. Novel-29b targeted the 3'UTR of Foxl2, which is involved in the maintenance of ovarian function and the transcriptional regulation of gonadal differentiation-related genes. Novel-62 and Novel-53 targeted the 3'UTR of ERbeta1 and ERbeta2 (which regulate the transcription of target genes), respectively. CONCLUSIONS Rare minnow is a widely used model for assessing the risk of environmental pollution in China. Identifying and characterizing rare minnow miRNA genes is necessary to discover the biological function of miRNAs and to screen for new molecule biomarkers to assess the risk of environmental pollution in the future.
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Affiliation(s)
- Xiangsheng Hong
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, People's Republic of China.,Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China
| | - Jianhui Qin
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China
| | - Rui Chen
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, People's Republic of China.,State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Lilai Yuan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, People's Republic of China.,State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jinmiao Zha
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, People's Republic of China. .,Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Zijian Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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13
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Yuan Z, Ding S, Yan M, Zhu X, Liu L, Tan S, Jin Y, Sun Y, Li Y, Huang T. Variability of miRNA expression during the differentiation of human embryonic stem cells into retinal pigment epithelial cells. Gene 2015; 569:239-49. [PMID: 26028588 DOI: 10.1016/j.gene.2015.05.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 05/23/2015] [Accepted: 05/25/2015] [Indexed: 01/08/2023]
Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells can be induced to differentiate into retinal pigment epithelium (RPE). MiRNAs have been characterized and found playing important roles in the differentiation process of ESCs, but their length and sequence heterogeneity (isomiRs), and their non-canonical forms of miRNAs are underestimated or ignored. In this report, we found some non-canonical miRNAs (dominant isomiRs) in all differentiation stages, and 27 statistically significant editing sites were identified in 24 different miRNAs. Moreover, we found marked major-to-minor arm-switching events in 14 pre-miRNAs during the hESC to RPE cell differentiation phases. Our study for the first time reports exploring the variability of miRNA expression during the differentiation of hESCs into RPE cells and the results show that miRNA variability is a ubiquitous phenomenon in the ESC differentiation.
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Affiliation(s)
- Zhidong Yuan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China.
| | - Suping Ding
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Mingli Yan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Xiao Zhu
- Guangdong Province Key Laboratory of Medical Molecular Diagnosis, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan 523808, China
| | - Lili Liu
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Shuhua Tan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Yuanchang Jin
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Yuandong Sun
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Yufeng Li
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Ting Huang
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
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14
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Evolutionary and expression analysis of miR-#-5p and miR-#-3p at the miRNAs/isomiRs levels. BIOMED RESEARCH INTERNATIONAL 2015; 2015:168358. [PMID: 26075215 PMCID: PMC4436453 DOI: 10.1155/2015/168358] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/27/2014] [Accepted: 09/29/2014] [Indexed: 11/18/2022]
Abstract
We mainly discussed miR-#-5p and miR-#-3p under three aspects: (1) primary evolutionary analysis of human miRNAs; (2) evolutionary analysis of miRNAs from different arms across the typical 10 vertebrates; (3) expression pattern analysis of miRNAs at the miRNA/isomiR levels using public small RNA sequencing datasets. We found that no bias can be detected between the numbers of 5p-miRNA and 3p-miRNA, while miRNAs from miR-#-5p and miR-#-3p show variable nucleotide compositions. IsomiR expression profiles from the two arms are always stable, but isomiR expressions in diseased samples are prone to show larger degree of dispersion. miR-#-5p and miR-#-3p have relative independent evolution/expression patterns and datasets of target mRNAs, which might also contribute to the phenomena of arm selection and/or arm switching. Simultaneously, miRNA/isomiR expression profiles may be regulated via arm selection and/or arm switching, and the dynamic miRNAome and isomiRome will adapt to functional and/or evolutionary pressures. A comprehensive analysis and further experimental study at the miRNA/isomiR levels are quite necessary for miRNA study.
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15
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Mione M, Bosserhoff A. MicroRNAs in melanocyte and melanoma biology. Pigment Cell Melanoma Res 2015; 28:340-54. [PMID: 25515738 DOI: 10.1111/pcmr.12346] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/15/2014] [Indexed: 12/18/2022]
Abstract
The importance of microRNAs as key molecular components of cellular processes is now being recognized. Recent reports have shown that microRNAs regulate processes as diverse as protein expression and nuclear functions inside cells and are able to signal extracellularly, delivered via exosomes, to influence cell fate at a distance. The versatility of microRNAs as molecular tools inspires the design of novel strategies to control gene expression, protein stability, DNA repair and chromatin accessibility that may prove very useful for therapeutic approaches due to the extensive manageability of these small molecules. However, we still lack a comprehensive understanding of the microRNA network and its interactions with the other layers of regulatory elements in cellular and extracellular functions. This knowledge may be necessary before we exploit microRNA versatility in therapeutic settings. To identify rules of interactions between microRNAs and other regulatory systems, we begin by reviewing microRNA activities in a single cell type: the melanocyte, from development to disease.
