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Wong EWP, Sahin M, Yang R, Lee U, Zhan YA, Misra R, Tomas F, Alomran N, Polyzos A, Lee CJ, Trieu T, Fundichely AM, Wiesner T, Rosowicz A, Cheng S, Liu C, Lallo M, Merghoub T, Hamard PJ, Koche R, Khurana E, Apostolou E, Zheng D, Chen Y, Leslie CS, Chi P. TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596845. [PMID: 38895201 PMCID: PMC11185511 DOI: 10.1101/2024.05.31.596845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Transposable elements (TEs) are abundant in the human genome, and they provide the sources for genetic and functional diversity. The regulation of TEs expression and their functional consequences in physiological conditions and cancer development remain to be fully elucidated. Previous studies suggested TEs are repressed by DNA methylation and chromatin modifications. The effect of 3D chromatin topology on TE regulation remains elusive. Here, by integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. In cancer, perturbation of the hierarchical chromatin topology can lead to co-option of LTRs as functional alternative promoters in a context-dependent manner and drive aberrant transcriptional activation of novel oncogenes and other divergent transcripts. These data uncovered a new layer of regulatory mechanism of TE expression beyond DNA and chromatin modification in human genome. They also posit the TAD hierarchy dysregulation as a novel mechanism for alternative promoter-mediated oncogene activation and transcriptional diversity in cancer, which may be exploited therapeutically.
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Zhao N, Yin G, Liu C, Zhang W, Shen Y, Wang D, Lin Z, Yang J, Mao J, Guo R, Zhang Y, Wang F, Liu Z, Lu X, Liu L. Critically short telomeres derepress retrotransposons to promote genome instability in embryonic stem cells. Cell Discov 2023; 9:45. [PMID: 37130870 PMCID: PMC10154409 DOI: 10.1038/s41421-023-00538-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/08/2023] [Indexed: 05/04/2023] Open
Abstract
Telomeres, at the ends of chromosomes, protect chromosomes from fusion and preserve genomic stability. However, the molecular mechanisms underlying telomere attrition-induced genome instability remain to be understood. We systematically analyzed the expression of retrotransposons and performed genomic sequencing of different cell and tissue types with telomeres of varying lengths due to telomerase deficiency. We found that critically short telomeres altered retrotransposon activity to promote genomic instability in mouse embryonic stem cells, as evidenced by elevated numbers of single nucleotide variants, indels and copy number variations (CNVs). Transpositions of retrotransposons such as LINE1 resulting from the short telomeres can also be found in these genomes with elevated number of mutations and CNVs. Retrotransposon activation is linked to increased chromatin accessibility, and reduced heterochromatin abundance correlates with short telomeres. Re-elongation of telomeres upon recovery of telomerase partly represses retrotransposons and heterochromatin accumulation. Together, our findings suggest a potential mechanism by which telomeres maintain genomic stability by suppressing chromatin accessibility and retrotransposon activity.
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Affiliation(s)
- Nannan Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Guoxing Yin
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Chun Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- College of Pharmacy, Nankai University, Tianjin, China
| | - Yang Shen
- Genome Institute of Singapore, Singapore, Singapore
| | - Dan Wang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Immunology, Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhenzhen Lin
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Immunology, Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jiao Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Jian Mao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Renpeng Guo
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Yongwang Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- College of Pharmacy, Nankai University, Tianjin, China
| | - Feng Wang
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhe Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Immunology, Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.
- College of Pharmacy, Nankai University, Tianjin, China.
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China.
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
- Institute of Translational Medicine, Tianjin Union Medical Center, Nankai University, Tianjin, China.
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Barberet J, Ducreux B, Bruno C, Guilleman M, Simonot R, Lieury N, Guilloteau A, Bourc’his D, Fauque P. Comparison of oocyte vitrification using a semi-automated or a manual closed system in human siblings: survival and transcriptomic analyses. J Ovarian Res 2022; 15:128. [PMID: 36464714 PMCID: PMC9720994 DOI: 10.1186/s13048-022-01064-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/21/2022] [Indexed: 12/07/2022] Open
Abstract
BACKGROUND Indications of oocyte vitrification increased substantially over the last decades for clinical and ethical reasons. A semi-automated vitrification system was recently developed making each act of vitrification reproducible. In this study, we evaluated the efficiency of the semi-automated technique of oocyte vitrification by survival rate, morphometric assessment and resistance to empty micro-injection gesture as compared with a manual method. Additionally, we intended to evaluate transcriptomic consequences of both techniques using single-cell RNA-seq technology. RESULTS Post-warming survival rate, oocyte surfaces and resistance to empty micro-injection were comparable between semi-automated and manual vitrification groups. Both oocyte vitrification techniques showed limited differences in the resulting transcriptomic profile of sibling oocytes since only 5 differentially expressed genes were identified. Additionally, there was no difference in median transcript integrity number or percentage of mitochondrial DNA between the two groups. However, a total of 108 genes were differentially expressed between fresh and vitrified oocytes (FDR < 0.05) and showed over-represented of genes related to important cellular process. CONCLUSIONS Our results provide reassurance about the influence of semi-automation as compared with the manual vitrification method. Concerning oocyte vitrification itself, no tight common transcriptomic signature associated has been observed across studies. TRIAL REGISTRATION NCT03570073.
