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Xing Z, Yu L, Li X, Su X. Anticancer bioactive peptide-3 inhibits human gastric cancer growth by targeting miR-338-5p. Cell Biosci 2016; 6:53. [PMID: 27688872 PMCID: PMC5034486 DOI: 10.1186/s13578-016-0112-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/30/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cancer incidence and mortality have been increasing in China, making cancer the leading cause of death since 2010 and a major public health concern in the country. Cancer stem cells have been studied in relation to the treatment of different malignancies, including gastric cancer. Anticancer bioactive peptide-3 (ACBP-3) can induce the apoptosis of gastric cancer stem cells (GCSCs) and reduce their tumorigenicity. In the present study, for the first time, we used a miRNA microarray and bioinformatics analysis to identify differentially expressed miRNAs in ACBP-3-treated GCSCs and GCSC-derived tumors in a xenograft model and functionally verified the identified miRNAs. miR-338-5p was selected based on its significant upregulation by ACBP-3 both in cultured GCSCs and in tumor tissues. RESULTS miR-338-5p was downregulated in GCSCs compared with normal gastric epithelial cells, and the ectopic restoration of miR-338-5p expression in GCSCs inhibited cell proliferation and induced apoptosis, which correlated with the upregulation of the pro-apoptotic Bcl-2 proteins BAK and BIM. We also found that ACBP-3-treated GCSCs could respond to lower effective doses of cisplatin (DDP) or 5-fluorouracil (5-FU), possibly because ACBP-3 induced the expression of miR-338-5p and the BAK and BIM proteins and promoted GCSC apoptosis. CONCLUSIONS Our data indicate that miR-338-5p is part of an important pathway for the inhibition of human gastric cancer stem cell proliferation by ACBP-3 combined with chemotherapeutics. ACBP-3 could suppress GCSC proliferation and lower the required effective dose of cisplatin or 5-fluorouracil. Therefore, this study provides not only further evidence for the remarkable anti-tumor effect of ACBP-3 but also a possible new approach for the development of GCSC-targeting therapies.
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Affiliation(s)
- Zhiwei Xing
- Department of Cell Biology, Capital Medical University, Beijing, China
| | - Lan Yu
- The Inner Mongolia Autonomous Region People’s Hospital, Hohhot, Inner Mongolia China
| | - Xian Li
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, Hohhot, Inner Mongolia China
| | - Xiulan Su
- Department of Cell Biology, Capital Medical University, Beijing, China
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, Hohhot, Inner Mongolia China
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Ma H, Wu Y, Niu Q, Zhang J, Jia G, Manjunath N, Wu H. A sliding-bulge structure at the Dicer processing site of pre-miRNAs regulates alternative Dicer processing to generate 5'-isomiRs. Heliyon 2016; 2:e00148. [PMID: 27656682 PMCID: PMC5021778 DOI: 10.1016/j.heliyon.2016.e00148] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/17/2016] [Accepted: 08/19/2016] [Indexed: 11/20/2022] Open
Abstract
5′-isomiRs expand the repertoire of miRNA targets. However, how they are generated is not well understood. Previously, we showed that for some miRNAs in mammalian cells, Drosha cleaves at multiple sites to generate multiple pre-miRNAs that give rise to multiple 5′-isomiRs. Here, we showed that for some other miRNAs, 5′-isomiRs are generated by alternative Dicer processing. In addition, we showed that in miR-203, alternative Dicer processing is regulated by a conserved sliding-bulge structure at the Dicer processing site, which allows the pre-miRNA molecule to fold into two different structures that are processed differently by Dicer. So far no RNA motif that slides to change conformation and alter a protein–RNA interaction has been reported. Thus, our study revealed a novel RNA motif that regulates 5′-isomiR generation in some miRNAs. It might also contribute to regulating protein–RNA interactions in other biological processes, since it takes only one point mutation to generate the sliding bulge, and there are a large number of different RNAs in the cell.
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Affiliation(s)
- Hongming Ma
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Yonggan Wu
- Labii Inc., Mountain View, CA 94043, USA
| | - Qi Niu
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Junli Zhang
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Gengxiang Jia
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - N Manjunath
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Haoquan Wu
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
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Salem O, Erdem N, Jung J, Münstermann E, Wörner A, Wilhelm H, Wiemann S, Körner C. The highly expressed 5'isomiR of hsa-miR-140-3p contributes to the tumor-suppressive effects of miR-140 by reducing breast cancer proliferation and migration. BMC Genomics 2016; 17:566. [PMID: 27502506 PMCID: PMC4977694 DOI: 10.1186/s12864-016-2869-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 07/01/2016] [Indexed: 02/06/2023] Open
Abstract
Background miRNAs are small noncoding RNA molecules that play an important role in post-transcriptional regulation of gene expression. Length and/or sequence variants of the same miRNA are termed isomiRs. While most isomiRs are functionally redundant compared to their canonical counterparts, the so-called 5’isomiRs exhibit a shifted 5’ end and therefore a shifted seed sequence resulting in a different target spectrum. However, not much is known about the functional relevance of these isoforms. Results Analysis of miRNA-seq data from breast cancer cell lines identified six pairs of highly expressed miRNAs and associated 5’isomiRs. Among them, hsa-miR-140-3p was of particular interest because its 5’isomiR showed higher expression compared to the canonical miRNA annotated in miRbase. This miRNA has previously been shown to control stemness of breast cancer cells. miRNAseq data of breast cancer patients (TCGA dataset) showed that both the canonical hsa-miR-140-3p and its 5’isomiR-140-3p were highly expressed in patients’ tumors compared to normal breast tissue. In the current work, we present the functional characterization of 5’isomiR-140-3p and the cellular phenotypes associated with its overexpression in MCF10A, MDA-MB-468 and MDA-MB-231 cell lines in comparison to the canonical hsa-miR-140-3p. Contrary to the effect of the canonical hsa-miR-140-3p, overexpression of the 5’isomiR-140-3p led to a decrease in cell viability. The latter observation was supported by cell cycle analysis, where the 5’isomiR-140-3p but not the hsa-miR-140-3p caused cell cycle arrest in G0/G1-phase. Additionally, 5’ismoiR-140-3p overexpression was found to cause a decrease in cell migration in the three cell lines. We identified three novel direct target genes of the 5’isomiR-140-3p; COL4A1, ITGA6 and MARCKSL1. Finally, we have shown that knocking down these genes partially phenocopied the effects of the 5’isomiR-140-4p overexpression, where COL4A1 and ITGA6 knockdown led to reduced cell viability and cell cycle arrest, while MARCKSL1 knockdown resulted in a decrease in the migratory potential of cells. Conclusions In summary, this work presents evidence that there is functional synergy between the canonical hsa-miR-140-3p and the newly identified 5’isomiR-140-3p in suppressing growth and progression of breast cancer by simultaneously targeting genes related to differentiation, proliferation, and migration. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2869-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Omar Salem
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), INF580, Heidelberg, 69120, Germany
| | - Nese Erdem
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), INF580, Heidelberg, 69120, Germany
| | - Janine Jung
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), INF580, Heidelberg, 69120, Germany
| | - Ewald Münstermann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), INF580, Heidelberg, 69120, Germany
| | - Angelika Wörner
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), INF580, Heidelberg, 69120, Germany
| | - Heike Wilhelm
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), INF580, Heidelberg, 69120, Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), INF580, Heidelberg, 69120, Germany
| | - Cindy Körner
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), INF580, Heidelberg, 69120, Germany.