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Affiliation(s)
- Marina Mione
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggestein-Leopoldshafen, Germany
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16
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Zhang H, Yang S, Guo L, Zhao Y, Shao F, Chen F. Comparisons of isomiR patterns and classification performance using the rank-based MANOVA and 10-fold cross-validation. Gene 2014; 569:21-6. [PMID: 25447923 DOI: 10.1016/j.gene.2014.11.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/07/2014] [Accepted: 11/11/2014] [Indexed: 12/29/2022]
Abstract
Next generation sequencing technology has identified a series of miRNA variants (named "isomiRs"), which might be associated with cancer progression. We provide a new strategy to reanalyze the miR-seq datasets through a view of the isomiR spectrum. Firstly, differentially expressed (DE) isomiRs were detected with the DESeq algorithm based on negative binomial distribution. Secondly, the rank-based MANOVA was adopted to compare the isomiR patterns between normal and tumor tissues. Moreover, a comprehensive survey on classification performance of three features was conducted, including the logistic regression, k-nearest neighbors and Random Forest. Finally, functional enrichment analysis was performed with the putative targets of specific isomiRs to elucidate their biological functions. Furthermore, the methods were applied to the downloaded miR-seq datasets of breast invasive carcinoma from TCGA. We found that the expression levels of multiple isomiRs derived from the same miRNA locus showed significant inconsistency between normal and tumor samples. In most cases, logistic regression with multiple DE isomiRs was superior to the others, with highest AUC and lowest AIC. Similarly, DE isomiRs performed best in the average accuracy of standard classifiers. Integrated targets were significantly enriched in some cancer-related pathways, including MAPK signaling pathway, and focal adhesion. Collectively, we could recommend the rank-based MANOVA for comparing different isomiR patterns, and further investigation on isomiRs needs to be considered in miRNA sequencing research.
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Affiliation(s)
- Hui Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Sheng Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Li Guo
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yang Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Fang Shao
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Feng Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
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17
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Qi P, Guo B, Zhu A, Wu C, Liu C. Identification and comparative analysis of the Pseudosciaena crocea microRNA transcriptome response to poly(I:C) infection using a deep sequencing approach. FISH & SHELLFISH IMMUNOLOGY 2014; 39:483-491. [PMID: 24945573 DOI: 10.1016/j.fsi.2014.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 06/03/2023]
Abstract
Two sRNA libraries with or without poly(I:C) infection of large yellow croaker Pseudosciaena crocea were constructed and sequenced using the high-throughput Illumina/Solexa deep sequencing technology. The high-throughput sequencing pipeline yielded 163,79,272 and 217,07,070 raw reads corresponding to 132,27,594 and 206,86,409 clean reads for the normal and infected libraries, respectively. Bioinfromatic analysis identified 534 miRNAs, of which, 158 miRNAs were known in miRBase 20.0 and the remaining 376 were not found homology to any known metazoan miRNAs, suggesting a possible species-specificity. We analyzed the significance of differently expressed miRNAs between two libraries using pairwise comparison. There was significant differential expression of 112 miRNAs (p < 0.001) between two libraries. Thereinto, a number of known miRNAs were identified immune-related. Real-time quantitative PCR experiments (RT-qPCR) were preformed for 6 miRNAs of the two samples, and agreement was found between the sequencing and RT-qPCR data. To our knowledge, this is the first comprehensive study of miRNAs in P. crocea and of expression analysis of P. crocea miRNAs in response to poly(I:C) infection, and many miRNAs were differentially regulated under normal and infection conditions. These findings deepened our understanding of the role of miRNAs in the intricate host's immune system, and should be useful to develop new control strategies for host immune defense against various foreign infection in P. crocea.
