3151
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Ibáñez-Ventoso C, Vora M, Driscoll M. Sequence relationships among C. elegans, D. melanogaster and human microRNAs highlight the extensive conservation of microRNAs in biology. PLoS One 2008; 3:e2818. [PMID: 18665242 PMCID: PMC2486268 DOI: 10.1371/journal.pone.0002818] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 06/19/2008] [Indexed: 12/15/2022] Open
Abstract
microRNAs act in a prevalent and conserved post-transcriptional gene regulatory mechanism that impacts development, homeostasis and disease, yet biological functions for the vast majority of miRNAs remain unknown. Given the power of invertebrate genetics to promote rapid evaluation of miRNA function, recently expanded miRNA identifications (miRBase 10.1), and the importance of assessing potential functional redundancies within and between species, we evaluated miRNA sequence relationships by 5' end match and overall homology criteria to compile a snapshot overview of miRNA families within the C. elegans and D. melanogaster genomes that includes their identified human counterparts. This compilation expands literature documentation of both the number of families and the number of family members, within and between nematode and fly models, and highlights sequences conserved between species pairs or among nematodes, flies and humans. Themes that emerge include the substantial potential for functional redundancy of miRNA sequences within species (84/139 C. elegans miRNAs and 70/152 D. melanogaster miRNAs share significant homology with other miRNAs encoded by their respective genomes), and the striking extent to which miRNAs are conserved across species--over half (73/139) C. elegans miRNAs share sequence homology with miRNAs encoded also in both fly and human genomes. This summary analysis of mature miRNA sequence relationships provides a quickly accessible resource that should facilitate functional and evolutionary analyses of miRNAs and miRNA families.
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Affiliation(s)
- Carolina Ibáñez-Ventoso
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Mehul Vora
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
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3152
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Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP. The impact of microRNAs on protein output. Nature 2008; 455:64-71. [PMID: 18668037 DOI: 10.1038/nature07242] [Citation(s) in RCA: 2843] [Impact Index Per Article: 177.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Accepted: 07/10/2008] [Indexed: 12/16/2022]
Abstract
MicroRNAs are endogenous approximately 23-nucleotide RNAs that can pair to sites in the messenger RNAs of protein-coding genes to downregulate the expression from these messages. MicroRNAs are known to influence the evolution and stability of many mRNAs, but their global impact on protein output had not been examined. Here we use quantitative mass spectrometry to measure the response of thousands of proteins after introducing microRNAs into cultured cells and after deleting mir-223 in mouse neutrophils. The identities of the responsive proteins indicate that targeting is primarily through seed-matched sites located within favourable predicted contexts in 3' untranslated regions. Hundreds of genes were directly repressed, albeit each to a modest degree, by individual microRNAs. Although some targets were repressed without detectable changes in mRNA levels, those translationally repressed by more than a third also displayed detectable mRNA destabilization, and, for the more highly repressed targets, mRNA destabilization usually comprised the major component of repression. The impact of microRNAs on the proteome indicated that for most interactions microRNAs act as rheostats to make fine-scale adjustments to protein output.
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Affiliation(s)
- Daehyun Baek
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
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3153
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Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A 2008. [PMID: 18663219 DOI: 10.1073/pnas.0804549105)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Improved approaches for the detection of common epithelial malignancies are urgently needed to reduce the worldwide morbidity and mortality caused by cancer. MicroRNAs (miRNAs) are small ( approximately 22 nt) regulatory RNAs that are frequently dysregulated in cancer and have shown promise as tissue-based markers for cancer classification and prognostication. We show here that miRNAs are present in human plasma in a remarkably stable form that is protected from endogenous RNase activity. miRNAs originating from human prostate cancer xenografts enter the circulation, are readily measured in plasma, and can robustly distinguish xenografted mice from controls. This concept extends to cancer in humans, where serum levels of miR-141 (a miRNA expressed in prostate cancer) can distinguish patients with prostate cancer from healthy controls. Our results establish the measurement of tumor-derived miRNAs in serum or plasma as an important approach for the blood-based detection of human cancer.