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Affiliation(s)
- Julie Barberet
- grid.493090.70000 0004 4910 6615Université Bourgogne Franche-Comté - Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France ,grid.31151.37CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction – CECOS, 14 rue Gaffarel, F-21000 Dijon, France
| | - Bastien Ducreux
- grid.493090.70000 0004 4910 6615Université Bourgogne Franche-Comté - Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France
| | - Céline Bruno
- grid.493090.70000 0004 4910 6615Université Bourgogne Franche-Comté - Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France ,grid.31151.37CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction – CECOS, 14 rue Gaffarel, F-21000 Dijon, France
| | - Magali Guilleman
- grid.493090.70000 0004 4910 6615Université Bourgogne Franche-Comté - Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France ,grid.31151.37CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction – CECOS, 14 rue Gaffarel, F-21000 Dijon, France
| | - Raymond Simonot
- grid.31151.37CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction – CECOS, 14 rue Gaffarel, F-21000 Dijon, France
| | - Nicolas Lieury
- grid.31151.37CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction – CECOS, 14 rue Gaffarel, F-21000 Dijon, France
| | - Adrien Guilloteau
- grid.31151.37USMR, Dijon Bourgogne University Hospital, F-21000 Dijon, France
| | - Déborah Bourc’his
- Institut Curie, PSL University, CNRS, INSERM, 26 rue d’Ulm, F-75248 Paris, France
| | - Patricia Fauque
- grid.493090.70000 0004 4910 6615Université Bourgogne Franche-Comté - Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France ,grid.31151.37CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction – CECOS, 14 rue Gaffarel, F-21000 Dijon, France ,grid.31151.37Laboratoire de Biologie de la Reproduction, CHU Dijon, BP 77908, 14, rue Gaffarel, 21079 Dijon Cedex, France
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Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements. BIOLOGY 2021; 10:biology10090896. [PMID: 34571773 PMCID: PMC8465862 DOI: 10.3390/biology10090896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/22/2022]
Abstract
Simple Summary Transposable elements (TEs) are DNA sequences that are, or were, able to move (transpose) within the genome of a single cell. They were first discovered by Barbara McClintock while working on maize, and they make up a large fraction of the genome. Transpositions can result in mutations and they can alter the genome size. Cells regulate the activity of TEs using a variety of mechanisms, such as chemical modifications of DNA and small RNAs. Machine learning (ML) is an interdisciplinary subject that studies computer algorithms that can improve through experience and by the use of data. ML has been successfully applied to a variety of problems in bioinformatics and has exhibited favorable precision and speed. Here, we provide a systematic and guided review on the ML and bioinformatic methods and tools that are used for the analysis of the regulation of TEs. Abstract Transposable elements (TEs, or mobile genetic elements, MGEs) are ubiquitous genetic elements that make up a substantial proportion of the genome of many species. The recent growing interest in understanding the evolution and function of TEs has revealed that TEs play a dual role in genome evolution, development, disease, and drug resistance. Cells regulate TE expression against uncontrolled activity that can lead to developmental defects and disease, using multiple strategies, such as DNA chemical modification, small RNA (sRNA) silencing, chromatin modification, as well as sequence-specific repressors. Advancements in bioinformatics and machine learning approaches are increasingly contributing to the analysis of the regulation mechanisms. A plethora of tools and machine learning approaches have been developed for prediction, annotation, and expression profiling of sRNAs, for methylation analysis of TEs, as well as for genome-wide methylation analysis through bisulfite sequencing data. In this review, we provide a guided overview of the bioinformatic and machine learning state of the art of fields closely associated with TE regulation and function.
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Pourrajab F, Hekmatimoghaddam S. Transposable elements, contributors in the evolution of organisms (from an arms race to a source of raw materials). Heliyon 2021; 7:e06029. [PMID: 33532648 PMCID: PMC7829209 DOI: 10.1016/j.heliyon.2021.e06029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/08/2020] [Accepted: 01/13/2021] [Indexed: 12/19/2022] Open
Abstract
There is a concept proposing that the primitive lineages of prokaryotes, eukaryotes, and viruses emerged from the primordial pool of primitive genetic elements. In this genetic pool, transposable elements (TEs) became a source of raw material for primitive genomes, tools of genetic innovation, and ancestors of modern genes (e.g. ncRNAs, tRNAs, and rRNAs). TEs contributed directly to the genome evolution of three forms of life on the earth. TEs now appear as tools that were used to giving rise to sexual dimorphism and sex determination, lineage-specific expression of genes and tissue differentiation and finally genome stability and lifespan determination.
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Affiliation(s)
- Fatemeh Pourrajab
- Nutrition and Food Security Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Department of Biochemistry and Molecular Biology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Seyedhossein Hekmatimoghaddam
- Department of Advanced Medical Sciences and Technologies, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Department of Laboratory Sciences, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Layton E, Fairhurst AM, Griffiths-Jones S, Grencis RK, Roberts IS. Regulatory RNAs: A Universal Language for Inter-Domain Communication. Int J Mol Sci 2020; 21:E8919. [PMID: 33255483 PMCID: PMC7727864 DOI: 10.3390/ijms21238919] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
In eukaryotes, microRNAs (miRNAs) have roles in development, homeostasis, disease and the immune response. Recent work has shown that plant and mammalian miRNAs also mediate cross-kingdom and cross-domain communications. However, these studies remain controversial and are lacking critical mechanistic explanations. Bacteria do not produce miRNAs themselves, and therefore it is unclear how these eukaryotic RNA molecules could function in the bacterial recipient. In this review, we compare and contrast the biogenesis and functions of regulatory RNAs in eukaryotes and bacteria. As a result, we discovered several conserved features and homologous components in these distinct pathways. These findings enabled us to propose novel mechanisms to explain how eukaryotic miRNAs could function in bacteria. Further understanding in this area is necessary to validate the findings of existing studies and could facilitate the use of miRNAs as novel tools for the directed remodelling of the human microbiota.
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Affiliation(s)
- Emma Layton
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
| | - Anna-Marie Fairhurst
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore;
| | - Sam Griffiths-Jones
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Richard K. Grencis
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
| | - Ian S. Roberts
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
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Arroyo M, Bautista R, Larrosa R, Cobo MÁ, Claros MG. Biomarker potential of repetitive-element transcriptome in lung cancer. PeerJ 2019; 7:e8277. [PMID: 31875158 PMCID: PMC6925957 DOI: 10.7717/peerj.8277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/22/2019] [Indexed: 12/11/2022] Open
Abstract
Since repetitive elements (REs) account for nearly 53% of the human genome, profiling its transcription after an oncogenic change might help in the search for new biomarkers. Lung cancer was selected as target since it is the most frequent cause of cancer death. A bioinformatic workflow based on well-established bioinformatic tools (such as RepEnrich, RepBase, SAMTools, edgeR and DESeq2) has been developed to identify differentially expressed RNAs from REs. It was trained and tested with public RNA-seq data from matched sequencing of tumour and healthy lung tissues from the same patient to reveal differential expression within the RE transcriptome. Healthy lung tissues express a specific set of REs whose expression, after an oncogenic process, is strictly and specifically changed. Discrete sets of differentially expressed REs were found for lung adenocarcinoma, for small-cell lung cancer, and for both cancers. Differential expression affects more HERV-than LINE-derived REs and seems biased towards down-regulation in cancer cells. REs behaving consistently in all patients were tested in a different patient cohort to validate the proposed biomarkers. Down-regulation of AluYg6 and LTR18B was confirmed as potential lung cancer biomarkers, while up-regulation of HERVK11D-Int is specific for lung adenocarcinoma and up-regulation of UCON88 is specific for small cell lung cancer. Hence, the study of RE transcriptome might be considered another research target in cancer, making REs a promising source of lung cancer biomarkers.