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Kasar S, Underbayev C, Hassan M, Ilev I, Degheidy H, Bauer S, Marti G, Lutz C, Raveche E, Batish M. Alterations in the mir-15a/16-1 Loci Impairs Its Processing and Augments B-1 Expansion in De Novo Mouse Model of Chronic Lymphocytic Leukemia (CLL). PLoS One 2016; 11:e0149331. [PMID: 26959643 PMCID: PMC4784815 DOI: 10.1371/journal.pone.0149331] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/29/2016] [Indexed: 12/26/2022] Open
Abstract
New Zealand Black (NZB) mice, a de novo model of CLL, share multiple characteristics with CLL patients, including decreased expression of miR-15a/16-1. We previously discovered a point mutation and deletion in the 3' flanking region of mir-16-1 of NZB and a similar mutation has been found in a small number of CLL patients. However, it was unknown whether the mutation is the cause for the reduced miR-15a/16-1 expression and CLL development. Using PCR and in vitro microRNA processing assays, we found that the NZB sequence alterations in the mir-15a/16-1 loci result in deficient processing of the precursor forms of miR-15a/16-1, in particular, we observe impaired conversion of pri-miR-15a/16-1 to pre-miR-15a/16-1. The in vitro data was further supported by derivation of congenic strains with replaced mir-15a/16-1 loci at one or both alleles: NZB congenic mice (NmiR+/-) and DBA congenic mice (DmiR-/-). The level of miR-15a/16-1 reflected the configuration of the mir-15a/16-1 loci with DBA congenic mice (DmiR-/-) showing reduced miR-15a levels compared to homozygous wild-type allele, while the NZB congenic mice (NmiR+/-) showed an increase in miR-15a levels relative to homozygous mutant allele. Similar to Monoclonal B-cell Lymphocytosis (MBL), the precursor stage of the human disease, an overall expansion of the B-1 population was observed in DBA congenic mice (DmiR-/-) relative to wild-type (DmiR+/+). These studies support our hypothesis that the mutations in the mir-15a/16-1 loci are responsible for decreased expression of this regulatory microRNA leading to B-1 expansion and CLL development.
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Affiliation(s)
- Siddha Kasar
- New Jersey Medical School, Rutgers University, Newark, New Jersey, 07103, United States of America
| | - Chingiz Underbayev
- New Jersey Medical School, Rutgers University, Newark, New Jersey, 07103, United States of America
| | | | - Ilko Ilev
- OSEL/CDRH/FDA White Oak, Maryland, United States of America
| | - Heba Degheidy
- CBER/FDA White Oak, Maryland, United States of America
| | - Steven Bauer
- CBER/FDA White Oak, Maryland, United States of America
| | - Gerald Marti
- OSEL/CDRH/FDA White Oak, Maryland, United States of America
| | - Carol Lutz
- New Jersey Medical School, Rutgers University, Newark, New Jersey, 07103, United States of America
| | - Elizabeth Raveche
- New Jersey Medical School, Rutgers University, Newark, New Jersey, 07103, United States of America
| | - Mona Batish
- New Jersey Medical School, Rutgers University, Newark, New Jersey, 07103, United States of America
- * E-mail:
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55
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Wang Y, Lv Y, Gao S, Zhang Y, Sun J, Gong C, Chen X, Li G. MicroRNA Profiles in Spontaneous Decidualized Menstrual Endometrium and Early Pregnancy Decidua with Successfully Implanted Embryos. PLoS One 2016; 11:e0143116. [PMID: 26735129 PMCID: PMC4703305 DOI: 10.1371/journal.pone.0143116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/31/2015] [Indexed: 01/16/2023] Open
Abstract
To comparatively analyze the human microRNA (miRNA) profiles between spontaneous decidualized menstrual endometrium and early pregnancy decidua by an in-depth sequencing of miRNAs. The specific miRNAs expressed at conception might be involved in pregnancy establishment and expression of let-7f-5p and let-7g-5p was experimentally up-regulated or inhibited to assess the effect on the expression of IGF2BP-1 and IGF2R in vitro, respectively. Samples of endometria and deciduas were obtained from 25 women who suffered from tubal or male factor subfertility and from 35 early pregnant women who underwent pregnancy termination at 6–8 weeks gestation were irrespectively collected and comparatively analyzed by miRNA sequencing and differential expression of known and novel miRNAs was analyzed using bioinformatics. The 2042 miRNA expression was analyzed in the study and the differential expression of six miRNAs was validated by qRT-PCR. The expression of four miRNAs in decidua samples was down-regulated (miR-34c, miR-92a, miR-181a-5p, and miR-191), whereas the expression of miR-10a-5p and let-7f-5p was significantly up-regulated. The expression of IGF2BP-1 and IGF2R declined and increased with overexpression and inhibition of let-7f-5p and let-7g-5p, respectively. Changes in the expression of particular miRNAs might play a role in the physiology of decidualization following successful embryo implantation, ultimately resulting in continuous decidualization.