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3154
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Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A 2008. [PMID: 18663219 DOI: 10.1073/pnas.0804549105;] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Improved approaches for the detection of common epithelial malignancies are urgently needed to reduce the worldwide morbidity and mortality caused by cancer. MicroRNAs (miRNAs) are small ( approximately 22 nt) regulatory RNAs that are frequently dysregulated in cancer and have shown promise as tissue-based markers for cancer classification and prognostication. We show here that miRNAs are present in human plasma in a remarkably stable form that is protected from endogenous RNase activity. miRNAs originating from human prostate cancer xenografts enter the circulation, are readily measured in plasma, and can robustly distinguish xenografted mice from controls. This concept extends to cancer in humans, where serum levels of miR-141 (a miRNA expressed in prostate cancer) can distinguish patients with prostate cancer from healthy controls. Our results establish the measurement of tumor-derived miRNAs in serum or plasma as an important approach for the blood-based detection of human cancer.
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3155
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Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A 2008; 105:10513-8. [PMID: 18663219 DOI: 10.1073/pnas.0804549105] [Citation(s) in RCA: 6151] [Impact Index Per Article: 384.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Improved approaches for the detection of common epithelial malignancies are urgently needed to reduce the worldwide morbidity and mortality caused by cancer. MicroRNAs (miRNAs) are small ( approximately 22 nt) regulatory RNAs that are frequently dysregulated in cancer and have shown promise as tissue-based markers for cancer classification and prognostication. We show here that miRNAs are present in human plasma in a remarkably stable form that is protected from endogenous RNase activity. miRNAs originating from human prostate cancer xenografts enter the circulation, are readily measured in plasma, and can robustly distinguish xenografted mice from controls. This concept extends to cancer in humans, where serum levels of miR-141 (a miRNA expressed in prostate cancer) can distinguish patients with prostate cancer from healthy controls. Our results establish the measurement of tumor-derived miRNAs in serum or plasma as an important approach for the blood-based detection of human cancer.
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3156
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Gottwein E, Cullen BR. Viral and cellular microRNAs as determinants of viral pathogenesis and immunity. Cell Host Microbe 2008; 3:375-87. [PMID: 18541214 DOI: 10.1016/j.chom.2008.05.002] [Citation(s) in RCA: 342] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 04/28/2008] [Accepted: 05/06/2008] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) have recently emerged as key posttranscriptional regulators of gene expression in multicellular eukaryotes. It is increasingly clear that miRNAs of both viral and cellular origin can positively or negatively influence viral replication. Viral miRNAs can directly alter host physiology, including components of the immune system, and host miRNAs can directly alter the virus life cycle. Here, we discuss what is known about how viral and cellular miRNAs influence viral replication and pathogenic potential through their regulation of viral mRNAs or by reshaping cellular gene expression.
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Affiliation(s)
- Eva Gottwein
- Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, NC 27710, USA
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3157
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Mellios N, Huang HS, Grigorenko A, Rogaev E, Akbarian S. A set of differentially expressed miRNAs, including miR-30a-5p, act as post-transcriptional inhibitors of BDNF in prefrontal cortex. Hum Mol Genet 2008; 17:3030-42. [PMID: 18632683 DOI: 10.1093/hmg/ddn201] [Citation(s) in RCA: 219] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Expression of brain-derived neurotrophic factor (BDNF) is developmentally regulated in prefrontal cortex (PFC). The underlying molecular mechanisms, however, remain unclear. Here, we explore the role of microRNAs (miRNAs) as post-transcriptional inhibitors of BDNF. A sequential approach involving in silico, miRNA microarray, in situ hybridization and qRT-PCR studies identified a group of 10 candidate miRNAs, segregating into five miRNA families (miR-30a-5p/b/c/d, miR-103/107, miR-191, miR-16/195, miR-495), which exhibited distinct developmental and lamina-specific expression in human PFC. Luciferase assays confirmed that at least two of these miRNAs, miR-30a-5p and miR-195, target specific sequences surrounding the proximal polyadenylation site within BDNF 3'-untranslated region. Furthermore, neuronal overexpression of miR-30a-5p, a miRNA enriched in layer III pyramidal neurons, resulted in down-regulation of BDNF protein. Notably, a subset of seven miRNAs, including miR-30a-5p, exhibited an inverse correlation with BDNF protein levels in PFC of subjects age 15-84 years. In contrast, the role of transcriptional mechanisms was more apparent during the transition from fetal to childhood and/or young adult stages, when BDNF mRNA up-regulation was accompanied by similar changes in (open chromatin-associated) histone H3-lysine 4 methylation at BDNF gene promoters I and IV. Collectively, our data highlight the multiple layers of regulation governing the developmental expression of BDNF in human PFC and suggest that miRNAs are involved in the fine-tuning of this neurotrophin particularly in adulthood.