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Affiliation(s)
- Macarena Arroyo
- U.G.C. Médico-Quirúrgica de Enfermedades Respiratorias, Hospital Regional Universitario de Málaga, Málaga, Spain.,Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, Spain
| | - Rocío Bautista
- Andalusian Platform for Bioinformatics-SCBI, Universidad de Málaga, Málaga, Spain
| | - Rafael Larrosa
- Andalusian Platform for Bioinformatics-SCBI, Universidad de Málaga, Málaga, Spain.,Department of Computer Architecture, Universidad de Málaga, Málaga, Spain
| | - Manuel Ángel Cobo
- Area of Oncology and Rare Diseases (IBIMA), Hospital Regional Universitario de Málaga, Málaga, Spain
| | - M Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, Spain.,Andalusian Platform for Bioinformatics-SCBI, Universidad de Málaga, Málaga, Spain.,Area of Oncology and Rare Diseases (IBIMA), Hospital Regional Universitario de Málaga, Málaga, Spain
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Computational Resources for Prediction and Analysis of Functional miRNA and Their Targetome. Methods Mol Biol 2019; 1912:215-250. [PMID: 30635896 DOI: 10.1007/978-1-4939-8982-9_9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
microRNAs are evolutionarily conserved, endogenously produced, noncoding RNAs (ncRNAs) of approximately 19-24 nucleotides (nts) in length known to exhibit gene silencing of complementary target sequence. Their deregulated expression is reported in various disease conditions and thus has therapeutic implications. In the last decade, various computational resources are published in this field. In this chapter, we have reviewed bioinformatics resources, i.e., miRNA-centered databases, algorithms, and tools to predict miRNA targets. First section has enlisted more than 75 databases, which mainly covers information regarding miRNA registries, targets, disease associations, differential expression, interactions with other noncoding RNAs, and all-in-one resources. In the algorithms section, we have compiled about 140 algorithms from eight subcategories, viz. for the prediction of precursor (pre-) and mature miRNAs. These algorithms are developed on various sequence, structure, and thermodynamic based features incorporated into different machine learning techniques (MLTs). In addition, computational identification of miRNAs from high-throughput next generation sequencing (NGS) data and their variants, viz. isomiRs, differential expression, miR-SNPs, and functional annotation, are discussed. Prediction and analysis of miRNAs and their associated targets are also evaluated under miR-targets section providing knowledge regarding novel miRNA targets and complex host-pathogen interactions. In conclusion, we have provided comprehensive review of in silico resources published in miRNA research to help scientific community be updated and choose the appropriate tool according to their needs.
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Jo A, Lee HE, Kim HS. Identification and expression analysis of a novel miRNA derived from ERV-E1 LTR in Equus caballus. Gene 2018; 687:238-245. [PMID: 30453070 DOI: 10.1016/j.gene.2018.11.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 12/12/2022]
Abstract
Horses (Equus caballus) have been domesticated and bred to enhance speed, strength, and agility. Members of the Equus caballus Endogenous Retrovirus (EqERV) family affect several of these abilities in horses. EqERV elements have been integrated in the horse genome during evolution and generate repeat elements such as long terminal repeats (LTRs). LTR sequences are involved in retrovirus replication and play an essential function in post-transcriptional control mechanisms, such as by providing binding sites for microRNAs (miRNAs) or generating miRNA precursors. In this study, we identified a novel miRNA derived from EqERV-E1 LTR using various bioinformatics tools. To examine the relationship between EqERV-E1 LTR and similar elements, we used BLAST2seq and phylogenetic analysis. LTR sequences were located in the untranslated region (UTR) of mRNAs and also formed the stem-loop secondary structure. The sequence was registered in the DDBJ database as LTR derived miRNA under the accession number corresponding to LC383797 (referred to eca-miR-1804). Quantitative polymerase chain reaction (qPCR) to confirm the expression of eca-miR-1804 and the similar miR-1255a, showed an almost identical expression pattern in eight different equine tissues. Therefore, these data imply that the LTR could function as an miRNA, which is expressed in the examined equine tissues. In addition, the current study provides inputs for additional functional studies concerning the LTR of other EqERV families.
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Affiliation(s)
- Ara Jo
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Institute of Systems Biology, 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; Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea.
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Serum microRNA Expression Profiling: Potential Diagnostic Implications of a Panel of Serum microRNAs for Clear Cell Renal Cell Cancer. Urology 2017; 104:64-69. [PMID: 28336290 DOI: 10.1016/j.urology.2017.03.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/20/2017] [Accepted: 03/07/2017] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To study the expression profiles of 5 microRNAs in tissue and serum of patients with clear cell renal cell cancer (ccRCC) and evaluate their diagnostic and prognostic potential. MATERIALS AND METHODS We prospectively analyzed 30 patients of histologically proven ccRCC and collected 3 mL of serum preoperatively and small pieces of tumor and adjacent non-tumor renal tissue intraoperatively. Control serum samples were obtained from 15 patients of non-renal benign diseases. We analyzed 5 miRNAs-miR-34a, miR-141, miR-200c, miR-1233, and miR-21-2. Freshly collected samples were immediately frozen in liquid nitrogen and total RNA was extracted. cDNA was synthesized by reverse transcription, and quantitative polymerase chain reaction was performed to determine relative miRNA expression. RESULTS In the renal tissue and serum samples, 3 out of 5 miRNAs were differentially expressed; that is, the expression levels of miR-34a and miR-141 were significantly decreased, whereas that of miR-1233 was significantly increased. Serum miR-34a, miR-141, and miR-1233 were able to diagnose ccRCC with a sensitivity of 80.76%, 75%, and 93.33%, and specificity of 80%, 73.33%, and 100%, respectively, as compared to histopathology. Using a panel of 2 serum miRNAs (miR-141 and miR-1233) ccRCC can be diagnosed with 100% sensitivity and 73.3% specificity. CONCLUSION miRNAs are differentially expressed in serum of patients with ccRCC and can be used to diagnose ccRCC with high sensitivity and specificity. Diagnostic sensitivity can be further improved by using a panel of miRNAs and has the potential to serve as novel diagnostic markers of ccRCC.