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Affiliation(s)
- Yu Wang
- The Key Laboratory of National Education Ministry for Mammalian Reproductive Biology and Biotechnology, Inner Mongolia University, Hohhot, China
- Department of Gynecology and Obstetrics, Inner Mongolia Medical University affiliated hospital, Hohhot, China
| | - Yang Lv
- The Key Laboratory of National Education Ministry for Mammalian Reproductive Biology and Biotechnology, Inner Mongolia University, Hohhot, China
| | - Shujun Gao
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yuanyuan Zhang
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Jiajia Sun
- The Key Laboratory of National Education Ministry for Mammalian Reproductive Biology and Biotechnology, Inner Mongolia University, Hohhot, China
| | - Chunling Gong
- The Key Laboratory of National Education Ministry for Mammalian Reproductive Biology and Biotechnology, Inner Mongolia University, Hohhot, China
| | - Xiujuan Chen
- Department of Gynecology and Obstetrics, Inner Mongolia Medical University affiliated hospital, Hohhot, China
- * E-mail: (XJC); (GPL)
| | - Guangpeng Li
- The Key Laboratory of National Education Ministry for Mammalian Reproductive Biology and Biotechnology, Inner Mongolia University, Hohhot, China
- * E-mail: (XJC); (GPL)
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56
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Starega-Roslan J, Galka-Marciniak P, Krzyzosiak WJ. Nucleotide sequence of miRNA precursor contributes to cleavage site selection by Dicer. Nucleic Acids Res 2015; 43:10939-51. [PMID: 26424848 PMCID: PMC4678860 DOI: 10.1093/nar/gkv968] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/15/2015] [Indexed: 12/21/2022] Open
Abstract
The ribonuclease Dicer excises mature miRNAs from a diverse group of precursors (pre-miRNAs), most of which contain various secondary structure motifs in their hairpin stem. In this study, we analyzed Dicer cleavage in hairpin substrates deprived of such motifs. We searched for the factors other than the secondary structure, which may influence the length diversity and heterogeneity of miRNAs. We found that the nucleotide sequence at the Dicer cleavage site influences both of these miRNA characteristics. With regard to cleavage mechanism, we demonstrate that the Dicer RNase IIIA domain that cleaves within the 3′ arm of the pre-miRNA is more sensitive to the nucleotide sequence of its substrate than is the RNase IIIB domain. The RNase IIIA domain avoids releasing miRNAs with G nucleotide and prefers to generate miRNAs with a U nucleotide at the 5′ end. We also propose that the sequence restrictions at the Dicer cleavage site might be the factor that contributes to the generation of miRNA duplexes with 3′ overhangs of atypical lengths. This finding implies that the two RNase III domains forming the single processing center of Dicer may exhibit some degree of flexibility, which allows for the formation of these non-standard 3′ overhangs.
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Affiliation(s)
- Julia Starega-Roslan
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | - Paulina Galka-Marciniak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
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Manzano M, Forte E, Raja AN, Schipma MJ, Gottwein E. Divergent target recognition by coexpressed 5'-isomiRs of miR-142-3p and selective viral mimicry. RNA (NEW YORK, N.Y.) 2015; 21:1606-20. [PMID: 26137849 PMCID: PMC4536321 DOI: 10.1261/rna.048876.114] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 06/08/2015] [Indexed: 05/28/2023]
Abstract
Sequence heterogeneity at the ends of mature microRNAs (miRNAs) is well documented, but its effects on miRNA function are largely unexplored. Here we studied the impact of miRNA 5'-heterogeneity, which affects the seed region critical for target recognition. Using the example of miR-142-3p, an emerging regulator of the hematopoietic lineage in vertebrates, we show that naturally coexpressed 5'-variants (5'-isomiRs) can recognize largely distinct sets of binding sites. Despite this, both miR-142-3p isomiRs regulate exclusive and shared targets involved in actin dynamics. Thus, 5'-heterogeneity can substantially broaden and enhance regulation of one pathway. Other 5'-isomiRs, in contrast, recognize largely overlapping sets of binding sites. This is exemplified by two herpesviral 5'-isomiRs that selectively mimic one of the miR-142-3p 5'-isomiRs. We hypothesize that other cellular and viral 5'-isomiRs can similarly be grouped into those with divergent or convergent target repertoires, based on 5'-sequence features. Taken together, our results provide a detailed characterization of target recognition by miR-142-3p and its 5'-isomiR-specific viral mimic. We furthermore demonstrate that miRNA 5'-end variation leads to differential targeting and can thus broaden the target range of miRNAs.
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Affiliation(s)
- Mark Manzano
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Eleonora Forte
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Archana N Raja
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Matthew J Schipma
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Eva Gottwein
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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58
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Agarwal V, Bell GW, Nam JW, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. eLife 2015; 4. [PMID: 26267216 PMCID: PMC4532895 DOI: 10.7554/elife.05005] [Citation(s) in RCA: 4955] [Impact Index Per Article: 550.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 07/12/2015] [Indexed: 12/20/2022] Open
Abstract
MicroRNA targets are often recognized through pairing between the miRNA seed region and complementary sites within target mRNAs, but not all of these canonical sites are equally effective, and both computational and in vivo UV-crosslinking approaches suggest that many mRNAs are targeted through non-canonical interactions. Here, we show that recently reported non-canonical sites do not mediate repression despite binding the miRNA, which indicates that the vast majority of functional sites are canonical. Accordingly, we developed an improved quantitative model of canonical targeting, using a compendium of experimental datasets that we pre-processed to minimize confounding biases. This model, which considers site type and another 14 features to predict the most effectively targeted mRNAs, performed significantly better than existing models and was as informative as the best high-throughput in vivo crosslinking approaches. It drives the latest version of TargetScan (v7.0; targetscan.org), thereby providing a valuable resource for placing miRNAs into gene-regulatory networks.
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Affiliation(s)
- Vikram Agarwal
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, United States
| | - George W Bell
- Bioinformatics and Research Computing, Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Jin-Wu Nam
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, United States
| | - David P Bartel
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, United States
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59
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Loo J, Wang SS, Peng F, He JA, He L, Guo YC, Gu DY, Kwok HC, Wu SY, Ho HP, Xie WD, Shao YH, Kong SK. A non-PCR SPR platform using RNase H to detect MicroRNA 29a-3p from throat swabs of human subjects with influenza A virus H1N1 infection. Analyst 2015; 140:4566-4575. [PMID: 26000345 DOI: 10.1039/c5an00679a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
As in all RNA viruses, influenza viruses change and mutate constantly because their RNA polymerase has no proofreading ability. This poses a serious threat to public health nowadays. In addition, traditional pathogen-based detection methods may not be able to report an infection from an unknown type or a subtype of virus if its nucleotide sequence is not known. Because of these factors, targeting host microRNA signatures may be an alternative to classify infections and distinguish types of pathogens as microRNAs are produced in humans shortly after infection. Although this approach is in its infant stage, there is an urgent need to develop a rapid reporter assay for microRNA for disease control and prevention. As a proof of concept, we report herein for the first time a non-PCR MARS (MicroRNA-RNase-SPR) assay to detect the microRNA miR-29a-3p from human subjects infected with influenza virus H1N1 by surface plasmon resonance (SPR). In our MARS assay, RNase H is employed to specifically hydrolyze the RNA probes immobilized on the gold surface where they hybridize with its cognate target cDNAs miR-29a-3p, where it was formed from reverse transcription with mature miR-29a-3p specific stem-looped primers. After the digestion of the RNA probe by RNase H, the intact cDNA was released from the RNA-DNA hybrid and bound to a new RNA probe for another enzymatic reaction cycle to amplify signals. With assay optimization, the detection limit of our MARS assay for miR-29a-3p was found to be 1 nM, and this new assay could be completed within 1 hour without thermal cycling. This non-PCR assay with high selectivity for mature microRNA provides a new platform for rapid disease diagnosis, quarantine and disease control.
