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Zhu S, Zhou R, Tang X, Fu W, Jia W. Hypoxia/inflammation-induced upregulation of HIF-1α and C/EBPβ promotes nephroblastoma cell EMT by improving HOXA11-AS transcription. Heliyon 2024; 10:e27654. [PMID: 38524550 PMCID: PMC10958367 DOI: 10.1016/j.heliyon.2024.e27654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 03/26/2024] Open
Abstract
Background Homeobox (HOX) A11 antisense RNA (HOXA11-AS) has been identified as a cancer promoting lncRNA and is overexpressed in nephroblastoma. However, how HOXA11-AS is regulated in a hypoxic inflammatory environment has not been studied. Methods In this study, gene expression and epithelial-mesenchymal transition (EMT) ability were detected in the nephroblastoma cell line WiT49 under conditions of hypoxia and inflammation. Next, HOXA11-AS transcription factors were predicted by datasets and subsequently confirmed by CHIP-QPCR, EMSA, and dual-luciferase reporter assays. Moreover, the regulatory relationships of HOXA11-AS and its transcription factors were further confirmed by rescue experiments. Results Our results showed that a hypoxic microenvironment promoted HOXA11-AS expression and nephroblastoma progression, induced EMT, and activated the Wnt signaling pathway. Combined hypoxia and inflammation had a more substantial effect on nephroblastoma than either hypoxia or inflammation alone. HIF-1α and C/EBPβ were confirmed to be the transcription factors for HOXA11-AS. Silencing of HIF-1α or C/EBPβ downregulated HOXA11-AS expression and suppressed EMT and the Wnt signaling pathway in nephroblastoma cells exposed to a hypoxic or inflammatory microenvironment. HOXA11-AS overexpression partly reversed the effect of HIF-1α or C/EBPβ knockdown. Conclusion We demonstrated that hypoxia/inflammation-induced upregulation of HIF-1α and C/EBPβ promoted nephroblastoma EMT by improving HOXA11-AS transcription. HOXA11-AS might be a therapy target for nephroblastoma.
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Affiliation(s)
- Shibo Zhu
- Department of Pediatric Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Rui Zhou
- Department of Pediatric Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiangliang Tang
- Department of Pediatric Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wen Fu
- Department of Pediatric Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wei Jia
- Department of Pediatric Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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2
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Wang S, Xu J, Zhao X, Feng Y, Xu W, Xue H, Wu M, Xu L. Small RNA-seq and hormones in the testes of dwarf hamsters ( Cricetulus barabensis) reveal the potential pathways in photoperiod regulated reproduction. Heliyon 2023; 9:e15687. [PMID: 37144180 PMCID: PMC10151367 DOI: 10.1016/j.heliyon.2023.e15687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 03/26/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023] Open
Abstract
Photoperiod regulates the functions and development of gonadal organs of seasonally breeding animals, resulting in breeding peaks in specific seasons. miRNA plays an important role in the regulation of testicular physiological functions. However, the relationship between photoperiods and miRNA levels in testes has yet to be conclusively determined. We investigated testicular miRNA of striped dwarf hamster (Cricetulus barabensis) responses to different photoperiods (long daylength [LD], moderate daylength [MD], and short daylength [SD]) and the potential pathways involved in photoperiod regulated reproduction. Testicular weights and reproductive hormone levels were measured in each of photoperiod treatments after 30 days. The concentrations of testosterone (T) and dihydrogen testosterone (DHT) in testes and Gonadotropin-releasing hormone (GnRH), follicle-stimulating hormone (FSH), and luteinizing hormone (LH) in serum were higher in MD than in the other two groups. Testicular weights were heaviest in MD. Small RNA-seq was performed for the testes of hamsters in three groups. A total of 769 miRNAs were identified, of which 83 were differentially expressed between LD, MD, and SD. GO and KEGG analysis of target genes revealed that some miRNAs influence testicular activities by regulating the pathways related to cell apoptosis and metabolism. Gene expression pattern analysis showed that the MAPK signaling pathway may be the core pathway for photoperiodic regulation of reproduction. These results suggest that moderate daylength is more suitable for hamster reproduction while long daylength and short daylength may regulate reproduction through different molecular pathways.
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3
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Yan F, Wang P, Yang X, Wang F. Long non-coding RNA HOXA11-AS regulates ischemic neuronal death by targeting miR-337-3p/YBX1 signaling pathway: protective effect of dexmedetomidine. Aging (Albany NY) 2023; 15:2797-2811. [PMID: 37059588 PMCID: PMC10120896 DOI: 10.18632/aging.204648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/24/2023] [Indexed: 04/16/2023]
Abstract
Cerebral ischemia/reperfusion (I/R) is a common neurological disease. Homeobox A11 antisense RNA (HOXA11-AS), a long non-coding RNA (lncRNA), has been demonstrated as an important regulator in diverse human cancers. However, its function and regulatory mechanism in ischemic stroke remains largely unknown. Dexmedetomidine (Dex) have received wide attraction because of its neuroprotective effects. This study aimed to explore the possible link between Dex and HOXA11-AS in protecting neuronal cells from by ischemia/reperfusion-induced apoptosis. We used oxygen-glucose deprivation and reoxygenation (OGD/R) in mouse neuroblastoma Neuro-2a cells and middle cerebral artery occlusion (MACO) mouse model to test the link. We found that Dex significantly alleviated OGD/R-induced DNA fragmentation, cell viability and apoptosis, and rescued the decreased HOXA11-AS expression after ischemic damage in Neuro-2a cells. Gain-/loss-of-function studies revealed that HOXA11-AS promoted proliferation, inhibited apoptosis in Neuro-2a cells exposed to OGD/R. Knockdown of HOXA11-AS decreased the protective effect of Dex on OGD/R cells. HOXA11-AS was found to transcriptionally regulate microRNA-337-3p (miR-337-3p) expression as evidenced by luciferase reporter assay, while miR-337-3p expression was upregulated following ischemia in vitro and in vivo. Besides, knockdown of miR-337-3p protected OGD/R-induced apoptotic death of Neuro-2a cells. Furthermore, HOXA11-AS functioned as a competing endogenous RNA (ceRNA) and competed with Y box protein 1 (Ybx1) mRNA for directly binding to miR-337-3p, which protected ischemic neuronal death. Dex treatment protected against ischemic damage and improved overall neurological functions in vivo. Our data suggest a novel mechanism of Dex neuroprotection for ischemic stroke through regulating lncRNA HOXA11-AS by targeting the miR-337-3p/Ybx1 signaling pathway, which might help develop new strategies for the therapeutic interventions in cerebral ischemic stroke.
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Affiliation(s)
- Fei Yan
- School of Pharmacy, Health Science Center, Xi’an Jiaotong University, Xi’an, Shaanxi 710115, China
| | - Pinxiao Wang
- Department of Urology, Xi’an Medical University, Xi’an, Shaanxi 710068, China
| | - Xiaojian Yang
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710000, China
| | - Fuli Wang
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710000, China
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4
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Segal D, Coulombe S, Sim J, Dostie J. A conserved HOTAIRM1-HOXA1 regulatory axis contributes early to neuronal differentiation. RNA Biol 2023; 20:1523-1539. [PMID: 37743644 PMCID: PMC10619521 DOI: 10.1080/15476286.2023.2258028] [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] [Accepted: 04/03/2023] [Indexed: 09/26/2023] Open
Abstract
HOTAIRM1 is unlike most long non-coding RNAs in that its sequence is highly conserved across mammals. Such evolutionary conservation points to it having a role in key cellular processes. We previously reported that HOTAIRM1 is required to curb premature activation of downstream HOXA genes in a cell model recapitulating their sequential induction during development. We found that it regulates 3' HOXA gene expression by a mechanism involving epigenetic and three-dimensional chromatin changes. Here we show that HOTAIRM1 participates in proper progression through the early stages of neuronal differentiation. We found that it can associate with the HOXA1 transcription factor and contributes to its downstream transcriptional program. Particularly, HOTAIRM1 affects the NANOG/POU5F1/SOX2 core pluripotency network maintaining an undifferentiated cell state. HOXA1 depletion similarly perturbed expression of these pluripotent factors, suggesting that HOTAIRM1 is a modulator of this transcription factor pathway. Also, given that binding of HOTAIRM1 to HOXA1 was observed in different cell types and species, our results point to this ribonucleoprotein complex as an integral part of a conserved HOTAIRM1-HOXA1 regulatory axis modulating the transition from a pluripotent to a differentiated neuronal state.