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Hu T, Zhu X, Pi W, Yu M, Shi H, Tuan D. Hypermethylated LTR retrotransposon exhibits enhancer activity. Epigenetics 2017; 12:226-237. [PMID: 28165867 DOI: 10.1080/15592294.2017.1289300] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
LTR retrotransposons are repetitive DNA elements comprising ∼10% of the human genome. They are silenced by hypermethylation of cytosines in CpG dinucleotides and are considered parasitic DNA serving no useful function for the host genome. However, hypermethylated LTRs contain enhancer and promoter sequences and can promote tissue-specific transcription of cis-linked genes. To resolve the apparent paradox of hypermethylated LTRs possessing transcriptional activities, we studied the ERV-9 LTR retrotransposon located at the 5' border of the transcriptionally active β-globin gene locus in human erythroid progenitor and erythroleukemia K562 cells. We found that the ERV-9 LTR, containing 65 CpGs in 1.7 kb DNA, was hypermethylated (with > 90% methylated CpGs). Hypermethylated LTR possessed transcriptional enhancer activity, since in vivo deletion of the LTR by CRISPR-cas9 suppressed transcription of the globin genes by > 50%. ChIP-qPCR and ChIP-seq studies showed that the hypermethylated LTR enhancer spanning recurrent CCAATCG and GATA motifs associated respectively with key transcription factors (TFs) NF-Y and GATA-1 and -2 at reduced levels, compared with the unmethylated LTR in transfected LTR-reporter gene plasmids. Electrophoretic mobility shift assays with methylated LTR enhancer probe showed that the methylated probe bound both NF-Y and GATA-1 and -2 with lower affinities than the unmethylated enhancer probe. Thus, hypermethylation drastically reduced, but did not totally abolish, the binding affinities of the enhancer motifs to the key TFs to assemble the LTR-pol II transcription complex that activated transcription of cis-linked genes at reduced efficiency.
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Affiliation(s)
- Tianxiang Hu
- a Department of Biochemistry and Molecular Biology , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Xingguo Zhu
- a Department of Biochemistry and Molecular Biology , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Wenhu Pi
- a Department of Biochemistry and Molecular Biology , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Miao Yu
- b Georgia Cancer Center , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Huidong Shi
- b Georgia Cancer Center , Medical College of Georgia, Augusta University , Augusta , GA , USA
| | - Dorothy Tuan
- a Department of Biochemistry and Molecular Biology , Medical College of Georgia, Augusta University , Augusta , GA , USA
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Nguyen TC, Cao X, Yu P, Xiao S, Lu J, Biase FH, Sridhar B, Huang N, Zhang K, Zhong S. Mapping RNA-RNA interactome and RNA structure in vivo by MARIO. Nat Commun 2016; 7:12023. [PMID: 27338251 PMCID: PMC4931010 DOI: 10.1038/ncomms12023] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 05/19/2016] [Indexed: 12/29/2022] Open
Abstract
The pervasive transcription of our genome presents a possibility of revealing new genomic functions by investigating RNA interactions. Current methods for mapping RNA–RNA interactions have to rely on an ‘anchor' protein or RNA and often require molecular perturbations. Here we present the MARIO (Mapping RNA interactome in vivo) technology to massively reveal RNA–RNA interactions from unperturbed cells. We mapped tens of thousands of endogenous RNA–RNA interactions from mouse embryonic stem cells and brain. We validated seven interactions by RNA antisense purification and one interaction using single-molecule RNA–FISH. The experimentally derived RNA interactome is a scale-free network, which is not expected from currently perceived promiscuity in RNA–RNA interactions. Base pairing is observed at the interacting regions between long RNAs, including transposon transcripts, suggesting a class of regulatory sequences acting in trans. In addition, MARIO data reveal thousands of intra-molecule interactions, providing in vivo data on high-order RNA structures. Current methods for mapping RNA-RNA interactions have to rely on an ‘anchor' protein or RNA. Here, the authors report the MARIO (Mapping RNA interactome in vivo) technology that can massively reveal RNA-RNA interactions and RNA structure from unperturbed cells.
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Affiliation(s)
- Tri C Nguyen
- Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA
| | - Xiaoyi Cao
- Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA
| | - Pengfei Yu
- Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA
| | - Shu Xiao
- Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA
| | - Jia Lu
- Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA
| | - Fernando H Biase
- Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA
| | - Bharat Sridhar
- Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA
| | - Norman Huang
- Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA
| | - Kang Zhang
- Department of Ophthalmology, University of California, San Diego, La Jolla, California 92093, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA
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Cabrera J, Barcala M, García A, Rio-Machín A, Medina C, Jaubert-Possamai S, Favery B, Maizel A, Ruiz-Ferrer V, Fenoll C, Escobar C. Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica: a functional role for miR390 and its TAS3-derived tasiRNAs. THE NEW PHYTOLOGIST 2016; 209:1625-40. [PMID: 26542733 DOI: 10.1111/nph.13735] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/25/2015] [Indexed: 05/20/2023]
Abstract
Root-knot nematodes (RKNs) induce inside the vascular cylinder the giant cells (GCs) embedded in the galls. The distinctive gene repression in early-developing GCs could be facilitated by small RNAs (sRNA) such as miRNAs, and/or epigenetic mechanisms mediated by 24nt-sRNAs, rasiRNAs and 21-22nt-sRNAs. Therefore, the sRNA-population together with the role of the miR390/TAS3/ARFs module were studied during early gall/GC formation. Three sRNA libraries from 3-d-post-inoculation (dpi) galls induced by Meloidogyne javanica in Arabidopsis and three from uninfected root segments were sequenced following Illumina-Solexa technology. pMIR390a::GUS and pTAS3::GUS lines were assayed for nematode-dependent promoter activation. A sensor line indicative of TAS3-derived tasiRNAs binding to the ARF3 sequence (pARF3:ARF3-GUS) together with a tasiRNA-resistant ARF3 line (pARF3:ARF3m-GUS) were used for functional analysis. The sRNA population showed significant differences between galls and controls, with high validation rate and correspondence with their target expression: 21-nt sRNAs corresponding mainly to miRNAs were downregulated, whilst 24-nt-sRNAs from the rasiRNA family were mostly upregulated in galls. The promoters of MIR390a and TAS3, active in galls, and the pARF3:ARF3-GUS line, indicated a role of TAS3-derived-tasiRNAs in galls. The regulatory module miR390/TAS3 is necessary for proper gall formation possibly through auxin-responsive factors, and the abundance of 24-nt sRNAs (mostly rasiRNAs) constitutes a gall hallmark.