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Affiliation(s)
- Pengzhi Qi
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316004, China
| | - Baoying Guo
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316004, China
| | - Aiyi Zhu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316004, China
| | - Changwen Wu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316004, China.
| | - Changlin Liu
- Yellow Sea Fisheries Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
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18
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Abstract
MicroRNAs (miRNAs) are transcriptional and posttranscriptional regulators involved in nearly all known biological processes in distant eukaryotic clades. Their discovery and functional characterization have broadened our understanding of biological regulatory mechanisms in animals and plants. They show both evolutionary conserved and unique features across Metazoa. Here, we present the current status of the knowledge about the role of miRNA in development, growth, and physiology of teleost fishes, in comparison to other vertebrates. Infraclass Teleostei is the most abundant group among vertebrate lineage. Fish are an important component of aquatic ecosystems and human life, being the prolific source of animal proteins worldwide and a vertebrate model for biomedical research. We review miRNA biogenesis, regulation, modifications, and mechanisms of action. Specific sections are devoted to the role of miRNA in teleost development, organogenesis, tissue differentiation, growth, regeneration, reproduction, endocrine system, and responses to environmental stimuli. Each section discusses gaps in the current knowledge and pinpoints the future directions of research on miRNA in teleosts.
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Affiliation(s)
| | - Igor Babiak
- Faculty of Aquaculture and Biosciences, University of Nordland, Bodø, Norway
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19
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A challenge for miRNA: multiple isomiRs in miRNAomics. Gene 2014; 544:1-7. [PMID: 24768184 DOI: 10.1016/j.gene.2014.04.039] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 04/11/2014] [Accepted: 04/18/2014] [Indexed: 11/22/2022]
Abstract
Accumulating evidence suggests that a single microRNA (miRNA) locus can generate a series of sequences during miRNA maturation process. These multiple sequences, called miRNA variants, or isomiRs, have different lengths and different 5' and 3' ends. Some of these isomiRs are detected as varied nucleotides and 3' additional non-template nucleotides. As physiological miRNA isoforms, they have drawn attention for possible regulatory biological roles. The present work mainly reviews miRNA/isomiR biogenesis, isomiR expression patterns, and functional and evolutionary implications, especially between isomiRs from homologous and clustered miRNA loci. The phenomenon of multiple isomiRs and their biological roles indicates that analysis performed at the miRNA and isomiR levels should be included in miRNA studies. This may enrich and complicate miRNA biogenesis and coding-non-coding RNA regulatory networks.
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20
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Xiao J, Zhong H, Zhou Y, Yu F, Gao Y, Luo Y, Tang Z, Guo Z, Guo E, Gan X, Zhang M, Zhang Y. Identification and characterization of microRNAs in ovary and testis of Nile tilapia (Oreochromis niloticus) by using solexa sequencing technology. PLoS One 2014; 9:e86821. [PMID: 24466258 PMCID: PMC3900680 DOI: 10.1371/journal.pone.0086821] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/14/2013] [Indexed: 01/01/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding small RNAs which play important roles in the regulation of gene expression by cleaving or inhibiting the translation of target gene transcripts. Thereinto, some specific miRNAs show regulatory activities in gonad development via translational control. In order to further understand the role of miRNA-mediated posttranscriptional regulation in Nile tilapia (Oreochromis niloticus) ovary and testis, two small RNA libraries of Nile tilapia were sequenced by Solexa small RNA deep sequencing methods. A total of 9,731,431 and 8,880,497 raw reads, representing 5,407,800 and 4,396,281 unique sequences were obtained from the sexually mature ovaries and testes, respectively. After comparing the small RNA sequences with the Rfam database, 1,432,210 reads in ovaries and 984,146 reads in testes were matched to the genome sequence of Nile tilapia. Bioinformatic analysis identified 764 mature miRNA, 209 miRNA-5p and 202 miRNA-3p were found in the two libraries, of which 525 known miRNAs are both expressed in the ovary and testis of Nile tilapia. Comparison of expression profiles of the testis, miR-727, miR-129 and miR-29 families were highly expressed in tilapia ovary. Additionally, miR-132, miR-212, miR-33a and miR-135b families, showed significant higher expression in testis compared with that in ovary. Furthermore, the expression patterns of the miRNAs were analyzed in different developmental stages of gonad. The result showed different expression patterns were observed during development of testis and ovary. In addition, the identification and characterization of differentially expressed miRNAs in the ovaries and testis of Nile tilapia provides important information on the role of miRNA in the regulation of the ovarian and testicular development and function. This data will be helpful to facilitate studies on the regulation of miRNAs during teleosts reproduction.