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Affiliation(s)
- Dana Segal
- Department of Biochemistry, and Rosalind & Morris Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
| | - Samy Coulombe
- Department of Biochemistry, and Rosalind & Morris Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
- School of Computer Science, and McGill Center for Bioinformatics, McGill University, Montréal, Québec, Canada
| | - Jasper Sim
- Department of Biochemistry, and Rosalind & Morris Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
| | - Josée Dostie
- Department of Biochemistry, and Rosalind & Morris Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
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5
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Ross CJ, Ulitsky I. Discovering functional motifs in long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1708. [PMID: 34981665 DOI: 10.1002/wrna.1708] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/19/2021] [Accepted: 12/04/2021] [Indexed: 12/27/2022]
Abstract
Long noncoding RNAs (lncRNAs) are products of pervasive transcription that closely resemble messenger RNAs on the molecular level, yet function through largely unknown modes of action. The current model is that the function of lncRNAs often relies on specific, typically short, conserved elements, connected by linkers in which specific sequences and/or structures are less important. This notion has fueled the development of both computational and experimental methods focused on the discovery of functional elements within lncRNA genes, based on diverse signals such as evolutionary conservation, predicted structural elements, or the ability to rescue loss-of-function phenotypes. In this review, we outline the main challenges that the different methods need to overcome, describe the recently developed approaches, and discuss their respective limitations. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Caroline Jane Ross
- Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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6
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Han W, Wang S, Qi Y, Wu F, Tian N, Qiang B, Peng X. Targeting HOTAIRM1 Ameliorates Glioblastoma by Disrupting Mitochondrial Oxidative Phosphorylation and Serine Metabolism. iScience 2022; 25:104823. [PMID: 35992092 PMCID: PMC9389257 DOI: 10.1016/j.isci.2022.104823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 06/12/2022] [Accepted: 07/19/2022] [Indexed: 12/02/2022] Open
Abstract
Serine hydroxymethyltransferase 2 (SHMT2), which catalyzes the conversion of serine to glycine and one-carbon transfer reactions in mitochondria, is significantly upregulated in glioblastoma (GBM). However, the mechanism by which the stability of SHMT2 gene expression is maintained to drive GBM tumorigenesis has not been clarified. Herein, through microarray screening, we identified that HOXA Transcript Antisense RNA, Myeloid-Specific 1 (HOTAIRM1) modulates the SHMT2 level in various GBM cell lines. Serine catabolism and mitochondrial oxidative phosphorylation activities were decreased by HOTAIRM1 inhibition. Mechanistically, according to our mass spectrometry and eCLIP-seq results, HOTAIRM1 can bind to PTBP1 and IGF2BP2. Furthermore, HOTAIRM1 maintains the stability of SHMT2 by promoting the recognition of an m6A site and the interaction of PTBP1/IGF2BP2 with SHMT2 mRNA. The stability of HOTAIRM1 can also be enhanced and results in positive feedback regulation to support the progression of GBM. Thus, targeting HOTAIRM1 could be a promising metabolic therapy for GBM. HOTAIRM1 regulates mitochondrial activity in GBM The target genes of HOTAIRM1 and the interacting RBPs were screened and identified SHMT2 mRNA has an m6A site that can be recognized by IGF2BP2 HOTAIRM1 regulates the stability of SHMT2 by binding to PTBP1 and IGF2BP2
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Affiliation(s)
- Wei Han
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
- Corresponding author
| | - Shanshan Wang
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Yingjiao Qi
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Fan Wu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Ningyu Tian
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Boqin Qiang
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Xiaozhong Peng
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
- National Human Diseases Animal Model Resource Center, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
- Corresponding author
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7
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Ma Q, Yang L, Tolentino K, Wang G, Zhao Y, Litzenburger UM, Shi Q, Zhu L, Yang C, Jiao H, Zhang F, Li R, Tsai MC, Chen JA, Lai I, Zeng H, Li L, Chang HY. Inducible lncRNA transgenic mice reveal continual role of HOTAIR in promoting breast cancer metastasis. eLife 2022; 11:79126. [PMID: 36579891 PMCID: PMC9831604 DOI: 10.7554/elife.79126] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022] Open
Abstract
HOTAIR is a 2.2-kb long noncoding RNA (lncRNA) whose dysregulation has been linked to oncogenesis, defects in pattern formation during early development, and irregularities during the process of epithelial-to-mesenchymal transition (EMT). However, the oncogenic transformation determined by HOTAIR in vivo and its impact on chromatin dynamics are incompletely understood. Here, we generate a transgenic mouse model with doxycycline-inducible expression of human HOTAIR in the context of the MMTV-PyMT breast cancer-prone background to systematically interrogate the cellular mechanisms by which human HOTAIR lncRNA acts to promote breast cancer progression. We show that sustained high levels of HOTAIR over time increased breast metastatic capacity and invasiveness in breast cancer cells, promoting migration and subsequent metastasis to the lung. Subsequent withdrawal of HOTAIR overexpression reverted the metastatic phenotype, indicating oncogenic lncRNA addiction. Furthermore, HOTAIR overexpression altered both the cellular transcriptome and chromatin accessibility landscape of multiple metastasis-associated genes and promoted EMT. These alterations are abrogated within several cell cycles after HOTAIR expression is reverted to basal levels, indicating an erasable lncRNA-associated epigenetic memory. These results suggest that a continual role for HOTAIR in programming a metastatic gene regulatory program. Targeting HOTAIR lncRNA may potentially serve as a therapeutic strategy to ameliorate breast cancer progression.
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Affiliation(s)
- Qing Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Liuyi Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Karen Tolentino
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Guiping Wang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Yang Zhao
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Ulrike M Litzenburger
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Quanming Shi
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Lin Zhu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Chen Yang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education,Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Huiyuan Jiao
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education,Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Feng Zhang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education,Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Rui Li
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Miao-Chih Tsai
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Jun-An Chen
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Ian Lai
- Transgenic, Knockout, and Tumor Model Center, Stanford University School of MedicineStanfordUnited States,Stanford Cancer Institute, Stanford University School of MedicineStanfordUnited States
| | - Hong Zeng
- Transgenic, Knockout, and Tumor Model Center, Stanford University School of MedicineStanfordUnited States,Stanford Cancer Institute, Stanford University School of MedicineStanfordUnited States
| | - Lingjie Li
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education,Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States,Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
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8
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Guo L, Huang Q, Zhao J, Liu H, Lu W, Wang J. microRNA-10b promotes the apoptosis of bovine ovarian granulosa cells by targeting plasminogen activator inhibitor-1. Theriogenology 2021; 176:206-216. [PMID: 34627051 DOI: 10.1016/j.theriogenology.2021.09.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/13/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Abstract
Granulosa cells (GCs) are essential somatic cells in the ovaries, and apoptosis of GCs causes follicular atresia. microRNA-10b (miR-10b) is pivotal for cell apoptosis. However, currently, little is known about the role of miR-10b in bovine ovarian GCs (BGCs). In this study, the effect of miR-10b on the apoptosis of BGCs was investigated. Our results showed that the overexpression of miR-10b could increase the apoptosis rate of BGCs, which is associated with the increased expression of Caspase-3 and decreased expression ratio of Bcl-2/Bax (P < 0.05). Furthermore, plasminogen activator inhibitor-1 (PAI-1) was confirmed to be a validated target of miR-10b in BGCs using dual-luciferase reporter analysis, and transfection of miR-10b mimics decreased the expression of PAI-1 (P < 0.05). In addition, overexpression of PAI-1 significantly inhibited BGC apoptosis (P < 0.05), and PAI-1 could alleviate BGC apoptosis induced by miR-10b (P < 0.05). Subsequently, phosphatidylinositol-3-kinase/protein kinase B (PI3K/AKT) was found to be the downstream pathway of PAI-1 by RNA-Seq analysis and verified by Western blot. Finally, a PI3K/AKT inhibitor (Miltefosine) was used to inhibit the PI3K/AKT pathway, which reversed the inhibitory effect of PAI-1 on the apoptosis of BGCs (P < 0.05), and enhanced the promotion effect of miR-10b on the apoptosis of BGCs (P < 0.05). Our results indicated that miR-10b promotes BGC apoptosis by targeting PAI-1 to regulate the PI3K/AKT pathway.