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Affiliation(s)
- Jacky Loo
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Room 609, Mong Man Wai Building, Shatin, NT, Hong Kong, China.
| | - S S Wang
- Shenzhen Entry-Exit Inspection and Quarantine Bureau, Shenzhen 518033, China.
| | - F Peng
- Shenzhen Entry-Exit Inspection and Quarantine Bureau, Shenzhen 518033, China.
| | - J A He
- Shenzhen Entry-Exit Inspection and Quarantine Bureau, Shenzhen 518033, China.
| | - L He
- Shenzhen Entry-Exit Inspection and Quarantine Bureau, Shenzhen 518033, China.
| | - Y C Guo
- Shenzhen Entry-Exit Inspection and Quarantine Bureau, Shenzhen 518033, China.
| | - D Y Gu
- Shenzhen Entry-Exit Inspection and Quarantine Bureau, Shenzhen 518033, China.
| | - H C Kwok
- Center for Advanced Research in Photonics, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
| | - S Y Wu
- Center for Advanced Research in Photonics, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
| | - H P Ho
- Center for Advanced Research in Photonics, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
| | - W D Xie
- Shenzhen Key Lab of Health Science and Technology, Division of Life Sciences & Health, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Y H Shao
- College of Optoelectronics Engineering, Key Laboratory of Optoelectronic Devices and Systems, Ministry of Education and Guangdong Province, Shenzhen Key Laboratory of Sensor Technology, Shenzhen University, Shenzhen 518060, China
| | - S K Kong
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Room 609, Mong Man Wai Building, Shatin, NT, Hong Kong, China.
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Kock KH, Kong KW, Hoon S, Seow Y. Functional VEGFA knockdown with artificial 3'-tailed mirtrons defined by 5' splice site and branch point. Nucleic Acids Res 2015; 43:6568-78. [PMID: 26089392 PMCID: PMC4513878 DOI: 10.1093/nar/gkv617] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/02/2015] [Indexed: 11/28/2022] Open
Abstract
Mirtrons are introns that form pre-miRNA hairpins after splicing to produce RNA interference (RNAi) effectors distinct from Drosha-dependent intronic miRNAs, and will be especially useful for co-delivery of coding genes and RNAi. A specific family of mirtrons – 3′-tailed mirtrons – has hairpins precisely defined on the 5′ end by the 5′ splice site and 3′ end by the branch point. Here, we present design principles for artificial 3′-tailed mirtrons and demonstrate, for the first time, efficient gene knockdown with tailed mirtrons within eGFP coding region. These artificial tailed mirtrons, unlike canonical mirtrons, have very few sequence design restrictions. Tailed mirtrons targeted against VEGFA mRNA, the misregulation of which is causative of several disorders including cancer, achieved significant levels of gene knockdown. Tailed mirtron-mediated knockdown was further shown to be splicing-dependent, and at least as effective as equivalent artificial intronic miRNAs, with the added advantage of very defined cleavage sites for generation of mature miRNA guide strands. Further development and exploitation of this unique mirtron biogenesis pathway for therapeutic RNAi coupled into protein-expressing genes can potentially enable the development of precisely controlled combinatorial gene therapy.
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Affiliation(s)
- Kian Hong Kock
- Molecular Engineering Laboratory, Biomedical Medical Sciences Institutes, 61 Biopolis Drive Proteos #03-13 Singapore 138673
| | - Kiat Whye Kong
- Molecular Engineering Laboratory, Biomedical Medical Sciences Institutes, 61 Biopolis Drive Proteos #03-13 Singapore 138673
| | - Shawn Hoon
- Molecular Engineering Laboratory, Biomedical Medical Sciences Institutes, 61 Biopolis Drive Proteos #03-13 Singapore 138673 School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Yiqi Seow
- Molecular Engineering Laboratory, Biomedical Medical Sciences Institutes, 61 Biopolis Drive Proteos #03-13 Singapore 138673
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61
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Yuan Z, Ding S, Yan M, Zhu X, Liu L, Tan S, Jin Y, Sun Y, Li Y, Huang T. Variability of miRNA expression during the differentiation of human embryonic stem cells into retinal pigment epithelial cells. Gene 2015; 569:239-49. [PMID: 26028588 DOI: 10.1016/j.gene.2015.05.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 05/23/2015] [Accepted: 05/25/2015] [Indexed: 01/08/2023]
Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells can be induced to differentiate into retinal pigment epithelium (RPE). MiRNAs have been characterized and found playing important roles in the differentiation process of ESCs, but their length and sequence heterogeneity (isomiRs), and their non-canonical forms of miRNAs are underestimated or ignored. In this report, we found some non-canonical miRNAs (dominant isomiRs) in all differentiation stages, and 27 statistically significant editing sites were identified in 24 different miRNAs. Moreover, we found marked major-to-minor arm-switching events in 14 pre-miRNAs during the hESC to RPE cell differentiation phases. Our study for the first time reports exploring the variability of miRNA expression during the differentiation of hESCs into RPE cells and the results show that miRNA variability is a ubiquitous phenomenon in the ESC differentiation.
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Affiliation(s)
- Zhidong Yuan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China.
| | - Suping Ding
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Mingli Yan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Xiao Zhu
- Guangdong Province Key Laboratory of Medical Molecular Diagnosis, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan 523808, China
| | - Lili Liu
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Shuhua Tan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Yuanchang Jin
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Yuandong Sun
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Yufeng Li
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Ting Huang
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
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Donohoe OH, Henshilwood K, Way K, Hakimjavadi R, Stone DM, Walls D. Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs. PLoS One 2015; 10:e0125434. [PMID: 25928140 PMCID: PMC4416013 DOI: 10.1371/journal.pone.0125434] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/17/2015] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in post-transcriptional gene regulation. Some viruses encode their own miRNAs and these are increasingly being recognized as important modulators of viral and host gene expression. Cyprinid herpesvirus 3 (CyHV-3) is a highly pathogenic agent that causes acute mass mortalities in carp (Cyprinus carpio carpio) and koi (Cyprinus carpio koi) worldwide. Here, bioinformatic analyses of the CyHV-3 genome suggested the presence of non-conserved precursor miRNA (pre-miRNA) genes. Deep sequencing of small RNA fractions prepared from in vitro CyHV-3 infections led to the identification of potential miRNAs and miRNA–offset RNAs (moRNAs) derived from some bioinformatically predicted pre-miRNAs. DNA microarray hybridization analysis, Northern blotting and stem-loop RT-qPCR were then used to definitively confirm that CyHV-3 expresses two pre-miRNAs during infection in vitro. The evidence also suggested the presence of an additional four high-probability and two putative viral pre-miRNAs. MiRNAs from the two confirmed pre-miRNAs were also detected in gill tissue from CyHV-3-infected carp. We also present evidence that one confirmed miRNA can regulate the expression of a putative CyHV-3-encoded dUTPase. Candidate homologues of some CyHV-3 pre-miRNAs were identified in CyHV-1 and CyHV-2. This is the first report of miRNA and moRNA genes encoded by members of the Alloherpesviridae family, a group distantly related to the Herpesviridae family. The discovery of these novel CyHV-3 genes may help further our understanding of the biology of this economically important virus and their encoded miRNAs may have potential as biomarkers for the diagnosis of latent CyHV-3.