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Affiliation(s)
- Nikolaos Mellios
- Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, 303 Belmont Street, Worcester, MA 01604, USA
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3158
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Studies of the interaction of the viral suppressor of RNA silencing protein p19 with small RNAs using fluorescence polarization. Biochemistry 2008; 47:8130-8. [PMID: 18597480 DOI: 10.1021/bi800401y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tombusviruses use a 19 kDa protein (p19) as a suppressor of the RNA silencing pathway during infection. The p19 protein binds to short-interfering RNA (siRNA) as a dimer and shows a high selectivity for short duplex RNAs over other RNA species. Since p19 can bind to synthetic and RNA silencing generated small RNAs with little sequence dependence and with size selectivity, this protein has utility as a tool for studying RNA silencing pathways in eukaryotes. However, the ability of p19 to serve as a tool for studying RNA silencing pathways may be complicated by the presence of other endogenous small RNAs such as micro-RNAs (miRNAs). To understand the importance of endogenous small RNA components with respect to p19's ability to bind to siRNAs, we examined the interactions of p19 with human miR-122, a 23-nucleotide duplex miRNA containing several mismatched base pairs that is highly abundant in the liver. The binding characteristics were compared with those of an siRNA optimized against the human kinase CSK. The binding studies were performed using fluorescence polarization experiments on duplex oligonucleotides containing Cy3 dye labels at the 5'-end of one of the strands of RNA as well as electrophoretic gel mobility shift assays. Both methods indicate that the synthetic siRNA with no mismatches in base pairing bound with >3-fold selectivity over that of miR-122. Our results suggest that p19 can distinguish between siRNAs and miRNA species, although the difference in binding constants is not so large that interactions with endogenous miRNAs can be totally ignored.
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3159
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Ornish D, Magbanua MJM, Weidner G, Weinberg V, Kemp C, Green C, Mattie MD, Marlin R, Simko J, Shinohara K, Haqq CM, Carroll PR. Changes in prostate gene expression in men undergoing an intensive nutrition and lifestyle intervention. Proc Natl Acad Sci U S A 2008; 105:8369-74. [PMID: 18559852 PMCID: PMC2430265 DOI: 10.1073/pnas.0803080105] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Indexed: 01/13/2023] Open
Abstract
Epidemiological and prospective studies indicate that comprehensive lifestyle changes may modify the progression of prostate cancer. However, the molecular mechanisms by which improvements in diet and lifestyle might affect the prostate microenvironment are poorly understood. We conducted a pilot study to examine changes in prostate gene expression in a unique population of men with low-risk prostate cancer who declined immediate surgery, hormonal therapy, or radiation and participated in an intensive nutrition and lifestyle intervention while undergoing careful surveillance for tumor progression. Consistent with previous studies, significant improvements in weight, abdominal obesity, blood pressure, and lipid profile were observed (all P < 0.05), and surveillance of low-risk patients was safe. Gene expression profiles were obtained from 30 participants, pairing RNA samples from control prostate needle biopsy taken before intervention to RNA from the same patient's 3-month postintervention biopsy. Quantitative real-time PCR was used to validate array observations for selected transcripts. Two-class paired analysis of global gene expression using significance analysis of microarrays detected 48 up-regulated and 453 down-regulated transcripts after the intervention. Pathway analysis identified significant modulation of biological processes that have critical roles in tumorigenesis, including protein metabolism and modification, intracellular protein traffic, and protein phosphorylation (all P < 0.05). Intensive nutrition and lifestyle changes may modulate gene expression in the prostate. Understanding the prostate molecular response to comprehensive lifestyle changes may strengthen efforts to develop effective prevention and treatment. Larger clinical trials are warranted to confirm the results of this pilot study.