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Affiliation(s)
- Lewei Guo
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Jilin, Changchun, 130118, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Qixuan Huang
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Jilin, Changchun, 130118, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Jing Zhao
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Jilin, Changchun, 130118, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Hongyu Liu
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Jilin, Changchun, 130118, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Wenfa Lu
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Jilin, Changchun, 130118, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China.
| | - Jun Wang
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Jilin, Changchun, 130118, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China.
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9
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Wu X, Wu G, Zhang H, Peng X, Huang B, Huang M, Ding J, Mao C, Peng C. MiR-196b Promotes the Invasion and Migration of Lung Adenocarcinoma Cells by Targeting AQP4. Technol Cancer Res Treat 2021; 20:1533033820985868. [PMID: 33455522 PMCID: PMC8097310 DOI: 10.1177/1533033820985868] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Objective: We aimed to investigate the mechanism of the regulatory axis of miR-196b/AQP4
underlying the invasion and migration of lung adenocarcinoma (LUAD)
cells. Methods: LUAD miRNA and mRNA expression profiles were downloaded from TCGA database
and then differential analysis was used to identify the target miRNA. Target
gene for the miRNA was obtained via prediction using 3 bioinformatics
databases and intersection with the differentially expressed mRNAs searched
from TCGA-LUAD. Then, qRT-PCR and western blot were used to validate the
expression of miR-196b and AQP4. Dual-luciferase reporter assay was
performed to confirm the targeting relationship between miR-196b and AQP4.
Transwell assay was used to investigate the migration and invasion of LUAD
cells. Results: MiR-196b was screened out by differential and survival analyses, and the
downstream target gene AQP4 was identified. In LUAD, miR-196b was highly
expressed while AQP4 was poorly expressed. Besides, overexpression of
miR-196b promoted cell invasion and migration, while overexpression of AQP4
had negative effects. Moreover, the results of the dual-luciferase reporter
assay suggested that AQP4 was a direct target of miR-196b. In addition, we
also found that overexpressing AQP4 could suppress the promotive effect of
miR-196b on cancer cell invasion and migration. Conclusion: MiR-196b promotes the invasion and migration of LUAD cells by down-regulating
AQP4, which helps us find new molecular targeted therapies for LUAD.
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Affiliation(s)
- Xuhui Wu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Gongzhi Wu
- Department of Cardiothoracic Surgery, Lishui City People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Huaizhong Zhang
- Department of Cardiothoracic Surgery, Lishui City People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Xuyang Peng
- Department of Cardiothoracic Surgery, Lishui City People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Bin Huang
- Department of Cardiothoracic Surgery, Lishui City People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Mingjiang Huang
- Department of Cardiothoracic Surgery, Lishui City People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Jianyang Ding
- Department of Cardiothoracic Surgery, Lishui City People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Chaofan Mao
- Department of Cardiothoracic Surgery, Lishui City People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Congxiong Peng
- Department of Cardiothoracic Surgery, Lishui City People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
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10
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Yang L, Shen K, Zhang M, Zhang W, Cai H, Lin L, Long X, Xing S, Tang Y, Xiong J, Wang J, Li D, Zhou J, Xiao M. Clinical Features and MicroRNA Expression Patterns Between AML Patients With DNMT3A R882 and Frameshift Mutations. Front Oncol 2019; 9:1133. [PMID: 31709191 PMCID: PMC6821681 DOI: 10.3389/fonc.2019.01133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/10/2019] [Indexed: 01/01/2023] Open
Abstract
Background: DNA methyltransferase 3A (DNMT3A) plays a unique role in hematopoiesis and acute myeloid leukemia (AML) pathogenesis. While the influences of DNMT3A mutation subtypes are still under debate. Purpose: Exploration of the clinical and molecular differences between AML patients carrying DNMT3A R882 mutations and DNMT3A frameshift mutations. Methods: Next generation of sequencing (NGS) and clinical data of 118 AML patients in our center were analyzed and compared. NGS, mRNA and miRNA profiling and clinical data from 12 patients in TCGA database were integrative analyzed. Results: Among all patients enrolled, 113 patients were positive for the variants of interest. Overall, a total of 295 variants were discovered, among which 24 DNMT3A mutations were detected, including 1 non-sense, 20 missense, 3 frameshift mutations. And 7 DNMT3A R882 mutations (3 R882H, 2 R882C, and 2 R882P) were found. Clinical analysis from our cohort and TCGA database indicated that patients carrying DNMT3A R882 mutation exhibited significantly higher levels of peripheral blood hemoglobin and non-significantly inferior prognosis compared with patients with DNMT3A frameshift mutations. Integrative analysis indicated that miR-10b, miR-143, and miR-30a were significantly decreased in the DNMT3A R882 group. High miR-143 expression is significantly associated with better prognosis in AML patients with DNMT3A mutations. Conclusion: Different molecular and clinical characteristics existed between patients with DNMT3A variant subtypes. The distinct microRNA expression pattern for DNMT3A R882 AML patients might not only act as markers to predict disease prognosis, but also could be further investigated to develop novel therapeutic targets for patients with DNMT3A mutations.
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Affiliation(s)
- Li Yang
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Ke'Feng Shen
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Mei'Lan Zhang
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Zhang
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Hao'Dong Cai
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Li'Man Lin
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao'Lu Long
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Shu'Gang Xing
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Tang
- Department of Oncology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Jie Xiong
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Jia'Chen Wang
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Deng'Ju Li
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Jian'Feng Zhou
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Min Xiao
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
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11
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Herrera-Úbeda C, Marín-Barba M, Navas-Pérez E, Gravemeyer J, Albuixech-Crespo B, Wheeler GN, Garcia-Fernàndez J. Microsyntenic Clusters Reveal Conservation of lncRNAs in Chordates Despite Absence of Sequence Conservation. BIOLOGY 2019; 8:E61. [PMID: 31450588 PMCID: PMC6784235 DOI: 10.3390/biology8030061] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 01/10/2023]
Abstract
Homologous long non-coding RNAs (lncRNAs) are elusive to identify by sequence similarity due to their fast-evolutionary rate. Here we develop LincOFinder, a pipeline that finds conserved intergenic lncRNAs (lincRNAs) between distant related species by means of microsynteny analyses. Using this tool, we have identified 16 bona fide homologous lincRNAs between the amphioxus and human genomes. We characterized and compared in amphioxus and Xenopus the expression domain of one of them, Hotairm1, located in the anterior part of the Hox cluster. In addition, we analyzed the function of this lincRNA in Xenopus, showing that its disruption produces a severe headless phenotype, most probably by interfering with the regulation of the Hox cluster. Our results strongly suggest that this lincRNA has probably been regulating the Hox cluster since the early origin of chordates. Our work pioneers the use of syntenic searches to identify non-coding genes over long evolutionary distances and helps to further understand lncRNA evolution.
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Affiliation(s)
- Carlos Herrera-Úbeda
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Marta Marín-Barba
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
| | - Enrique Navas-Pérez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Jan Gravemeyer
- German Cancer Research Center, 69120 Heidelberg, Germany
| | - Beatriz Albuixech-Crespo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Grant N Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
| | - Jordi Garcia-Fernàndez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain.
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12
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Han N, Zuo L, Chen H, Zhang C, He P, Yan H. Long non-coding RNA homeobox A11 antisense RNA (HOXA11-AS) promotes retinoblastoma progression via sponging miR-506-3p. Onco Targets Ther 2019; 12:3509-3517. [PMID: 31123409 PMCID: PMC6511239 DOI: 10.2147/ott.s195404] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/16/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Long non-coding RNA homeobox A11 antisense RNA (HOXA11-AS) has been reported to be involved in initiation and development of multiple cancers. However, the detailed biological roles and underlying molecular mechanism of HOXA11-AS remain unclear in retinoblastoma (RB). Herein, the goals of this study were to explore the biological function and the potential mechanism of HOXA11-AS in RB. Materials and methods: The expression of HOXA11-AS in RB tissues and cell lines was detected using real-time PCR (qRT-PCR). Cell proliferation, cycle arrest and apoptosis were measured using a cell counting kit 8 and flow cytometry. The target miRNAs of HOXA11-AS was predicted by Starbase2.0 software and was confirmed using a dual-luciferase reporter assay. Result: We found that HOXA11-AS expression was markedly elevated in RB tissues and cell lines compared to normal retina tissues and human retinal epithelial cells, respectively. Functional analysis showed that knockdown of HOXA11-AS in RB cells significantly suppressed cell proliferation, and induced cell cycle arrest at G1/G0 phase and promoted cell apoptosis. We also found that HOXA11-AS could serve as a competing endogenous RNA (ceRNA) that inhibited miR-506-3p expression, which regulated its downstream target NIMA-related kinase 6 (NEK6) in RB. In addition, miR-506-3p inhibitors partially reversed the effect of HOXA11-AS depletion on proliferation, cycle arrest and apoptosis in RB cells. Conclusion: Taken together, these findings demonstrated that HOXA11-AS could promote RB progression by sponging miR-506-3p, suggesting that HOXA-11-AS might be a potential therapeutic target for RB.