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Affiliation(s)
- Jun Xiao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning, Guangxi, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
- State Key Laboratory of Genetic Resources and Evolution and Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Huan Zhong
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning, Guangxi, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
| | - Yi Zhou
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning, Guangxi, China
| | - Fan Yu
- Key Laboratory for Genetic Breeding of Aquatic Animals, Aquaculture Biology, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution and Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Yongju Luo
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning, Guangxi, China
| | - Zhanyang Tang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning, Guangxi, China
| | - Zhongbao Guo
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning, Guangxi, China
| | - Enyan Guo
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning, Guangxi, China
| | - Xi Gan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning, Guangxi, China
- * E-mail: (XG); (MZ)
| | - Ming Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
- * E-mail: (XG); (MZ)
| | - Yaping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Kunming, Yunnan, China
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21
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Abstract
A mature miRNA may be generated from 5p or 3p arm of a hairpin precursor. The selection may be flexible via "arm switching". However, accumulating evidences suggest that both arms of many pre-miRNAs can yield mature functional miRNAs. Herein, we attempted to compare the isomiR expression profiles between the two arms through analyzing in-house and published small RNA deep sequencing datasets. Although many miR-#-5p and miR-#-3p have been reported as functional miRNAs, fewer miRNA pairs (11 and 6 pairs are collected in tumor and normal cells, respectively) are simultaneously identified as abundant miRNA species. According to isomiR types and dominant isomiR species, miR-#-5p and miR-#-3p show various isomiR expression profiles as well as diverse enrichment levels. IsomiR profiles of non-dominant arm are not well-conserved in 5' ends as well as isomiR profiles of dominant arm. If both the miR-#-5p and miR-#-3p are abundantly expressed, their isomiR expression profiles are always stable across different samples. Similar to diverse enrichment levels of miR-#-5p and miR-#-3p, the isomiR expression patterns may also be influenced by the phenomenon of "arm switching". The diverged isomiR expression profiles further enrich the complexity of multiple isomiRs, and complicate the coding-non-coding RNA regulatory network.
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22
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Identification and characterization of microRNAs in channel catfish (Ictalurus punctatus) by using Solexa sequencing technology. PLoS One 2013; 8:e54174. [PMID: 23342099 PMCID: PMC3546936 DOI: 10.1371/journal.pone.0054174] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 12/07/2012] [Indexed: 11/19/2022] Open
Abstract
Channel catfish (Ictalurus spp.) is an economically important species in freshwater aquaculture around the world and occupies a prominent position in the aquaculture industry of the United States. MicroRNAs (miRNAs) play important roles in the regulation of almost every biological process in eukaryotes; however, there is little information available concerning miRNAs in channel catfish. In this study, a small-RNA cDNA library was constructed from 10 tissues of channel catfish, and Solexa sequencing technology was used to perform high-throughput sequencing of the library. A total of 14,919,026 raw reads, representing 161,288 unique sequences, were obtained from the small-cDNA library. After comparing the small RNA sequences with the RFam database, 4,542,396 reads that represent 25,538 unique sequences were mapped to the genome sequence of zebrafish to perform distribution analysis and to screen for candidate miRNA genes. Subsequent bioinformatic analysis identified 237 conserved miRNAs and 45 novel miRNAs in the channel catfish. Stem-loop RT-PCR was applied to validate and profile the expression of the novel miRNAs in 10 tissues. Some novel miRNAs, such as ipu-miR-129b, ipu-miR-7562 and ipu-miR-7553, were expressed in all tissues examined. However, some novel miRNAs appear to be tissue specific. Ipu-miR-7575 is predominantly expressed in stomach. Ipu-miR-7147 and ipu-miR-203c are highly expressed in heart, but are relatively weakly expressed in other tissues. Based on sequence complementarity between miRNAs and mRNA targets, potential target sequences for the 45 novel miRNAs were identified by searching for antisense hits in the reference RNA sequences of the channel catfish. These potential target sequences are involved in immune regulation, transcriptional regulation, metabolism and many other biological functions. The discovery of miRNAs in the channel catfish genome by this study contributes to a better understanding of the role miRNAs play in regulating diverse biological processes in fish and vertebrates.