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Affiliation(s)
- Javier Cabrera
- Universidad de Castilla-La Mancha, Facultad de Ciencias Ambientales y Bioquímica, Avda. Carlos III, s/n 45071, Toledo, Spain
| | - Marta Barcala
- Universidad de Castilla-La Mancha, Facultad de Ciencias Ambientales y Bioquímica, Avda. Carlos III, s/n 45071, Toledo, Spain
| | - Alejandra García
- Universidad de Castilla-La Mancha, Facultad de Ciencias Ambientales y Bioquímica, Avda. Carlos III, s/n 45071, Toledo, Spain
| | - Ana Rio-Machín
- Molecular Cytogenetics Group, Human Cancer Genetics Programme, Centro Nacional Investigaciones Oncológicas (CNIO), C/Melchor Fernández Almagro, 3, 28029 , Madrid, Spain
| | - Clémence Medina
- INRA, Université Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Stephanie Jaubert-Possamai
- INRA, Université Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Bruno Favery
- INRA, Université Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Alexis Maizel
- Centre for Organismal Studies University of Heidelberg, Im Neuenheimer Feld, 230-69120, Heidelberg, Germany
| | - Virginia Ruiz-Ferrer
- Centro de Investigaciones Biológicas, CSIC, Av. Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Carmen Fenoll
- Universidad de Castilla-La Mancha, Facultad de Ciencias Ambientales y Bioquímica, Avda. Carlos III, s/n 45071, Toledo, Spain
| | - Carolina Escobar
- Universidad de Castilla-La Mancha, Facultad de Ciencias Ambientales y Bioquímica, Avda. Carlos III, s/n 45071, Toledo, Spain
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14
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Gebert D, Rosenkranz D. RNA-based regulation of transposon expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:687-708. [DOI: 10.1002/wrna.1310] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/08/2015] [Accepted: 09/13/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Daniel Gebert
- Institute of Anthropology; Johannes Gutenberg University; Mainz Germany
| | - David Rosenkranz
- Institute of Anthropology; Johannes Gutenberg University; Mainz Germany
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15
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Morales ME, Servant G, Ade C, Roy-Enge AM. Altering Genomic Integrity: Heavy Metal Exposure Promotes Transposable Element-Mediated Damage. Biol Trace Elem Res 2015; 166:24-33. [PMID: 25774044 PMCID: PMC4696754 DOI: 10.1007/s12011-015-0298-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/03/2015] [Indexed: 12/13/2022]
Abstract
Maintenance of genomic integrity is critical for cellular homeostasis and survival. The active transposable elements (TEs) composed primarily of three mobile element lineages LINE-1, Alu, and SVA comprise approximately 30% of the mass of the human genome. For the past 2 decades, studies have shown that TEs significantly contribute to genetic instability and that TE-caused damages are associated with genetic diseases and cancer. Different environmental exposures, including several heavy metals, influence how TEs interact with its host genome increasing their negative impact. This mini-review provides some basic knowledge on TEs, their contribution to disease, and an overview of the current knowledge on how heavy metals influence TE-mediated damage.
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Affiliation(s)
- Maria E. Morales
- Department of Epidemiology and Tulane Cancer Center, SL-66, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Geraldine Servant
- Department of Epidemiology and Tulane Cancer Center, SL-66, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Catherine Ade
- Department of Cellular and Molecular Biology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Astrid M. Roy-Enge
- Department of Epidemiology and Tulane Cancer Center, SL-66, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
- Corresponding author: Astrid M. Roy-Engel, Ph.D., Department of Epidemiology, Tulane Cancer Center, SL66, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112. , Phone: (504) 988-6316, Fax: (504) 988-5516
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16
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Sadovsky Y, Mouillet JF, Ouyang Y, Bayer A, Coyne CB. The Function of TrophomiRs and Other MicroRNAs in the Human Placenta. Cold Spring Harb Perspect Med 2015; 5:a023036. [PMID: 25877393 DOI: 10.1101/cshperspect.a023036] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In eutherian organisms, the placenta interfaces the fetal and maternal environments. Located at the placental villous surface, in direct contact with maternal blood, is the trophoblast layer, which mediates the crucial maternal-fetal exchange of gases, nutrients, and waste products, produces hormones that support the pregnancy, and provides immunologic defense. Discovery of microRNAs (miRNAs) and their role in development, differentiation, and homeostatic resilience has increased our understanding of genomic and epigenomic networks that regulate placental function. Moreover, unique miRNA species, which are expressed by human trophoblasts and are termed "trophomiRs," may show specialized functions during normal and pathological pregnancies. Placental miRNAs, packaged within exosomes and other vesicles or bound in protein complexes, are capable of communicating distinctive signals to maternal and/or fetal tissues. Additional research may usher in the use of circulating miRNAs as pregnancy-related disease biomarkers, providing new diagnostic and therapeutic options during pregnancy.