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Affiliation(s)
- Ning Han
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin 130041, People's Republic of China
| | - Ling Zuo
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin 130041, People's Republic of China
| | - Han Chen
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin 130041, People's Republic of China
| | - Chunxia Zhang
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin 130041, People's Republic of China
| | - Pei He
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin 130041, People's Republic of China
| | - Hongtao Yan
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin 130041, People's Republic of China
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13
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Graves JAM. Marsupial genomics meet marsupial reproduction. Reprod Fertil Dev 2018; 31:1181-1188. [PMID: 30482268 DOI: 10.1071/rd18234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/08/2018] [Indexed: 11/23/2022] Open
Abstract
We came from very different backgrounds, with different skills and interests. Marilyn Renfree was recognised as 'a giant of marsupial embryology'; I had spent my working life studying genes and chromosomes. We teamed up out of mutual respect (awe on my side) to form, with Des Cooper, the ARC Centre of Excellence in Kangaroo Genomics. This is the story of how our collaboration came to be, and what it has produced for our knowledge of some of the world's most remarkable animals.
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14
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Xue JY, Huang C, Wang W, Li HB, Sun M, Xie M. HOXA11-AS: a novel regulator in human cancer proliferation and metastasis. Onco Targets Ther 2018; 11:4387-4393. [PMID: 30100744 PMCID: PMC6067783 DOI: 10.2147/ott.s166961] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Multiple studies have demonstrated that lncRNAs extensively participate in human cancer proliferation and metastasis. Epigenetic modification, transcriptional and posttranscriptional regulatory mechanisms are involved in lncRNA-led tumorigenesis and transfer. Recently, a novel identified homeobox (HOX) A11 antisense lncRNA, HOXA11-AS, 1,628 bp in length, has been excessively highlighted to be an essential initiator and facilitator in the process of malignant tumor proliferation and metastasis. As found in many reports, HOXA11-AS can not only act as a molecular scaffold of PRC2, LSD1 and DNMT1 to epigenetically modify chromosomes in the nucleus but also occur as ceRNA competitively sponging miRNAs in the cytoplasm. Furthermore, HOXA11-AS may function as a potential biomarker for cancer diagnosis and prognosis. In this review, we summarize the evolvement and mechanisms of HOXA11-AS in proliferation and metastasis of various human cancers.
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Affiliation(s)
- Jiang-Yang Xue
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
| | - Chao Huang
- Central Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China,
| | - Wei Wang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
| | - Hai-Bo Li
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
| | - Ming Sun
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA,
| | - Min Xie
- Central Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China,
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15
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Bi L, Sun L, Jin Z, Zhang S, Shen Z. MicroRNA-10a/b are regulators of myeloid differentiation and acute myeloid leukemia. Oncol Lett 2018; 15:5611-5619. [PMID: 29552198 PMCID: PMC5840650 DOI: 10.3892/ol.2018.8050] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 09/07/2017] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRs) have been demonstrated to perform important roles in normal hematopoiesis and leukemogenesis. Accumulating evidence suggests that miR-10a and miR-10b may behave as novel oncogenes or tumor suppressors in human cancer. The present study reported the function of the miR-10 family in myeloid differentiation and acute myeloid leukemia (AML). The levels of miR-10a/b expression were increased in AML cases compared with normal controls, particularly in M1, M2 and M3 subtypes. The levels of miR-10a/b expression were also upregulated in patients with nucleophosmin-mutated AML and AML patients with t(8;21) and t(9;11), compared with the normal control. In addition, the role of miR-10a/b in regulating myeloid differentiation and leukemogenesis was investigated. The results indicated that miR-10a/b expression was able to promote the proliferation of human promyelocytic leukemia cells, while suppressing the granulocytic and monocytic differentiation of the leukemia cells. These findings suggested that abnormal high expression of miR-10a/b may result in unlimited proliferation of immature blood progenitors and repression of mature blood cell differentiation and maturation, thus leading to the occurrence of AML. miR-10a/b may be developed as novel therapeutic targets for the treatment of AML.
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Affiliation(s)
- Laixi Bi
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Lan Sun
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Zhenlin Jin
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Shenghui Zhang
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Zhijian Shen
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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16
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Long non-coding RNA HOXA11-AS promotes the proliferation HCC cells by epigenetically silencing DUSP5. Oncotarget 2017; 8:109509-109521. [PMID: 29312625 PMCID: PMC5752538 DOI: 10.18632/oncotarget.22723] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/26/2017] [Indexed: 01/11/2023] Open
Abstract
Hepatocellular carcinoma has been identified as the fifth most common cancer in men and the ninth in women worldwide. Despite many efforts have been made in recent years, the overall survival rate of patients with hepatocellular carcinoma still remain unsatisfied. Therefore, exploring the mechanisms underlying the progression of hepatocellular carcinoma is essential for developing novel treatments to improve patient prognosis. HOXA11-AS, transcribed from the opposite strand of the protein-coding gene HOXA11, has been identified to be associated with the malignant characteristics of several cancers. However, the biological role and molecular mechanism of HOXA11-AS in hepatocellular carcinoma still need to be further investigated. In the current study, the expression of HOXA11-AS in the hepatocellular carcinoma cell lines and tissues was measured by quantitative real-time PCR. Loss-of-function and gain-of-function approaches were applied to investigate the proliferative function of HOXA11-AS in hepatocellular carcinoma cells. Results from flow cytometric analysis of apoptosis and cell cycle distribution revealed that HOXA11-AS promoted hepatocellular carcinoma cells proliferation through regulating cell cycle and apoptosis. Gene chip technology and quantitative real-time PCR confirmed that DUSP5 was a downstream target of HOXA11-AS. RNA immune co-precipitation assays, RNA pull-down and Chromatin immunoprecipitation assays confirmed that HOXA11-AS could recruit EZH2 to the promoter region of DUSP5, which therefore suppressed the transcription of DUSP5. Collectively, these findings revealed that HOXA11-AS functions as an oncogene in hepatocellular carcinoma through interacting with polycomb-repressive complex2.
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17
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Genome-wide screen for differentially methylated long noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as regulated by enhancer DNA methylation with prognostic relevance for human breast cancer. Oncogene 2017; 36:6446-6461. [PMID: 28759043 PMCID: PMC5701091 DOI: 10.1038/onc.2017.246] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 06/05/2017] [Accepted: 06/08/2017] [Indexed: 12/14/2022]
Abstract
The majority of long noncoding RNAs (lncRNAs) is still poorly characterized with respect to function, interactions with protein-coding genes, and mechanisms that regulate their expression. As for protein-coding RNAs, epigenetic deregulation of lncRNA expression by alterations in DNA methylation might contribute to carcinogenesis. To provide genome-wide information on lncRNAs aberrantly methylated in breast cancer we profiled tumors of the C3(1) SV40TAg mouse model by MCIp-seq (Methylated CpG Immunoprecipitation followed by sequencing). This approach detected 69 lncRNAs differentially methylated between tumor tissue and normal mammary glands, with 26 located in antisense orientation of a protein-coding gene. One of the hypomethylated lncRNAs, 1810019D21Rik (now called Esrp2-antisense (as)) was identified in proximity to the epithelial splicing regulatory protein 2 (Esrp2) that is significantly elevated in C3(1) tumors. ESRPs were shown previously to have a dual role in carcinogenesis. Both gain and loss have been associated with poor prognosis in human cancers, but the mechanisms regulating expression are not known. In-depth analyses indicate that coordinate overexpression of Esrp2 and Esrp2-as inversely correlates with DNA methylation. Luciferase reporter gene assays support co-expression of Esrp2 and the major short Esrp2-as variant from a bidirectional promoter, and transcriptional regulation by methylation of a proximal enhancer. Ultimately, this enhancer-based regulatory mechanism provides a novel explanation for tissue-specific expression differences and upregulation of Esrp2 during carcinogenesis. Knockdown of Esrp2-as reduced Esrp2 protein levels without affecting mRNA expression and resulted in an altered transcriptional profile associated with extracellular matrix (ECM), cell motility and reduced proliferation, whereas overexpression enhanced proliferation. Our findings not only hold true for the murine tumor model, but led to the identification of an unannotated human homolog of Esrp2-as which is significantly upregulated in human breast cancer and associated with poor prognosis.