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23
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Chang HT, Li SC, Ho MR, Pan HW, Ger LP, Hu LY, Yu SY, Li WH, Tsai KW. Comprehensive analysis of microRNAs in breast cancer. BMC Genomics 2012; 13 Suppl 7:S18. [PMID: 23281739 PMCID: PMC3521236 DOI: 10.1186/1471-2164-13-s7-s18] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs (miRNAs) are short noncoding RNAs (approximately 22 nucleotides in length) that play important roles in breast cancer progression by downregulating gene expression. The detailed mechanisms and biological functions of miRNA molecules in breast carcinogenesis have yet to be fully elucidated. This study used bioinformatics and experimental approaches to conduct detailed analysis of the dysregulated miRNAs, arm selection preferences, 3' end modifications, and position shifts in isoforms of miRNAs (isomiRs) in breast cancer. Methods Next-generation sequencing (NGS) data on breast cancer was obtained from the NCBI Sequence Read Archive (SRA). The miRNA expression profiles and isomiRs in normal breast and breast tumor tissues were determined by mapping the clean reads back to human miRNAs. Differences in miRNA expression and pre-miRNA 5p/3p arm usage between normal and breast tumor tissues were further investigated using stem-loop reverse transcription and real-time polymerase chain reaction. Results The analysis identified and confirmed the aberrant expression of 22 miRNAs in breast cancer. Results from pathway enrichment analysis further indicated that the aberrantly expressed miRNAs play important roles in breast carcinogenesis by regulating the mitogen-activated protein kinase (MAPK) signaling pathway. Data also indicated that the position shifts in isomiRs and 3' end modifications were consistent in breast tumor and adjacent normal tissues, and that 5p/3p arm usage of some miRNAs displayed significant preferences in breast cancer. Conclusions Expression pattern and arm selection of miRNAs are significantly varied in breast cancers through analyzing NGS data and experimental approach. These miRNA candidates have high potential to play critical roles in the progression of breast cancer and could potentially provide as targets for future therapy.
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Affiliation(s)
- Hong-Tai Chang
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, Republic of China
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Li SC, Tsai KW, Pan HW, Jeng YM, Ho MR, Li WH. MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues. BMC SYSTEMS BIOLOGY 2012; 6 Suppl 2:S14. [PMID: 23282006 PMCID: PMC3521178 DOI: 10.1186/1752-0509-6-s2-s14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Background The expression of microRNA (miRNA) genes undergoes several maturation steps. Recent studies brought new insights into the maturation process, but also raised debates on the maturation mechanism. To understand the mechanism better, we downloaded small RNA sequence reads from NCBI SRA and quantified the expression profiles of miRNAs in normal and tumor liver tissues. Results From these miRNA expression profiles, we studied several issues related to miRNA biogenesis. First of all, the 3' ends of mature miRNAs usually carried modified nucleotides, generated from nucleotide addition or RNA editing. We found that adenine accounted for more than 50% of all miRNA 3' end modification events in all libraries. However, uracil dominated over adenine in several miRNA types. Moreover, the miRNA reads in the HBV-associated libraries have much lower rates of nucleotide modification. These results indicate that miRNA 3' end modifications are miRNA specific and may differ between normal and tumor tissues. Secondly, according to the hydrogen-bonding theory, the expression ratio of 5p arm to 3p arm miRNAs, derived from the same pre-miRNA, should be constant over tissues. However, a comparison of the expression profiles of the 5p arm and 3p arm miRNAs showed that one arm is preferred in the normal liver tissue whereas the other is preferred in the tumor liver tissue. In other words, different liver tissues have their own preferences on selecting either arm to be mature miRNAs. Conclusions The results suggest that besides the traditional miRNA biogenesis theory, another mechanism may also participate in the miRNA biogenesis pathways.
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Affiliation(s)
- Sung-Chou Li
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
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Cheng WC, Chung IF, Huang TS, Chang ST, Sun HJ, Tsai CF, Liang ML, Wong TT, Wang HW. YM500: a small RNA sequencing (smRNA-seq) database for microRNA research. Nucleic Acids Res 2012. [PMID: 23203880 PMCID: PMC3531161 DOI: 10.1093/nar/gks1238] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
MicroRNAs (miRNAs) are small RNAs ∼22 nt in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next-generation sequencing applications, have reshaped the miRNA research landscape. In this study, we established an integrative database, the YM500 (http://ngs.ym.edu.tw/ym500/), containing analysis pipelines and analysis results for 609 human and mice smRNA-seq results, including public data from the Gene Expression Omnibus (GEO) and some private sources. YM500 collects analysis results for miRNA quantification, for isomiR identification (incl. RNA editing), for arm switching discovery, and, more importantly, for novel miRNA predictions. Wetlab validation on >100 miRNAs confirmed high correlation between miRNA profiling and RT-qPCR results (R = 0.84). This database allows researchers to search these four different types of analysis results via our interactive web interface. YM500 allows researchers to define the criteria of isomiRs, and also integrates the information of dbSNP to help researchers distinguish isomiRs from SNPs. A user-friendly interface is provided to integrate miRNA-related information and existing evidence from hundreds of sequencing datasets. The identified novel miRNAs and isomiRs hold the potential for both basic research and biotech applications.
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Affiliation(s)
- Wei-Chung Cheng
- Division of Pediatric Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei 11217, Taiwan
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