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Affiliation(s)
- Yoel Sadovsky
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15213 Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
| | - Jean-Francois Mouillet
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Yingshi Ouyang
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Avraham Bayer
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Carolyn B Coyne
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
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17
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Hoffman Y, Pilpel Y, Oren M. microRNAs and Alu elements in the p53-Mdm2-Mdm4 regulatory network. J Mol Cell Biol 2015; 6:192-7. [PMID: 24868102 DOI: 10.1093/jmcb/mju020] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
p53 is a transcription factor that governs numerous stress response pathways within the cell. Maintaining the right levels of p53 is crucial for cell survival and proper cellular homeostasis. The tight regulation of p53 involves many cellular components, most notably its major negative regulators Mdm2 and Mdm4, which maintain p53 protein amount and activity in tight check. microRNAs (miRNAs) are small non-coding RNAs that target specific mRNAs to translational arrest and degradation. miRNAs are also key components of the normal p53 pathway, joining forces with Mdm2 and Mdm4 to maintain proper p53 activity. Here we review the current knowledge of miRNAs targeting Mdm2 and Mdm4, and their importance in different tissues and in pathological states such as cancer. In addition, we address the role of Alu sequences-highly abundant retroelements spread throughout the human genome, and their impact on gene regulation via the miRNA machinery. Alus occupy a significant portion of genes' 3'UTR, and as such they have the potential to impact mRNA regulation. Since Alus are primate-specific, they introduce a new regulatory layer into primate genomes. Alus can influence and alter gene regulation, creating primate-specific cancer-preventive regulatory mechanisms to sustain the transition to longer life span in primates. We review the possible influence of Alu sequences on miRNA functionality in general and specifically within the p53 network.
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Affiliation(s)
- Yonit Hoffman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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18
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Mouillet JF, Ouyang Y, Bayer A, Coyne CB, Sadovsky Y. The role of trophoblastic microRNAs in placental viral infection. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2015; 58:281-9. [PMID: 25023694 DOI: 10.1387/ijdb.130349ys] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During the past decade, various types of small non-coding RNAs were found to be expressed in all kingdoms and phyla of life. Intense research efforts have begun to shed light on their biological functions, although much remains to be determined in order to fully characterize their scope of biological action. Typically, small RNAs provide sequence specificity to a protein complex that is driven to silence a long target RNA. MicroRNAs (miRNAs) are small RNAs that are coded in the genome of most eukaryotes, and contribute to the cellular identity by regulating cell-specific gene networks by translational repression or degradation of mRNA. These effects commonly fine-tune gene expression associated with developmental or environmental cues. Different cell types can be characterized by their distinctive cellular miRNA landscape. The human placenta expresses a unique set of miRNAs, a high proportion of which is derived from a large cluster located on chromosome 19, (termed chromosome 19 miRNA cluster, or C19MC). Interestingly, a fraction of these placenta-enriched miRNAs are released to the extracellular environment through exosomes that were recently found to induce an antiviral immunity. In this review, we explore relevant placental viral infections and discuss the antiviral role of exosome-packaged placental C19MC miRNAs in this context.
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Affiliation(s)
- Jean-Francois Mouillet
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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19
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Kan CWS, Howell VM, Hahn MA, Marsh DJ. Genomic alterations as mediators of miRNA dysregulation in ovarian cancer. Genes Chromosomes Cancer 2014; 54:1-19. [PMID: 25280227 DOI: 10.1002/gcc.22221] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 09/10/2014] [Indexed: 12/18/2022] Open
Abstract
Ovarian cancer is the fifth most common cause of cancer death in women worldwide. Serous epithelial ovarian cancer (SEOC) is the most common and aggressive histological subtype. Widespread genomic alterations go hand-in-hand with aberrant DNA damage signaling and are a hallmark of high-grade SEOC. MicroRNAs (miRNAs) are a class of small noncoding RNA molecules that are nonrandomly distributed in the genome. They are frequently located in chromosomal regions susceptible to copy number variation (CNV) associated with malignancy that can influence their expression. Widespread changes in miRNA expression have been reported in multiple cancer types including ovarian cancer. This review examines CNV and single nucleotide polymorphisms, two common types of genomic alterations that occur in ovarian cancer, in the context of their influence on the expression of miRNA and the ability of miRNA to bind to and regulate their target genes. This includes genes encoding proteins involved in DNA repair and the maintenance of genomic stability. Improved understanding of mechanisms of miRNA dysregulation and the role of miRNA in ovarian cancer will provide further insight into the pathogenesis and treatment of this disease.
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Affiliation(s)
- Casina W S Kan
- Hormones and Cancer Group, Kolling Institute of Medical Research, University of Sydney, Royal North Shore Hospital, St Leonards, Sydney, NSW 2065, Australia
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20
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Sedivy JM, Kreiling JA, Neretti N, De Cecco M, Criscione SW, Hofmann JW, Zhao X, Ito T, Peterson AL. Death by transposition - the enemy within? Bioessays 2013; 35:1035-43. [PMID: 24129940 PMCID: PMC3922893 DOI: 10.1002/bies.201300097] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Here we present and develop the hypothesis that the derepression of endogenous retrotransposable elements (RTEs) – genomic parasites – is an important and hitherto under-unexplored molecular aging process that can potentially occur in most tissues. We further envision that the activation and continued presence of retrotransposition contribute to age-associated tissue degeneration and pathology. Chromatin is a complex and dynamic structure that needs to be maintained in a functional state throughout our lifetime. Studies of diverse species have revealed that chromatin undergoes extensive rearrangements during aging. Cellular senescence, an important component of mammalian aging, has recently been associated with decreased heterochromatinization of normally silenced regions of the genome. These changes lead to the expression of RTEs, culminating in their transposition. RTEs are common in all kingdoms of life, and comprise close to 50% of mammalian genomes. They are tightly controlled, as their activity is highly destabilizing and mutagenic to their resident genomes.
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Affiliation(s)
- John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
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21
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De Cecco M, Criscione SW, Peckham EJ, Hillenmeyer S, Hamm EA, Manivannan J, Peterson AL, Kreiling JA, Neretti N, Sedivy JM. Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements. Aging Cell 2013; 12:247-56. [PMID: 23360310 DOI: 10.1111/acel.12047] [Citation(s) in RCA: 295] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2013] [Indexed: 11/28/2022] Open
Abstract
Replicative cellular senescence is an important tumor suppression mechanism and also contributes to aging. Progression of both cancer and aging include significant epigenetic components, but the chromatin changes that take place during cellular senescence are not known. We used formaldehyde assisted isolation of regulatory elements (FAIRE) to map genome-wide chromatin conformations. In contrast to growing cells, whose genomes are rich with features of both open and closed chromatin, FAIRE profiles of senescent cells are significantly smoothened. This is due to FAIRE signal loss in promoters and enhancers of active genes, and FAIRE signal gain in heterochromatic gene-poor regions. Chromatin of major retrotransposon classes, Alu, SVA and L1, becomes relatively more open in senescent cells, affecting most strongly the evolutionarily recent elements, and leads to an increase in their transcription and ultimately transposition. Constitutive heterochromatin in centromeric and peri-centromeric regions also becomes relatively more open, and the transcription of satellite sequences increases. The peripheral heterochromatic compartment (PHC) becomes less prominent, and centromere structure becomes notably enlarged. These epigenetic changes progress slowly after the onset of senescence, with some, such as mobilization of retrotransposable elements becoming prominent only at late times. Many of these changes have also been noted in cancer cells.