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18
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Jo A, Im J, Lee HE, Jang D, Nam GH, Mishra A, Kim WJ, Kim W, Cha HJ, Kim HS. Evolutionary conservation and expression of miR-10a-3p in olive flounder and rock bream. Gene 2017; 628:16-23. [PMID: 28698161 DOI: 10.1016/j.gene.2017.07.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/01/2017] [Accepted: 07/07/2017] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) that mainly bind to the seed sequences located within the 3' untranslated region (3' UTR) of target genes. They perform an important biological function as regulators of gene expression. Different genes can be regulated by the same miRNA, whilst different miRNAs can be regulated by the same genes. Here, the evolutionary conservation and expression pattern of miR-10a-3p in olive flounder and rock bream was examined. Binding sites (AAAUUC) to seed region of the 3' UTR of target genes were highly conserved in various species. The expression pattern of miR-10a-3p was ubiquitous in the examined tissues, whilst its expression level was decreased in gill tissues infected by viral hemorrhagic septicemia virus (VHSV) compared to the normal control. In the case of rock bream, the spleen, kidney, and liver tissues showed dominant expression levels of miR-10a-3p. Only the liver tissues in the rock bream samples infected by the iridovirus indicated a dominant miR-10a-3p expression. The gene ontology (GO) analysis of predicted target genes for miR-10a-3p revealed that multiple genes are related to binding activity, catalytic activity, cell components as well as cellular and metabolic process. Overall the results imply that the miR-10a-3p could be used as a biomarker to detect VHSV infection in olive flounder and iridovirus infection in rock bream. In addition, the data provides fundamental information for further study of the complex interaction between miR-10a-3p and gene expression.
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Affiliation(s)
- Ara Jo
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Jennifer Im
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Dongmin Jang
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Gyu-Hwi Nam
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Anshuman Mishra
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Woo-Jin Kim
- Genetics and Breeding Research Center, National Institute of Fisheries Science, Geoje 53334, Republic of Korea
| | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul 08824, Republic of Korea
| | - Hee-Jae Cha
- Departments of Parasitology and Genetics, College of Medicine, Kosin University, Busan 49267, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 46241, Republic of Korea.
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19
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Kanno S, Nosho K, Ishigami K, Yamamoto I, Koide H, Kurihara H, Mitsuhashi K, Shitani M, Motoya M, Sasaki S, Tanuma T, Maguchi H, Hasegawa T, Kimura Y, Takemasa I, Shinomura Y, Nakase H. MicroRNA-196b is an independent prognostic biomarker in patients with pancreatic cancer. Carcinogenesis 2017; 38:425-431. [DOI: 10.1093/carcin/bgx013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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20
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HOTAIR functions as a competing endogenous RNA to regulate PTEN expression by inhibiting miR-19 in cardiac hypertrophy. Mol Cell Biochem 2017; 432:179-187. [PMID: 28316060 DOI: 10.1007/s11010-017-3008-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/07/2017] [Indexed: 01/18/2023]
Abstract
Sustained cardiac hypertrophy (CH) is related to a variety of physiological as well as pathological stimuli and eventually increases the risk of heart failure. HOTAIR has been identified as a competing endogenous RNA in multiple human biological processes. Whether lncRNA-HOTAIR is involved in the progress of CH and how it works still remain unknown. Herein, we found that HOTAIR was down-regulated, while miR-19 was up-regulated in both heart tissues from TAC-operated mice in vivo and cultural cardiomyocytes treated with Ang-II in vitro by real-time PCR. Meanwhile, HOTAIR expression was negatively correlated with miR-19 in TAC-operated mice. HOTAIR overexpression reduced cell surface area and the expression of hypertrophic markers ANP, BNP, and β-MHC in response to Ang-II stimulation as well as knockdown of miR-19. The further molecular mechanisms of HOTAIR action in CH demonstrated that HOTAIR may act as a competing endogenous RNA (ceRNA) for miR-19, thereby modulating the dis-inhibition of its endogenous target PTEN and playing an important role in inhibiting CH progress. These findings reveal a novel function of LncRNAs, which conduce to an extensive understanding of CH and provide novel research directions and therapeutic options for treating this disease.
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21
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Xu C, Gu L. The diagnostic effect of serum miR-196b as biomarker in colorectal cancer. Biomed Rep 2016; 6:39-45. [PMID: 28123705 PMCID: PMC5244757 DOI: 10.3892/br.2016.815] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/11/2016] [Indexed: 12/11/2022] Open
Abstract
The microRNA, miR-196b, serves a role in normal cell differentiation, proliferation and tumorigenesis of different types of cancer. The aim of the present study was to explore the serum expression of miR-196b in colorectal cancer (CRC) and its correlation with clinicopathological features. Sera samples were obtained from 103 patients with CRC, 51 patients with colorectal adenoma (Ad) and 100 healthy individuals for the present study. The serum expression of miR-196b in sera samples of the three cohorts was detected using reverse transcription-quantitative polymerase chain reaction. The diagnostic value of miR-196b in the serum of the patients with CRC was evaluated by receiver operating characteristic (ROC) curve and survival analysis, using the Kaplan-Meier method, which was performed with the data from a 5-year follow-up. The expression of miR-196b in the serum of patients with CRC was significantly higher compared with that in Ad patients or healthy individuals (all P<0.001), and the overexpression of serum miR-196b was clearly associated with lymph node invasion, differentiation, and the tumor-lymph nodes-metastasis stage (all P<0.05). ROC curve analysis demonstrated that, comparing patients with CRC with healthy individuals, the area under the curve of serum miR-196b was 0.8135, and its specificity and sensitivity were 63 and 87.38%, respectively, at a diagnostic threshold of −4.785. Patients with CRC of miR-196b-high status had shorter overall survival and disease-free survival rates compared with those of miR-196b-low status. In conclusion, the results of the present study demonstrated that serum miR-196b is upregulated in CRC, and may have an application as a diagnostic and prognostic biomarker for patients with CRC.
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Affiliation(s)
- Chunjie Xu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Lei Gu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
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22
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Li T, Xu C, Cai B, Zhang M, Gao F, Gan J. Expression and clinicopathological significance of the lncRNA HOXA11-AS in colorectal cancer. Oncol Lett 2016; 12:4155-4160. [PMID: 27895785 DOI: 10.3892/ol.2016.5129] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 07/12/2016] [Indexed: 01/16/2023] Open
Abstract
HOXA11 antisense RNA (HOXA11-AS) is a long non-coding RNA (lncRNA) that is important in determining cancer progression. HOXA11-AS was recently identified as a novel biomarker in lung cancer progression. However, its role in colorectal cancer (CRC) remains poorly understood. The present study aimed to analyze lncRNA HOXA11-AS expression in CRC and investigate a possible association between HOXA11-AS and clinicopathological factors. HOXA11-AS expression was examined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in 84 CRC tissues and adjacent non-cancerous tissues, in addition to 3 CRC cell lines and 1 human normal colorectal cell line. The results demonstrated that HOXA11-AS expression was decreased in the CRC tissues and cell lines compared with that of the controls (P<0.05). Clinicopathological analysis indicated that low HOXA11-AS expression was significantly correlated with tumor size, advanced tumor-node-metastasis stage, lymph node metastasis and carcinoembryonic antigen level of patients with CRC (P<0.05). Furthermore, the areas under the curve (AUC) were 0.613 and 0.628 for HOXA11-AS, indicating that the lncRNA is able to distinguish CRC tissue from non-cancerous tissue, and CRC tissue with lymph node metastasis from CRC without lymph node metastasis. Therefore, HOXA11-AS may function as a potential biomarker and target for novel therapeutic strategies to treat CRC.