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Affiliation(s)
- Owen H. Donohoe
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland
| | | | - Keith Way
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Weymouth, Dorset, the United Kingdom
| | - Roya Hakimjavadi
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland
| | - David M. Stone
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Weymouth, Dorset, the United Kingdom
| | - Dermot Walls
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland
- * E-mail:
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63
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Bajan S, Hutvagner G. Regulation of miRNA processing and miRNA mediated gene repression in cancer. Microrna 2015; 3:10-7. [PMID: 25069508 PMCID: PMC4260356 DOI: 10.2174/2211536602666140110234046] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/13/2013] [Accepted: 12/20/2013] [Indexed: 12/19/2022]
Abstract
The majority of human protein-coding genes are predicted to be targets of miRNA-mediated post-transcriptional regulation. The widespread influence of miRNAs is illustrated by their essential roles in all biological processes. Regulated miRNA expression is essential for maintaining cellular differentiation; therefore alterations in miRNA expression patterns are associated with several diseases, including various cancers. High-throughput sequencing technologies revealed low level expressing miRNA isoforms, termed isomiRs. IsomiRs may differ in sequence, length, target preference and expression patterns from their parental miRNA and can arise from differences in miRNA biosynthesis, RNA editing, or SNPs inherent to the miRNA gene. The association between isomiR expression and disease progression is largely unknown. Misregulated miRNA expression is thought to contribute to the formation and/or progression of cancer. However, due to the diversity of targeted transcripts, miRNAs can function as both tumor-suppressor genes and oncogenes as defined by cellular context. Despite this, miRNA profiling studies concluded that the differential expression of particular miRNAs in diseased tissue could aid the diagnosis and treatment of some cancers.
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Affiliation(s)
| | - Gyorgy Hutvagner
- Correspondence: Faculty of Engineering and Information Technology, Centre of Health Technology, University of Technology Sydney, Sydney, Australia
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Abstract
In considering an overview of microRNA biology, it is useful to consider microRNAs as a part of cellular communication. At the simplest level, microRNAs act to decrease the expression of messenger RNAs that contain stretches of sequence complementary to the microRNA. This function can be likened to the function of endogenous or synthetic short interfering RNA. However, microRNA function is more complicated and nuanced than this "on-off" model would suggest. Further, many microRNA targets are themselves noncoding RNAs. In this review, the authors discuss the role of microRNAs in shaping the proteome of the cell in a way that is consistent with microRNA involvement in a highly regulated conversation, sensitive to outside influence and internal feedback.
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Affiliation(s)
- Justin L. Mott
- Assistant Professor, Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, Tel: 402-559-3177, Fax: 402-559-6650
| | - Ashley M. Mohr
- Postdoctoral Fellow, Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, Tel: 402-559-3170, Fax: 402-559-6650
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Song J, Jin EH, Kim D, Kim KY, Chun CH, Jin EJ. MicroRNA-222 regulates MMP-13 via targeting HDAC-4 during osteoarthritis pathogenesis. BBA CLINICAL 2014; 3:79-89. [PMID: 26673737 PMCID: PMC4661531 DOI: 10.1016/j.bbacli.2014.11.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/27/2014] [Accepted: 11/29/2014] [Indexed: 12/21/2022]
Abstract
Background Even though increasing evidences on miRNA involvement in human pathological responses, the distinct roles and related mechanisms of miRNAs in the pathology of osteoarthritis (OA) are not yet fully understood. Method RNA levels or protein levels of Apoptotic genes, HDACs, MMP-13, and miRNAs in human chondrocytes isolated from normal biopsy sample and OA cartilages were analyzed by real-time PCR or western blotting. Exogenous modulation of miR-222 level was performed using delivery of its specific precursor or specific inhibitor and target validation assay was applied to identify its potent target. In vivo study using DMM mice model was performed and assessed the degree of cartilage degradation. Results According to miRNA profiling, miR-222 was significantly down-regulated in OA chondrocytes. Over-expression of miR-222 significantly suppressed apoptotic death by down-regulating HDAC-4 and MMP-13 level. Moreover, 3′-UTR reporter assays showed that HDAC-4 is a direct target of miR-222. The treatment of chondrocytes with the HDAC inhibitor, trichostatin A (TSA), suppressed MMP-13 protein level and apoptosis, whereas the over-expression of HDAC-4 displayed opposite effects. The introduction of miR-222 into the cartilage of medial meniscus destabilized mice significantly reduced cartilage destruction and MMP-13 level. Conclusion Taken together, our data suggest that miR-222 may be involved in cartilage destruction by targeting HDAC-4 and regulating MMP-13 level. MiR-222 controls OA pathogenesis by targeting HDAC-4. HADC-4 regulated by miR-222 modulates MMP-13 expression during cartilage destruction. Our study indicates the possibility that miR-222 could act as a protective factor against OA.
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Affiliation(s)
- Jinsoo Song
- Department of Biological Sciences, College of Natural Sciences, Wonkwang University, Iksan, Chunbuk 570-749, Korea
| | - Eun-Heui Jin
- Department of Biological Sciences, College of Natural Sciences, Wonkwang University, Iksan, Chunbuk 570-749, Korea
| | - Dongkyun Kim
- Department of Biological Sciences, College of Natural Sciences, Wonkwang University, Iksan, Chunbuk 570-749, Korea
| | - Keun Young Kim
- Department of Surgery, Wonkwang University School of Medicine, Iksan, Chunbuk 570-749, Korea
| | - Churl-Hong Chun
- Department of Orthopedic Surgery, Wonkwang University School of Medicine, Iksan, Chunbuk 570-749, Korea
| | - Eun-Jung Jin
- Department of Biological Sciences, College of Natural Sciences, Wonkwang University, Iksan, Chunbuk 570-749, Korea ; Integrated Omics Institute, Wonkwang University, Iksan, Chunbuk 570-749, Korea
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66
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Cheng WC, Chung IF, Tsai CF, Huang TS, Chen CY, Wang SC, Chang TY, Sun HJ, Chao JYC, Cheng CC, Wu CW, Wang HW. YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research. Nucleic Acids Res 2014; 43:D862-7. [PMID: 25398902 PMCID: PMC4383957 DOI: 10.1093/nar/gku1156] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We previously presented YM500, which is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from 468 human smRNA-seq datasets. Here in this updated YM500v2 database (http://ngs.ym.edu.tw/ym500/), we focus on the cancer miRNome to make the database more disease-orientated. New miRNA-related algorithms developed after YM500 were included in YM500v2, and, more significantly, more than 8000 cancer-related smRNA-seq datasets (including those of primary tumors, paired normal tissues, PBMC, recurrent tumors, and metastatic tumors) were incorporated into YM500v2. Novel miRNAs (miRNAs not included in the miRBase R21) were not only predicted by three independent algorithms but also cleaned by a new in silico filtration strategy and validated by wetlab data such as Cross-Linked ImmunoPrecipitation sequencing (CLIP-seq) to reduce the false-positive rate. A new function 'Meta-analysis' is additionally provided for allowing users to identify real-time differentially expressed miRNAs and arm-switching events according to customer-defined sample groups and dozens of clinical criteria tidying up by proficient clinicians. Cancer miRNAs identified hold the potential for both basic research and biotech applications.