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Affiliation(s)
- Dean Ornish
- *Preventive Medicine Research Institute, 900 Bridgeway, Sausalito, CA 94965
- Department of Medicine, School of Medicine, University of California, 505 Parnassus Avenue, San Francisco, CA 94143; and
| | | | - Gerdi Weidner
- *Preventive Medicine Research Institute, 900 Bridgeway, Sausalito, CA 94965
| | - Vivian Weinberg
- Biostatistics Core, The Helen Diller Family Comprehensive Cancer Center, University of California, 513 Parnassus Avenue, Box 0127, San Francisco, CA 94143
| | - Colleen Kemp
- *Preventive Medicine Research Institute, 900 Bridgeway, Sausalito, CA 94965
| | - Christopher Green
- Department of Urology, The Helen Diller Family Comprehensive Cancer Center, and
| | - Michael D. Mattie
- Department of Urology, The Helen Diller Family Comprehensive Cancer Center, and
| | - Ruth Marlin
- *Preventive Medicine Research Institute, 900 Bridgeway, Sausalito, CA 94965
| | - Jeff Simko
- Department of Pathology, University of California, 2340 Sutter Street, San Francisco, CA 94115
| | - Katsuto Shinohara
- Department of Urology, The Helen Diller Family Comprehensive Cancer Center, and
| | - Christopher M. Haqq
- Department of Urology, The Helen Diller Family Comprehensive Cancer Center, and
| | - Peter R. Carroll
- Department of Urology, The Helen Diller Family Comprehensive Cancer Center, and
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3160
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Kim J, Cho IS, Hong JS, Choi YK, Kim H, Lee YS. Identification and characterization of new microRNAs from pig. Mamm Genome 2008; 19:570-80. [PMID: 18548309 DOI: 10.1007/s00335-008-9111-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 04/29/2008] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs that direct the posttranscriptional repression of cognate messenger RNAs. Despite increasing evidence for diverse roles of miRNAs in biological processes, little is known about miRNAs in pig. We describe the first experimental identification of porcine miRNAs by sequence analysis of a cDNA library of small RNAs from porcine fibroblast cells. We identified 25 distinct porcine miRNAs, of which 19 are previously unreported, and define 14 new miRNA families in pig. Most of the cloned miRNAs are expressed ubiquitously in all porcine tissues examined, whereas some miRNAs are expressed preferentially in specific tissues. Our results enrich the porcine miRNA database and provide useful information for investigating biological functions of miRNAs in pig.
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Affiliation(s)
- Jung Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, South Korea
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3161
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Callis TE, Wang DZ. Taking microRNAs to heart. Trends Mol Med 2008; 14:254-60. [DOI: 10.1016/j.molmed.2008.03.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 03/19/2008] [Accepted: 03/19/2008] [Indexed: 01/04/2023]
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3162
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Abstract
Recognition of the importance of noncoding RNAs has risen exponentially since the discovery that small molecules of 20–26 nucleotides in length were at the core of all RNA silencing phenomena. Among those small RNAs, miRNAs clearly represent the most prominent family and have been implicated in a wide range of biological processes. Recently, it has been recognized that even viruses encode their own miRNAs, and this finding has unveiled a new level in the study of host–virus interactions. Viral miRNAs have been mainly described in herpesviruses, including the oncogenic gammaherpesviruses, such as Epstein–Barr virus or Kaposi’s sarcoma-associated herpesvirus, and they have been shown to regulate the expression of both viral and cellular genes. We are only just starting to elucidate the function of viral miRNAs, however, the results obtained so far clearly indicate that they play a prominent role in the virus life cycle.