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Affiliation(s)
- Tong Li
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Chengfei Xu
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Bin Cai
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Meng Zhang
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Feng Gao
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Jialiang Gan
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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23
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The function of homeobox genes and lncRNAs in cancer. Oncol Lett 2016; 12:1635-1641. [PMID: 27588114 DOI: 10.3892/ol.2016.4901] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/24/2016] [Indexed: 02/02/2023] Open
Abstract
Recently, the homeobox (HOX) gene family has been reported as a factor in tumorigenesis. In the human genome, the HOX gene family contains 4 clusters with 39 genes and multiple transcripts. Mutation or abnormal expression of genes is responsible for developmental disorders. In addition, changes in the levels and activation of certain HOX genes has been associated with the development of cancer. Long non-coding RNAs (lncRNAs) have also been identified to serve critical functions in cancer. Although a limited number of lncRNAs have been previously investigated, the list of functional lncRNA genes has recently grown. Two of the most important and well-studied lncRNAs and HOX transcript genes are HOX transcript antisense RNA (HOTAIR) and HOXA distal transcript antisense RNA (HOTTIP). The present study aimed to review not only the function of the HOTAIR and HOTTIP genes in certain forms of cancer, but also to review other HOX genes and protein functions in cancer, particularly HOX family genes associated with lncRNAs.
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24
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Nitsche A, Stadler PF. Evolutionary clues in lncRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27436689 DOI: 10.1002/wrna.1376] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/06/2016] [Accepted: 06/09/2016] [Indexed: 12/13/2022]
Abstract
The diversity of long non-coding RNAs (lncRNAs) in the human transcriptome is in stark contrast to the sparse exploration of their functions concomitant with their conservation and evolution. The pervasive transcription of the largely non-coding human genome makes the evolutionary age and conservation patterns of lncRNAs to a topic of interest. Yet it is a fairly unexplored field and not that easy to determine as for protein-coding genes. Although there are a few experimentally studied cases, which are conserved at the sequence level, most lncRNAs exhibit weak or untraceable primary sequence conservation. Recent studies shed light on the interspecies conservation of secondary structures among lncRNA homologs by using diverse computational methods. This highlights the importance of structure on functionality of lncRNAs as opposed to the poor impact of primary sequence changes. Further clues in the evolution of lncRNAs are given by selective constraints on non-coding gene structures (e.g., promoters or splice sites) as well as the conservation of prevalent spatio-temporal expression patterns. However, a rapid evolutionary turnover is observable throughout the heterogeneous group of lncRNAs. This still gives rise to questions about its functional meaning. WIREs RNA 2017, 8:e1376. doi: 10.1002/wrna.1376 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Anne Nitsche
- Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany.,Institute de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Cedex, France
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology - IZI, Leipzig, Germany.,Center for Non-Coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.,Department of Theoretical Chemistry, University of Vienna, Wien, Austria.,Santa Fe Institute, Santa Fe, NM, USA
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25
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Tellez CS, Juri DE, Do K, Picchi MA, Wang T, Liu G, Spira A, Belinsky SA. miR-196b Is Epigenetically Silenced during the Premalignant Stage of Lung Carcinogenesis. Cancer Res 2016; 76:4741-51. [PMID: 27302168 DOI: 10.1158/0008-5472.can-15-3367] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/16/2016] [Indexed: 02/06/2023]
Abstract
miRNA silencing by promoter hypermethylation may represent a mechanism by which lung cancer develops and progresses, but the miRNAs involved during malignant transformation are unknown. We previously established a model of premalignant lung cancer wherein we treated human bronchial epithelial cells (HBEC) with low doses of tobacco carcinogens. Here, we demonstrate that next-generation sequencing of carcinogen-transformed HBECs treated with the demethylating agent 5-aza-2'deoxycytidine revealed miR-196b and miR-34c-5p to be epigenetic targets. Bisulfite sequencing confirmed dense promoter hypermethylation indicative of silencing in multiple malignant cell lines and primary tumors. Chromatin immunoprecipitation studies further demonstrated an enrichment in repressive histone marks on the miR-196b promoter during HBEC transformation. Restoration of miR-196b expression by transfecting transformed HBECs with specific mimics led to cell-cycle arrest mediated in part through transcriptional regulation of the FOS oncogene, and miR-196b reexpression also significantly reduced the growth of tumor xenografts. Luciferase assays demonstrated that forced expression of miR-196b inhibited the FOS promoter and AP-1 reporter activity. Finally, a case-control study revealed that methylation of miR-196b in sputum was strongly associated with lung cancer (OR = 4.7, P < 0.001). Collectively, these studies highlight miR-196b as a tumor suppressor whose silencing early in lung carcinogenesis may provide a selective growth advantage to premalignant cells. Targeted delivery of miR-196b could therefore serve as a preventive or therapeutic strategy for the management of lung cancer. Cancer Res; 76(16); 4741-51. ©2016 AACR.
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Affiliation(s)
- Carmen S Tellez
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico.
| | - Daniel E Juri
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Kieu Do
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Teresa Wang
- Department of Medicine, Boston University, Boston, Massachusetts
| | - Gang Liu
- Department of Medicine, Boston University, Boston, Massachusetts
| | - Avrum Spira
- Department of Medicine, Boston University, Boston, Massachusetts
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico.
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26
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HoxA Genes and the Fin-to-Limb Transition in Vertebrates. J Dev Biol 2016; 4:jdb4010010. [PMID: 29615578 PMCID: PMC5831813 DOI: 10.3390/jdb4010010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/27/2016] [Accepted: 02/04/2016] [Indexed: 12/12/2022] Open
Abstract
HoxA genes encode for important DNA-binding transcription factors that act during limb development, regulating primarily gene expression and, consequently, morphogenesis and skeletal differentiation. Within these genes, HoxA11 and HoxA13 were proposed to have played an essential role in the enigmatic evolutionary transition from fish fins to tetrapod limbs. Indeed, comparative gene expression analyses led to the suggestion that changes in their regulation might have been essential for the diversification of vertebrates' appendages. In this review, we highlight three potential modifications in the regulation and function of these genes that may have boosted appendage evolution: (1) the expansion of polyalanine repeats in the HoxA11 and HoxA13 proteins; (2) the origin of +a novel long-non-coding RNA with a possible inhibitory function on HoxA11; and (3) the acquisition of cis-regulatory elements modulating 5' HoxA transcription. We discuss the relevance of these mechanisms for appendage diversification reviewing the current state of the art and performing additional comparative analyses to characterize, in a phylogenetic framework, HoxA11 and HoxA13 expression, alanine composition within the encoded proteins, long-non-coding RNAs and cis-regulatory elements.
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27
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Swellam M, El-Khazragy N. Clinical impact of circulating microRNAs as blood-based marker in childhood acute lymphoblastic leukemia. Tumour Biol 2016; 37:10571-6. [PMID: 26857279 DOI: 10.1007/s13277-016-4948-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/29/2016] [Indexed: 01/03/2023] Open
Abstract
Aberrant microRNA (miRNA) expression participates in childhood acute lymphoblastic leukemia (ALL). This study aimed to investigate the expression of miRNA-100, miRNA-196a, and miRNA-146a among childhood ALL and study their correlation with other hematological parameters and different phenotypes. Peripheral blood mononuclear cells (PMNCs) were obtained from 85 childhood ALL and 25 healthy children for the detection of miRNA expression using quantitative real-time PCR. Significant higher median levels were reported for ALL compared to control children. The diagnostic efficacy for miRNA-146a was superior as both sensitivity and specificity were absolute. A significant correlation was observed between higher expression of miRNA-100 and lower platelet and lymphocyte counts; high expression of miRNA-146a showed significant correlation with low total leukocyte count (TLC) and lymphocyte counts. Significant relation was reported between studied miRNAs and different phenotyping. miRNA-100, miRNA-196a, and miRNA-146a have significant role in childhood ALL leukemogenesis, and they may be useful as biological diagnostic molecular markers.
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Affiliation(s)
- Menha Swellam
- Department of Biochemistry, Genetic Engineering and Biotechnology Research Division, National Research Centre, Giza, 12622, Dokki, Egypt.
| | - Nashwa El-Khazragy
- Department of Clinical Pathology, Oncology Diagnostic Unit, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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28
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De Kumar B, Krumlauf R. HOXs and lincRNAs: Two sides of the same coin. SCIENCE ADVANCES 2016; 2:e1501402. [PMID: 27034976 PMCID: PMC4805430 DOI: 10.1126/sciadv.1501402] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/28/2015] [Indexed: 05/13/2023]
Abstract
The clustered Hox genes play fundamental roles in regulation of axial patterning and elaboration of the basic body plan in animal development. There are common features in the organization and regulatory landscape of Hox clusters associated with their highly conserved functional roles. The presence of transcribed noncoding sequences embedded within the vertebrate Hox clusters is providing insight into a new layer of regulatory information associated with Hox genes.