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Affiliation(s)
- Wei-Chung Cheng
- Research Center for Tumor Medical Science, China Medical University, Taichung 40402, Taiwan
| | - I-Fang Chung
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
| | - Cheng-Fong Tsai
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan
| | - Tse-Shun Huang
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chen-Yang Chen
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan
| | - Shao-Chuan Wang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
| | - Ting-Yu Chang
- VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan
| | - Hsing-Jen Sun
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
| | - Jeffrey Yung-Chuan Chao
- Institute of Clinical Medicine, Medical College, National Yang-Ming University, Taipei 11221, Taiwan Department of Radiation Oncology, Taichung Veterans' General Hospital, Taichung 40705, Taiwan
| | - Cheng-Chung Cheng
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defence Medical Center, Taipei 11490, Taiwan
| | - Cheng-Wen Wu
- Institute of Clinical Medicine, Medical College, National Yang-Ming University, Taipei 11221, Taiwan Institute of Biomedical Science, Academia Sinica, Taipei 11529, Taiwan Institute of Biochemistry and Molecular Biology, National Yang Ming University, Taipei 11221, Taiwan
| | - Hsei-Wei Wang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan Institute of Clinical Medicine, Medical College, National Yang-Ming University, Taipei 11221, Taiwan Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 11221, Taiwan Department of Education and Research, Taipei City Hospital, Taipei 10341, Taiwan
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Seong Y, Lim DH, Kim A, Seo JH, Lee YS, Song H, Kwon YS. Global identification of target recognition and cleavage by the Microprocessor in human ES cells. Nucleic Acids Res 2014; 42:12806-21. [PMID: 25326327 PMCID: PMC4227787 DOI: 10.1093/nar/gku957] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Microprocessor plays an essential role in canonical miRNA biogenesis by facilitating cleavage of stem-loop structures in primary transcripts to yield pre-miRNAs. Although miRNA biogenesis has been extensively studied through biochemical and molecular genetic approaches, it has yet to be addressed to what extent the current miRNA biogenesis models hold true in intact cells. To address the issues of in vivo recognition and cleavage by the Microprocessor, we investigate RNAs that are associated with DGCR8 and Drosha by using immunoprecipitation coupled with next-generation sequencing. Here, we present global protein–RNA interactions with unprecedented sensitivity and specificity. Our data indicate that precursors of canonical miRNAs and miRNA-like hairpins are the major substrates of the Microprocessor. As a result of specific enrichment of nascent cleavage products, we are able to pinpoint the Microprocessor-mediated cleavage sites per se at single-nucleotide resolution. Unexpectedly, a 2-nt 3′ overhang invariably exists at the ends of cleaved bases instead of nascent pre-miRNAs. Besides canonical miRNA precursors, we find that two novel miRNA-like structures embedded in mRNAs are cleaved to yield pre-miRNA-like hairpins, uncoupled from miRNA maturation. Our data provide a framework for in vivo Microprocessor-mediated cleavage and a foundation for experimental and computational studies on miRNA biogenesis in living cells.
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Affiliation(s)
- Youngmo Seong
- Department of Bioscience & Biotechnology, Sejong University, Seoul 143-747, Korea
| | - Do-Hwan Lim
- College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Korea
| | - Augustine Kim
- Department of Food Science & Technology, Sejong University, Seoul 143-747, Korea
| | - Jae Hong Seo
- Department of Internal Medicine, Korea University Guro Hospital, Seoul 152-703, Korea
| | - Young Sik Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Korea
| | - Hoseok Song
- Department of Biomedical Sciences, Korea University, Seoul 136-705, Korea
| | - Young-Soo Kwon
- Department of Bioscience & Biotechnology, Sejong University, Seoul 143-747, Korea
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Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that function as guide molecules in RNA silencing. Targeting most protein-coding transcripts, miRNAs are involved in nearly all developmental and pathological processes in animals. The biogenesis of miRNAs is under tight temporal and spatial control, and their dysregulation is associated with many human diseases, particularly cancer. In animals, miRNAs are ∼22 nucleotides in length, and they are produced by two RNase III proteins--Drosha and Dicer. miRNA biogenesis is regulated at multiple levels, including at the level of miRNA transcription; its processing by Drosha and Dicer in the nucleus and cytoplasm, respectively; its modification by RNA editing, RNA methylation, uridylation and adenylation; Argonaute loading; and RNA decay. Non-canonical pathways for miRNA biogenesis, including those that are independent of Drosha or Dicer, are also emerging.
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69
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Warnefors M, Liechti A, Halbert J, Valloton D, Kaessmann H. Conserved microRNA editing in mammalian evolution, development and disease. Genome Biol 2014; 15:R83. [PMID: 24964909 PMCID: PMC4197820 DOI: 10.1186/gb-2014-15-6-r83] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 06/25/2014] [Indexed: 01/31/2023] Open
Abstract
Background Mammalian microRNAs (miRNAs) are sometimes subject to adenosine-to-inosine RNA editing, which can lead to dramatic changes in miRNA target specificity or expression levels. However, although a few miRNAs are known to be edited at identical positions in human and mouse, the evolution of miRNA editing has not been investigated in detail. In this study, we identify conserved miRNA editing events in a range of mammalian and non-mammalian species. Results We demonstrate deep conservation of several site-specific miRNA editing events, including two that date back to the common ancestor of mammals and bony fishes some 450 million years ago. We also find evidence of a recent expansion of an edited miRNA family in placental mammals and show that editing of these miRNAs is associated with changes in target mRNA expression during primate development and aging. While global patterns of miRNA editing tend to be conserved across species, we observe substantial variation in editing frequencies depending on tissue, age and disease state: editing is more frequent in neural tissues compared to heart, kidney and testis; in older compared to younger individuals; and in samples from healthy tissues compared to tumors, which together suggests that miRNA editing might be associated with a reduced rate of cell proliferation. Conclusions Our results show that site-specific miRNA editing is an evolutionarily conserved mechanism, which increases the functional diversity of mammalian miRNA transcriptomes. Furthermore, we find that although miRNA editing is rare compared to editing of long RNAs, miRNAs are greatly overrepresented among conserved editing targets.