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Affiliation(s)
- Sébastien Pfeffer
- IBMP–CNRS, 12, Rue Du Général Zimmer, 67084 Strasbourg Cedex, France
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3163
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Walker JC, Harland RM. Expression of microRNAs during embryonic development of Xenopus tropicalis. Gene Expr Patterns 2008; 8:452-456. [PMID: 18440877 DOI: 10.1016/j.gep.2008.03.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Revised: 03/15/2008] [Accepted: 03/25/2008] [Indexed: 11/16/2022]
Abstract
microRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression and have prominent roles during early embryo development and organogenesis. We set out to determine the expression pattern of miRNAs in the developmental model system, Xenopus tropicalis. We made probes to predicted primary-miRNA transcripts and performed in situ hybridization. Our data show conserved and novel tissue-specific expression patterns during embryogenesis that suggest functional roles during development.
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Affiliation(s)
- James C Walker
- Department of Molecular and Cell Biology, 579 Life Sciences Addition, University of California, Berkeley, CA 94720-3200, USA
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3164
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Interspecies regulation of microRNAs and their targets. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1779:735-42. [PMID: 18407843 DOI: 10.1016/j.bbagrm.2008.03.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 03/16/2008] [Accepted: 03/17/2008] [Indexed: 11/20/2022]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide RNA molecules that play essential roles in posttranscriptional regulation of target genes. In animals, miRNAs bind to target mRNA through imperfect complementary sequences that are usually located at the 3' untranslated regions (UTRs), leading to translational repression or transcript degradation. In plants, miRNAs predominately mediate degradation of target mRNAs via perfect or near-perfect complementary sequences. MicroRNA targets include a large number of transcription factors, suggesting a role of miRNAs in the control of regulatory networks and cellular growth and development. Many miRNAs and their targets are conserved among plants or animals, whereas some are specific to a few plant or animal lineages. Conserved miRNAs do not necessarily exhibit the same expression levels or patterns in different species or at different stages within a species. Therefore, sequence and expression divergence in miRNAs between species may affect miRNA accumulation and target regulation in interspecific hybrids and allopolyploids that contain two or more divergent genomes, leading to developmental changes and phenotypic variation in the new species.
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3165
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Lehrbach NJ, Miska EA. Functional genomic, computational and proteomic analysis of C. elegans microRNAs. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:228-35. [DOI: 10.1093/bfgp/eln024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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3166
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MicroRNA profile of Marek's disease virus-transformed T-cell line MSB-1: predominance of virus-encoded microRNAs. J Virol 2008; 82:4007-15. [PMID: 18256158 DOI: 10.1128/jvi.02659-07] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Research over the last few years has demonstrated the increasing role of microRNAs (miRNAs) as major regulators of gene expression in diverse cellular processes and diseases. Several viruses, particularly herpesviruses, also use the miRNA pathway of gene regulation by encoding their own miRNAs. Marek's disease (MD) is a widespread lymphomatous neoplastic disease of poultry caused by the highly contagious Marek's disease virus type 1 (MDV-1). Recent studies using virus-infected chicken embryo fibroblasts have identified at least eight miRNAs that map to the R(L)/R(S) region of the MDV genome. Since MDV is a lymphotropic virus that induces T-cell lymphomas, analysis of the miRNA profile in T-cell lymphoma would be more relevant for examining their role in oncogenesis. We determined the viral and host miRNAs expressed in MSB-1, a lymphoblastoid cell line established from an MDV-induced lymphoma of the spleen. In this paper, we report the identification of 13 MDV-1-encoded miRNAs (12 by direct cloning and 1 by Northern blotting) from MSB-1 cells. These miRNAs, five of which are novel MDV-1 miRNAs, map to the Meq and latency-associated transcript regions of the MDV genome. Furthermore, we show that miRNAs encoded by MDV-1 and the coinfected MDV-2 accounted for >60% of the 5,099 sequences of the MSB-1 "miRNAome." Several chicken miRNAs, some of which are known to be associated with cancer, were also cloned from MSB-1 cells. High levels of expression of MDV-1-encoded miRNAs and potentially oncogenic host miRNAs suggest that miRNAs may have major roles in MDV pathogenesis and neoplastic transformation.
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3167
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Affiliation(s)
- Jamison D Feramisco
- Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
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