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Affiliation(s)
- Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
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29
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Quah S, Holland PWH. The Hox cluster microRNA miR-615: a case study of intronic microRNA evolution. EvoDevo 2015; 6:31. [PMID: 26451238 PMCID: PMC4597612 DOI: 10.1186/s13227-015-0027-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/25/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Introns represent a potentially rich source of existing transcription for the evolution of novel microRNAs (miRNAs). Within the Hox gene clusters, a miRNA gene, miR-615, is located within the intron of the Hoxc5 gene. This miRNA has a restricted phylogenetic distribution, providing an opportunity to examine the origin and evolution of a new miRNA within the intron of a developmentally-important homeobox gene. RESULTS Alignment and structural analyses show that the sequence is highly conserved across eutherian mammals and absent in non-mammalian tetrapods. Marsupials possess a similar sequence which we predict will not be efficiently processed as a miRNA. Our analyses suggest that transcription of HOXC5 in humans is accompanied by expression of miR-615 in all cases, but that the miRNA can also be transcribed independently of its host gene through the use of an intragenic promoter. We present scenarios for the evolution of miR-615 through intronic exaptation, and speculate on the acquisition of independent transcriptional regulation. Target prediction and transcriptomic analyses suggest that the dominant product of miR-615 is involved in the regulation of growth and a range of developmental processes. CONCLUSIONS The miR-615 gene evolved within the intron of Hoxc5 in the ancestor of placental mammals. Using miR-615 as a case study, we propose a model by which a functional miRNA can emerge within an intron gradually, by selection on secondary structure followed by evolution of an independent miRNA promoter. The location within a Hox gene intron is of particular interest as the miRNA is specific to placental mammals, is co-expressed with its host gene and may share complementary functions.
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Affiliation(s)
- Shan Quah
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | - Peter W. H. Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
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30
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Ye P, Wang T, Liu WH, Li XC, Tang LJ, Tian FZ. Enhancing HOTAIR/MiR-10b Drives Normal Liver Stem Cells Toward a Tendency to Malignant Transformation Through Inducing Epithelial- to-Mesenchymal Transition. Rejuvenation Res 2015; 18:332-40. [PMID: 25708830 DOI: 10.1089/rej.2014.1642] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Ping Ye
- Third Military Medical University, Chongqing, China
| | - Tao Wang
- General Surgery Center, Chengdu Military General Hospital, Chengdu, Sichuan Province, China
| | - Wei-hui Liu
- General Surgery Center, Chengdu Military General Hospital, Chengdu, Sichuan Province, China
| | - Xiu-chuan Li
- Department of Cardiology, Chengdu Military General Hospital, Chengdu, Sichuan, Province, China
| | - Li-jun Tang
- General Surgery Center, Chengdu Military General Hospital, Chengdu, Sichuan Province, China
| | - Fu-zhou Tian
- General Surgery Center, Chengdu Military General Hospital, Chengdu, Sichuan Province, China
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31
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Gardner PP, Fasold M, Burge SW, Ninova M, Hertel J, Kehr S, Steeves TE, Griffiths-Jones S, Stadler PF. Conservation and losses of non-coding RNAs in avian genomes. PLoS One 2015; 10:e0121797. [PMID: 25822729 PMCID: PMC4378963 DOI: 10.1371/journal.pone.0121797] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/03/2015] [Indexed: 11/21/2022] Open
Abstract
Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase. We identify 34 lncRNA-associated loci that are conserved between birds and mammals and validate 12 of these in chicken. We report several intriguing cases where a reported mammalian lncRNA, but not its function, is conserved. We also demonstrate extensive conservation of classical ncRNAs (e.g., tRNAs) and more recently discovered ncRNAs (e.g., snoRNAs and miRNAs) in birds. Furthermore, we describe numerous “losses” of several RNA families, and attribute these to either genuine loss, divergence or missing data. In particular, we show that many of these losses are due to the challenges associated with assembling avian microchromosomes. These combined results illustrate the utility of applying homology-based methods for annotating novel vertebrate genomes.
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Affiliation(s)
- Paul P. Gardner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- * E-mail:
| | - Mario Fasold
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
- ecSeq Bioinformatics, Brandvorwerkstr.43, D-04275 Leipzig, Germany
| | - Sarah W. Burge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Ninova
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Jana Hertel
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Stephanie Kehr
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Tammy E. Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sam Griffiths-Jones
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany
- Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria
- Center for RNA in Technology and Health, Univ. Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, USA
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
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32
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Ge J, Chen Z, Li R, Lu T, Xiao G. Upregulation of microRNA-196a and microRNA-196b cooperatively correlate with aggressive progression and unfavorable prognosis in patients with colorectal cancer. Cancer Cell Int 2014; 14:128. [PMID: 25525411 PMCID: PMC4269845 DOI: 10.1186/s12935-014-0128-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 11/11/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Both microRNA (miR)-196a and miR-196b are implicated in normal cell differentiation, proliferation, and in tumorigenesis of various cancer types. Especially, miR-196a exerts a pro-oncogenic influence in colorectal cancer (CRC) cells and miR-196b expression is upregulated in CRC tissues. The aim of this study was to evaluate the associations of miR-196a and miR-196b dysregulation with clinicopathological characteristics and prognosis in patients with CRC. METHODS Quantitative real time-PCR (qRT-PCR) was performed to detect the expression levels of miR-196a and miR-196b in 126 pairs of fresh tumor samples matched with adjacent colorectal mucosa obtained from 126 patients with CRC. RESULTS miR-196a and miR-196b expression levels in CRC tissues were significantly higher than those in adjacent colorectal mucosa (both P < 0.002). Interestingly, the expression levels of miR-196a in CRC tissues were positively correlated with those of miR-196b. Then, high miR-196a expression and high miR-196b expression, alone or in combination, were all statistically linked to the presence of lymph node metastasis, the poor differentiation grade, and the advanced TNM stage of CRC. Moreover, overall and disease-free survivals of CRC patients with high miR-196a expression, high miR-196b expression and miR-196a-high/miR-196b-high expression tended to be shorter than the corresponding control groups (log-rank statistic, all P < 0.001). Furthermore, multivariate analysis indicated miR-196a and/or miR-196b expression as independent prognostic indicators for CRC patients (all P < 0.05). CONCLUSIONS Both miR-196a and miR-196b may be correlated with aggressive progression and unfavorable clinical outcome in CRC patients. Combined expression of miR-196a and miR-196b may be a promising biomarker in identifying a poor prognosis group of CRC.
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Affiliation(s)
- Jie Ge
- Department of General Surgery, Xiangya Hospital, Central South University, 87# Xiangya Road, Changsha, Hunan 410008 China
| | - Zihua Chen
- Department of General Surgery, Xiangya Hospital, Central South University, 87# Xiangya Road, Changsha, Hunan 410008 China
| | - Ruixing Li
- Department of General Surgery, Xiangya Hospital, Central South University, 87# Xiangya Road, Changsha, Hunan 410008 China
| | - Tailiang Lu
- Department of General Surgery, Xiangya Hospital, Central South University, 87# Xiangya Road, Changsha, Hunan 410008 China
| | - Guangfa Xiao
- Department of General Surgery, Xiangya Hospital, Central South University, 87# Xiangya Road, Changsha, Hunan 410008 China
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33
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Combined elevation of microRNA-196a and microRNA-196b in sera predicts unfavorable prognosis in patients with osteosarcomas. Int J Mol Sci 2014; 15:6544-55. [PMID: 24747591 PMCID: PMC4013646 DOI: 10.3390/ijms15046544] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 03/28/2014] [Accepted: 04/09/2014] [Indexed: 12/31/2022] Open
Abstract
AIM To investigate whether the aberrant expression of microRNA (miR)-196a and miR-196b can be used as potential prognostic markers of human osteosarcoma. METHODS Quantitative real-time reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis was performed to detect the expression levels of miR-196a and miR-196b in osteosarcoma tissues and patients' sera. RESULTS Expression levels of miR-196a and miR-196b in osteosarcoma tissues were both significantly higher than those in noncancerous bone tissues (both p<0.001), in line with which, the serum levels of the two miRNAs were also markedly upregulated in patients with osteosarcomas compared with healthy controls (both p<0.001). Then, the elevation of serum miR-196a and miR-196b levels both more frequently occurred in osteosarcoma patients with high tumor grade (p=0.008 and 0.01, respectively), positive metastasis (p=0.001 and 0.006, respectively) and recurrence (p=0.001 and 0.006, respectively). Moreover, high serum miR-196a, high serum miR-196b and conjoined expression of miR-196a/miR-196b were all independent prognostic factors for OS (overall survival) and DFS (disease-free survival) of osteosarcoma patients. CONCLUSION Our present data indicate the involvement of miR-196a and miR-196b upregulation in the pathogenesis of osteosarcoma. More importantly, the altered levels of circulating miR-196a and miR-196b might have great potential to serve as novel and non-invasive prognostic factors for this malignancy.