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Ma H, Wu Y, Dang Y, Choi JG, Zhang J, Wu H. Pol III Promoters to Express Small RNAs: Delineation of Transcription Initiation. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e161. [PMID: 24803291 PMCID: PMC4040628 DOI: 10.1038/mtna.2014.12] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 03/10/2014] [Indexed: 12/17/2022]
Abstract
Pol III promoters such as U6 are commonly used to express small RNAs, including small interfering RNA, short hairpin RNA, and guide RNA, for the clustered regularly interspaced short palindromic repeats genome-editing system. However, whether the small RNAs were precisely expressed as desired has not been studied. Here, using deep sequencing to analyze small RNAs, we show that, for mouse U6 promoter, sequences immediately upstream of the putative initiation site, which is often modified to accommodate the restriction enzyme sites that enable easy cloning of small RNAs, are critical for precise transcription initiation. When the promoter is kept unmodified, transcription starts precisely from the first available A or G within the range of positions −1 to +2. In addition, we show that transcription from another commonly used pol III promoter, H1, starts at multiple sites, which results in variability at the 5′ end of the transcripts. Thus, inaccuracy of 5′ end of small RNA transcripts might be a common problem when using these promoters to express small RNAs based on currently believed concepts. Our study provides general guidelines for minimizing the variability of initiation, thereby enabling more accurate expression of small RNAs.
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Affiliation(s)
- Hongming Ma
- Center of Excellence for Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Yonggan Wu
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Ying Dang
- Center of Excellence for Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Jang-Gi Choi
- Center of Excellence for Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Junli Zhang
- Center of Excellence for Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Haoquan Wu
- Center of Excellence for Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
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Xia J, Zhang W. A meta-analysis revealed insights into the sources, conservation and impact of microRNA 5'-isoforms in four model species. Nucleic Acids Res 2014; 42:1427-41. [PMID: 24178030 PMCID: PMC3919606 DOI: 10.1093/nar/gkt967] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 09/12/2013] [Accepted: 10/01/2013] [Indexed: 12/20/2022] Open
Abstract
MicroRNA (miRNA) 5'-isoforms, or 5'-isomiRs, are small-RNA species that originate from the same genomic loci as the major miRNAs with their 5' ends shifted from the 5' ends of the miRNAs by a few nucleotides. Although 5'-isomiRs have been reported, their origins, properties and potential functions remain to be examined. We systematically studied 5'-isomiRs in human, mouse, fruitfly and worm by analysing a large collection of small non-coding RNA and mRNA profiling data. The results revealed a broad existence of 5'-isomiRs in the four species, many of which were conserved and could arise from genomic loci of canonical and non-canonical miRNAs. The well-conserved 5'-isomiRs have several features, including a preference of the 3p over the 5p arms of hairpins of conserved mammalian miRNAs, altered 5'-isomiRs across species and across tissues, and association with structural variations of miRNA hairpins. Importantly, 5'-isomiRs and their major miRNAs may have different mRNA targets and thus potentially play distinct roles of gene regulation, as shown by an integrative analysis combining miRNA and mRNA profiling data from psoriatic and normal human skin and from murine miRNA knockout assays. Indeed, 18 5'-isomiRs had aberrant expression in psoriatic human skin, suggesting their potential function in psoriasis pathogenesis. The results of the current study deepened our understanding of the diversity and conservation of miRNAs, their plasticity in gene regulation and potential broad function in complex diseases.
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Affiliation(s)
- Jing Xia
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China, Department of Computer Science and Engineering, Washington University in Saint Louis, One Brookings Drive, St. Louis, MO 63130, USA and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China, Department of Computer Science and Engineering, Washington University in Saint Louis, One Brookings Drive, St. Louis, MO 63130, USA and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
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Stroynowska-Czerwinska A, Fiszer A, Krzyzosiak WJ. The panorama of miRNA-mediated mechanisms in mammalian cells. Cell Mol Life Sci 2014; 71:2253-70. [PMID: 24468964 PMCID: PMC4031385 DOI: 10.1007/s00018-013-1551-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/02/2013] [Accepted: 12/30/2013] [Indexed: 12/21/2022]
Abstract
MicroRNAs comprise a large family of short, non-coding RNAs that are present in most eukaryotic organisms and are typically involved in downregulating the expression of protein-coding genes. The detailed mechanisms of miRNA functioning in animals and plants have been under investigation for more than decade. In mammalian cells, miRNA guides the effector complex miRISC to bind with partially complementary sequences, usually within the 3′UTR of mRNAs, and inhibit protein synthesis with or without transcript degradation. In addition to these main mechanisms, several other modes of miRNA-mediated gene expression regulation have been described, but their scale and importance remain a matter of debate. In this review, we briefly summarize the pathway of miRNA precursor processing during miRNA biogenesis and continue with the description of the miRISC assembly process. Then, we present the miRNA-mediated mechanisms of gene expression regulation in detail, and we gather information concerning the proteins involved in these processes. In addition, we briefly refer to the current applications of miRNA mechanisms in therapeutic strategies. Finally, we highlight some of the remaining controversies surrounding the regulation of mammalian gene expression by miRNAs.
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Affiliation(s)
- Anna Stroynowska-Czerwinska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
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Guennewig B, Roos M, Dogar AM, Gebert LF, Zagalak JA, Vongrad V, Metzner KJ, Hall J. Synthetic pre-microRNAs reveal dual-strand activity of miR-34a on TNF-α. RNA (NEW YORK, N.Y.) 2014; 20:61-75. [PMID: 24249224 PMCID: PMC3866645 DOI: 10.1261/rna.038968.113] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 09/26/2013] [Indexed: 06/02/2023]
Abstract
Functional microRNAs (miRNAs) are produced from both arms of their precursors (pre-miRNAs). Their abundances vary in context-dependent fashion spatiotemporarily and there is mounting evidence of regulatory interplay between them. Here, we introduce chemically synthesized pre-miRNAs (syn-pre-miRNAs) as a general class of accessible, easily transfectable mimics of pre-miRNAs. These are RNA hairpins, identical in sequence to natural pre-miRNAs. They differ from commercially available miRNA mimics through their complete hairpin structure, including any regulatory elements in their terminal-loop regions and their potential to introduce both strands into RISC. They are distinguished from transcribed pre-miRNAs by their terminal 5' hydroxyl groups and their precisely defined terminal nucleotides. We demonstrate with several examples how they fully recapitulate the properties of pre-miRNAs, including their processing by Dicer into functionally active 5p; and 3p-derived mature miRNAs. We use syn-pre-miRNAs to show that miR-34a uses its 5p and 3p miRNAs in two pathways: apoptosis during TGF-β signaling, where SIRT1 and SP4 are suppressed by miR-34a-5p and miR-34a-3p, respectively; and the lipopolysaccharide (LPS)-activation of primary human monocyte-derived macrophages, where TNF (TNFα) is suppressed by miR-34a-5p indirectly and miR-34a-3p directly. Our results add to growing evidence that the use of both arms of a miRNA may be a widely used mechanism. We further suggest that syn-pre-miRNAs are ideal and affordable tools to investigate these mechanisms.