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Affiliation(s)
- Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Steven W. Criscione
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Edward J. Peckham
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Sara Hillenmeyer
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Eliza A. Hamm
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Jayameenakshi Manivannan
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Abigail L. Peterson
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Jill A. Kreiling
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - John M. Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
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22
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Hoffman Y, Dahary D, Bublik DR, Oren M, Pilpel Y. The majority of endogenous microRNA targets within Alu elements avoid the microRNA machinery. Bioinformatics 2013; 29:894-902. [DOI: 10.1093/bioinformatics/btt044] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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23
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Wang JW, Li K, Hellermann G, Lockey RF, Mohapatra S, Mohapatra S. Regulating the Regulators: microRNA and Asthma. World Allergy Organ J 2013; 4:94-103. [PMID: 23282474 PMCID: PMC3651079 DOI: 10.1186/1939-4551-4-6-94] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
One obstacle to developing an effective therapeutic strategy to treat or prevent asthma is that the fundamental causes of asthma are not totally understood. Asthma is thought to be a chronic TH2 immune-mediated inflammatory disease. Epigenetic changes are recognized to play a role in the initiation and maintenance of a TH2 response. MicroRNAs (miRNAs) are key epigenetic regulators of gene expression, and their expression is highly regulated, therefore, deregulation of miRNAs may play an important role in the pathogenesis of asthma. Profiling circulating miRNA might provide the highest specificity and sensitivity to diagnose asthma; similarly, correcting potential defects in the miRNA regulation network may lead to new therapeutic modalities to treat this disease.
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Affiliation(s)
- Jia-Wang Wang
- Department of Internal Medicine Division of Translational Medicine and Nanomedicine Research Center1, and Division of Allergy and Immunology2, Department of Molecular Medicine3, University of South Florida College of Medicine, and James A. Haley VA Hospital and Medical Research Center4, Tampa, FL 33612
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24
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Santana MF, Silva JCF, Batista AD, Ribeiro LE, da Silva GF, de Araújo EF, de Queiroz MV. Abundance, distribution and potential impact of transposable elements in the genome of Mycosphaerella fijiensis. BMC Genomics 2012; 13:720. [PMID: 23260030 PMCID: PMC3562529 DOI: 10.1186/1471-2164-13-720] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 12/20/2012] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Mycosphaerella fijiensis is a ascomycete that causes Black Sigatoka in bananas. Recently, the M. fijiensis genome was sequenced. Repetitive sequences are ubiquitous components of fungal genomes. In most genomic analyses, repetitive sequences are associated with transposable elements (TEs). TEs are dispersed repetitive DNA sequences found in a host genome. These elements have the ability to move from one location to another within the genome, and their insertion can cause a wide spectrum of mutations in their hosts. Some of the deleterious effects of TEs may be due to ectopic recombination among TEs of the same family. In addition, some transposons are physically linked to genes and can control their expression. To prevent possible damage caused by the presence of TEs in the genome, some fungi possess TE-silencing mechanisms, such as RIP (Repeat Induced Point mutation). In this study, the abundance, distribution and potential impact of TEs in the genome of M. fijiensis were investigated. RESULTS A total of 613 LTR-Gypsy and 27 LTR-Copia complete elements of the class I were detected. Among the class II elements, a total of 28 Mariner, five Mutator and one Harbinger complete elements were identified. The results of this study indicate that transposons were and are important ectopic recombination sites. A distribution analysis of a transposable element from each class of the M. fijiensis isolates revealed variable hybridization profiles, indicating the activity of these elements. Several genes encoding proteins involved in important metabolic pathways and with potential correlation to pathogenicity systems were identified upstream and downstream of transposable elements. A comparison of the sequences from different transposon groups suggested the action of the RIP silencing mechanism in the genome of this microorganism. CONCLUSIONS The analysis of TEs in M. fijiensis suggests that TEs play an important role in the evolution of this organism because the activity of these elements, as well as the rearrangements caused by ectopic recombination, can result in deletion, duplication, inversion and translocation. Some of these changes can potentially modify gene structure or expression and, thus, facilitate the emergence of new strains of this pathogen.
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Affiliation(s)
- Mateus F Santana
- Present address: Laboratório de Genética Molecular e de Microrganismo, Universidade Federal de Viçosa, Viçosa, Brazil
| | - José CF Silva
- Present address: Diretoria de Tecnologia da Informação, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Aline D Batista
- Present address: Laboratório de Genética Molecular e de Microrganismo, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Lílian E Ribeiro
- Present address: Laboratório de Genética Molecular e de Microrganismo, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Elza F de Araújo
- Present address: Laboratório de Genética Molecular e de Microrganismo, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Marisa V de Queiroz
- Present address: Laboratório de Genética Molecular e de Microrganismo, Universidade Federal de Viçosa, Viçosa, Brazil
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25
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Ahn K, Gim JA, Ha HS, Han K, Kim HS. The novel MER transposon-derived miRNAs in human genome. Gene 2012; 512:422-8. [PMID: 22926102 DOI: 10.1016/j.gene.2012.08.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 08/16/2012] [Accepted: 08/17/2012] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are small RNA molecules (~20-30 nucleotides) that generally act in gene silencing and translational repression through the RNA interference pathway. They generally originate from intergenic genomic regions, but some are found in genomic regions that have been characterized such as introns, exons, and transposable elements (TE). To identify the miRNAs that are derived from palindromic MERs, we analyzed MER paralogs in human genome. The structures of the palindromic MERs were similar to the hairpin structure of miRNA in humans. Three miRNAs derived from MER96 located on chromosome 3, and MER91C paralogs located on chromosome 8 and chromosome 17 were identified in HeLa, HCT116, and HEK293 cell lines. The interactions between these MER-derived miRNAs and AGO1, AGO2, and AGO3 proteins were validated by immunoprecipitation assays. The data suggest that miRNAs derived from transposable elements could widely affect various target genes in the human genome.