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Bhan A, Mandal SS. Long noncoding RNAs: emerging stars in gene regulation, epigenetics and human disease. ChemMedChem 2014; 9:1932-56. [PMID: 24677606 DOI: 10.1002/cmdc.201300534] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Indexed: 12/19/2022]
Abstract
Noncoding RNAs (ncRNAs) are classes of transcripts that are encoded by the genome and transcribed but never get translated into proteins. Though not translated into proteins, ncRNAs play pivotal roles in a variety of cellular functions. Here, we review the functions of long noncoding RNAs (lncRNAs) and their implications in various human diseases. Increasing numbers of studies demonstrate that lncRNAs play critical roles in regulation of protein-coding genes, maintenance of genomic integrity, dosage compensation, genomic imprinting, mRNA processing, cell differentiation, and development. Misregulation of lncRNAs is associated with a variety of human diseases, including cancer, immune and neurological disorders. Different classes of lncRNAs, their functions, mechanisms of action, and associations with different human diseases are summarized in detail, highlighting their as yet untapped potential in therapy.
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Affiliation(s)
- Arunoday Bhan
- Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019 (USA)
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35
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Li L, Liu B, Wapinski OL, Tsai MC, Qu K, Zhang J, Carlson JC, Lin M, Fang F, Gupta RA, Helms JA, Chang HY. Targeted disruption of Hotair leads to homeotic transformation and gene derepression. Cell Rep 2013; 5:3-12. [PMID: 24075995 DOI: 10.1016/j.celrep.2013.09.003] [Citation(s) in RCA: 258] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/30/2013] [Accepted: 09/02/2013] [Indexed: 12/22/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are thought to be prevalent regulators of gene expression, but the consequences of lncRNA inactivation in vivo are mostly unknown. Here, we show that targeted deletion of mouse Hotair lncRNA leads to derepression of hundreds of genes, resulting in homeotic transformation of the spine and malformation of metacarpal-carpal bones. RNA sequencing and conditional inactivation reveal an ongoing requirement of Hotair to repress HoxD genes and several imprinted loci such as Dlk1-Meg3 and Igf2-H19 without affecting imprinting choice. Hotair binds to both Polycomb repressive complex 2, which methylates histone H3 at lysine 27 (H3K27), and Lsd1 complex, which demethylates histone H3 at lysine 4 (H3K4) in vivo. Hotair inactivation causes H3K4me3 gain and, to a lesser extent, H3K27me3 loss at target genes. These results reveal the function and mechanisms of Hotair lncRNA in enforcing a silent chromatin state at Hox and additional genes.
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Affiliation(s)
- Lingjie Li
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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36
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Affiliation(s)
- Jennifer A. Marshall Graves
- La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne 3186, Australia
- Research School of Biology, Australian National University, Canberra 2060, Australia;
- Department of Zoology, University of Melbourne, Melbourne 3010, Australia
| | - Marilyn B. Renfree
- Department of Zoology, University of Melbourne, Melbourne 3010, Australia
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37
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Graves JAM. Kangaroo gene mapping and sequencing: insights into mammalian genome evolution. AUST J ZOOL 2013. [DOI: 10.1071/zo13002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The deep divergence of marsupials and eutherian mammals 160 million years ago provides genetic variation to explore the evolution of DNA sequence, gene arrangement and regulation of gene expression in mammals. Following the pioneering work of Professor Desmond W. Cooper, emerging techniques in cytogenetics and molecular biology have been adapted to characterise the genomes of kangaroos and other marsupials. In particular, genetic and genomic work over four decades has shown that marsupial sex chromosomes differ significantly from the eutherian XY chromosome pair in their size, gene content and activity. These differences can be exploited to deduce how mammalian sex chromosomes, sex determination and epigenetic silencing evolved.
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38
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Lindsay J, Carone DM, Brown J, Hall L, Qureshi S, Mitchell SE, Jannetty N, Hannon G, Renfree M, Pask A, O'Neill M, O'Neill R. Unique small RNA signatures uncovered in the tammar wallaby genome. BMC Genomics 2012; 13:559. [PMID: 23075437 PMCID: PMC3576234 DOI: 10.1186/1471-2164-13-559] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 10/08/2012] [Indexed: 12/12/2022] Open
Abstract
Background Small RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. The tammar wallaby, a marsupial mammal, is a powerful comparative model for studying the evolution of regulatory networks. As part of the genome sequencing initiative for the tammar, we have explored the evolution of each of the major classes of mammalian small RNAs in an Australian marsupial for the first time, including the first genome-scale analysis of the newest class of small RNAs, centromere repeat associated short interacting RNAs (crasiRNAs). Results Using next generation sequencing, we have characterized the major classes of small RNAs, micro (mi) RNAs, piwi interacting (pi) RNAs, and the centromere repeat associated short interacting (crasi) RNAs in the tammar. We examined each of these small RNA classes with respect to the newly assembled tammar wallaby genome for gene and repeat features, salient features that define their canonical sequences, and the constitution of both highly conserved and species-specific members. Using a combination of miRNA hairpin predictions and co-mapping with miRBase entries, we identified a highly conserved cluster of miRNA genes on the X chromosome in the tammar and a total of 94 other predicted miRNA producing genes. Mapping all miRNAs to the tammar genome and comparing target genes among tammar, mouse and human, we identified 163 conserved target genes. An additional nine genes were identified in tammar that do not have an orthologous miRNA target in human and likely represent novel miRNA-regulated genes in the tammar. A survey of the tammar gonadal piRNAs shows that these small RNAs are enriched in retroelements and carry members from both marsupial and tammar-specific repeat classes. Lastly, this study includes the first in-depth analyses of the newly discovered crasiRNAs. These small RNAs are derived largely from centromere-enriched retroelements, including a novel SINE. Conclusions This study encompasses the first analyses of the major classes of small RNAs for the newly completed tammar genome, validates preliminary annotations using deep sequencing and computational approaches, and provides a foundation for future work on tammar-specific as well as conserved, but previously unknown small RNA progenitors and targets identified herein. The characterization of new miRNA target genes and a unique profile for crasiRNAs has allowed for insight into multiple RNA mediated processes in the tammar, including gene regulation, species incompatibilities, centromere and chromosome function.
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Affiliation(s)
- James Lindsay
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
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Deakin JE. Marsupial genome sequences: providing insight into evolution and disease. SCIENTIFICA 2012; 2012:543176. [PMID: 24278712 PMCID: PMC3820666 DOI: 10.6064/2012/543176] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 09/26/2012] [Indexed: 05/08/2023]
Abstract
Marsupials (metatherians), with their position in vertebrate phylogeny and their unique biological features, have been studied for many years by a dedicated group of researchers, but it has only been since the sequencing of the first marsupial genome that their value has been more widely recognised. We now have genome sequences for three distantly related marsupial species (the grey short-tailed opossum, the tammar wallaby, and Tasmanian devil), with the promise of many more genomes to be sequenced in the near future, making this a particularly exciting time in marsupial genomics. The emergence of a transmissible cancer, which is obliterating the Tasmanian devil population, has increased the importance of obtaining and analysing marsupial genome sequence for understanding such diseases as well as for conservation efforts. In addition, these genome sequences have facilitated studies aimed at answering questions regarding gene and genome evolution and provided insight into the evolution of epigenetic mechanisms. Here I highlight the major advances in our understanding of evolution and disease, facilitated by marsupial genome projects, and speculate on the future contributions to be made by such sequences.
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Affiliation(s)
- Janine E. Deakin
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
- *Janine E. Deakin:
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