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Affiliation(s)
- Kung Ahn
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
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Abstract
MicroRNAs (miRNAs) are aiding our understanding of cancer biology, and are now coming close to therapeutic use as well. Here, we focus specifically on the interaction between miRNAs and genomic instability. MiRNA regulation is essential to many cellular processes, and escape from this regulatory network seems to be a common characteristic of malignant transformation. Genomic instability may preferentially target miRNAs either because of selective pressure or because of inherent vulnerability related to their location near fragile sites. Furthermore, disruption of miRNA processing elements affords a more global release from miRNA regulation. Finally, we review how miRNAs function as both effectors and modulators of the DNA damage response, intricately weaved with traditional elements such as ATM, P53, and MMR. Thus, miRNAs are important substrates for genomic instability and play a crucial role in cellular DNA sensing and repair mechanisms.
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Affiliation(s)
- Dan-Avi Landau
- Department of Hematology, Yale University School of Medicine and the Yale Cancer Center, New Haven, CT, USA
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Sokolova OA, Yakushev EY, Stolyarenko AD, Mikhaleva EA, Gvozdev VA, Klenov MS. Interplay of transposon-silencing genes in the germline of Drosophila melanogaster. Mol Biol 2011. [DOI: 10.1134/s0026893311030174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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A brief history of the status of transposable elements: from junk DNA to major players in evolution. Genetics 2011; 186:1085-93. [PMID: 21156958 DOI: 10.1534/genetics.110.124180] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The idea that some genetic factors are able to move around chromosomes emerged more than 60 years ago when Barbara McClintock first suggested that such elements existed and had a major role in controlling gene expression and that they also have had a major influence in reshaping genomes in evolution. It was many years, however, before the accumulation of data and theories showed that this latter revolutionary idea was correct although, understandably, it fell far short of our present view of the significant influence of what are now known as "transposable elements" in evolution. In this article, I summarize the main events that influenced my thinking about transposable elements as a young scientist and the influence and role of these specific genomic elements in evolution over subsequent years. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work.
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Meng HX, Hackett JA, Nestor C, Dunican DS, Madej M, Reddington JP, Pennings S, Harrison DJ, Meehan RR. Apoptosis and DNA methylation. Cancers (Basel) 2011; 3:1798-820. [PMID: 24212783 PMCID: PMC3757391 DOI: 10.3390/cancers3021798] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 03/11/2011] [Accepted: 03/11/2011] [Indexed: 01/05/2023] Open
Abstract
Epigenetic mechanisms assist in maintaining gene expression patterns and cellular properties in developing and adult tissues. The molecular pathology of disease states frequently includes perturbation of DNA and histone methylation patterns, which can activate apoptotic pathways associated with maintenance of genome integrity. This perspective focuses on the pathways linking DNA methyltransferases and methyl-CpG binding proteins to apoptosis, and includes new bioinformatic analyses to characterize the evolutionary origin of two G/T mismatch-specific thymine DNA glycosylases, MBD4 and TDG.
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Affiliation(s)
- Huan X. Meng
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - James A. Hackett
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - Colm Nestor
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
- Breakthrough Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mail: (D.J.H.)
| | - Donncha S. Dunican
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - Monika Madej
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - James P. Reddington
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - Sari Pennings
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK; E-Mail: (S.P.)
| | - David J. Harrison
- Breakthrough Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mail: (D.J.H.)
| | - Richard R. Meehan
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
- Breakthrough Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mail: (D.J.H.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +44 (0)-332-2471; Fax: +44 (0) 131 467 8456
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White NMA, Yousef GM. MicroRNAs: exploring a new dimension in the pathogenesis of kidney cancer. BMC Med 2010; 8:65. [PMID: 20964839 PMCID: PMC2978114 DOI: 10.1186/1741-7015-8-65] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 10/21/2010] [Indexed: 01/07/2023] Open
Abstract
Renal cell carcinoma (RCC) is the most common neoplasm of the adult kidney. The role of the von-Hippel-Lindeau (VHL) tumour suppressor gene is well established in RCC with a loss of VHL protein leading to accumulated hypoxia-induced factor (HIF) and the subsequent transcriptional activation of multiple downstream targets. Recently, microRNAs (miRNAs) have been shown to be differentially expressed in RCC and their role in RCC pathogenesis is emerging. This month, in BMC Medicine, Gleadle and colleagues show that certain miRNAs are regulated by VHL in either a hypoxia-inducible factor (HIF)-dependent or HIF-independent manner in RCC. They also show that miRNA expression correlates with the survival of RCC patients.In this commentary, we discuss the current understanding of the role of miRNAs in RCC and the different possible scenarios of their involvement in RCC pathogenesis. We also address their clinical significance as tumour markers, together with the potential use of miRNAs as therapeutic targets. Finally, we discuss some of the challenges that face the fast-evolving field of miRNAs, including the identification and validation of miRNA targets and the difficulties associated with establishing a link between miRNA expression and biological effects. A more thorough understanding of the biological nature of miRNAs and careful experimental planning will help us to reveal the complex role that miRNAs play in RCC pathogenesis. See research article: http://www.biomedcentral.com/1741-7015/8/64.
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Affiliation(s)
- Nicole M A White
- Department of Laboratory Medicine and the Keenan Research Centre in the Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto M5B 1W8, Canada
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Wilkins AS. The enemy within: an epigenetic role of retrotransposons in cancer initiation. Bioessays 2010; 32:856-65. [PMID: 20715060 DOI: 10.1002/bies.201000008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This article proposes that cancers can be initiated by retrotransposon (RTN) activation through changes in the transcriptional regulation of nearby genes. I first detail the hypothesis and then discuss the nature of physiological stress(es) in RTN activation; the role of DNA demethylation in the initiation and propagation of new RTN states; the connection between ageing and cancer incidence and the involvement of activated RTNs in the chromosomal aberrations that feature in cancer progression. The hypothesis neither replaces nor invalidates other theories of cancer, in particular the somatic mutation theory, but helps clarify and unify much of the hitherto poorly integrated, complex phenomenology of cancer.
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