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Affiliation(s)
- Boris Guennewig
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Martina Roos
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Afzal M. Dogar
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Luca F.R. Gebert
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Julian A. Zagalak
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Valentina Vongrad
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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74
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Lower and upper stem-single-stranded RNA junctions together determine the Drosha cleavage site. Proc Natl Acad Sci U S A 2013; 110:20687-92. [PMID: 24297910 DOI: 10.1073/pnas.1311639110] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microprocessor [Drosha-DGCR8 (DiGeorge syndrome critical region gene 8) complex] processing of primary microRNA (pri-miRNA) is the critical first step in miRNA biogenesis, but how the Drosha cleavage site is determined has been unclear. Previous models proposed that the Drosha-DGCR8 complex measures either ~22 nt from the upper stem-single-stranded RNA (ssRNA, terminal loop) junction or ~11 nt from the lower stem-ssRNA junction to determine the cleavage site. Here, using miRNA-offset RNAs to determine the Drosha cleavage site, we show that the Microprocessor measures the distances from both the lower and upper stem-ssRNA junctions to determine the cleavage site in human cells, and optimal distances from both structures are critical to the precision of Drosha processing. If the distances are not optimal, Drosha tends to cleave at multiple sites, which can, in turn, generate multiple 5' isomiRs. Thus, our results also reveal a mechanism of 5' isomiR generation.
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75
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Shen XB, Xu D, Li JL, Lu LQ. Molecular cloning and immune responsive expression of a ribonuclease III orthologue involved in RNA interference, dicer, in grass carp Ctenopharyngodon idella. JOURNAL OF FISH BIOLOGY 2013; 83:1234-1248. [PMID: 24580665 DOI: 10.1111/jfb.12219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 07/19/2013] [Indexed: 06/03/2023]
Abstract
In this study, the dicer gene (designated as cidicer) was identified and characterized from grass carp Ctenopharyngodon idella. The complementary DNA (cDNA) of cidicer contained an open reading frame (ORF) of 5646 nucleotides (nts) encoding a putative protein of 1881 amino acids (aa). The deduced Dicer protein contained all known functional domains identified in other organisms. Tissue tropism analysis indicated that cidicer is abundantly expressed in brain, gill, head kidney, liver, spleen, heart, muscle and intestine. In the C. idella kidney (CIK) cells, messenger RNA (mRNA) expression of cidicer was significantly up-regulated at 24 h (6·36-fold, P < 0·01) after grass carp reovirus (GCRV) infection, and its transcriptional expression level was also transiently induced to a high level (6·54-fold, P < 0·01) at 2 h post-stimulation of synthetic double-stranded polyinosinic-polycytidylic potassium salt [poly(I:C)]. In vivo analysis further showed that the expression of cidicer mRNA in the liver was induced to a significantly high level at 12 h (8·46-fold, P < 0·01), and then dropped to normal level at 72 h post-challenge with GCRV. The transcriptional expression pattern of cidicer in the spleen tissue was similar to that of liver tissue upon GCRV challenge. These results collectively implied that the identified cidicer was an inducible gene responding to viral infection both in vitro and in vivo, and the data would shed light on the interaction between RNA interference (RNAi) antiviral pathway and aquareovirus infection.
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Affiliation(s)
- X B Shen
- Key Laboratory of Freshwater Fishery Germplasm Resources, Ministry of Agriculture of P. R. China, Shanghai Ocean University, Shanghai 201306, China
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76
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Regulation of huntingtin gene expression by miRNA-137, -214, -148a, and their respective isomiRs. Int J Mol Sci 2013; 14:16999-7016. [PMID: 23965969 PMCID: PMC3759948 DOI: 10.3390/ijms140816999] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 08/06/2013] [Accepted: 08/08/2013] [Indexed: 12/21/2022] Open
Abstract
With the advent of deep sequencing technology, a variety of miRNA length and sequence variants, termed isomiRNAs (isomiRs), have been discovered. However, the functional roles of these commonly detected isomiRs remain unknown. In this paper, we demonstrated that miRNAs regulate the expression of the HTT gene, whose mutation leads to Huntington’s disease (HD), a hereditary degenerative disorder. Specifically, we validated the interactions of canonical miRNAs, miR-137, miR-214, and miR-148a, with the HTT 3′UTR using a luciferase assay. Moreover, we applied synthetic miRNA mimics to examine whether a slight shifting of miRNA seed regions might alter the regulation of the HTT transcript. We also examined miR-137, miR-214, and miR-148a isomiRs and showed the activity of these isoforms on reporter constructs bearing appropriate sequences from the HTT 3′UTR. Hence, we demonstrated that certain 5′-end variants of miRNAs might be functional for the regulation of the same targets as canonical miRNAs.
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77
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Bettencourt P, Marion S, Pires D, Santos LF, Lastrucci C, Carmo N, Blake J, Benes V, Griffiths G, Neyrolles O, Lugo-Villarino G, Anes E. Actin-binding protein regulation by microRNAs as a novel microbial strategy to modulate phagocytosis by host cells: the case of N-Wasp and miR-142-3p. Front Cell Infect Microbiol 2013; 3:19. [PMID: 23760605 PMCID: PMC3672780 DOI: 10.3389/fcimb.2013.00019] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 05/17/2013] [Indexed: 12/26/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is a successful intracellular pathogen that thrives in macrophages (Mφs). There is a need to better understand how Mtb alters cellular processes like phagolysosome biogenesis, a classical determinant of its pathogenesis. A central feature of this bacteria's strategy is the manipulation of Mφ actin. Here, we examined the role of microRNAs (miRNAs) as a potential mechanism in the regulation of actin-mediated events leading to phagocytosis in the context of mycobacteria infection. Given that non-virulent Mycobacterium smegmatis also controls actin filament assembly to prolong its intracellular survival inside host cells, we performed a global transcriptomic analysis to assess the modulation of miRNAs upon M. smegmatis infection of the murine Mφ cell line, J774A.1. This approach identified miR-142-3p as a key candidate to be involved in the regulation of actin dynamics required in phagocytosis. We unequivocally demonstrate that miR-142-3p targets N-Wasp, an actin-binding protein required during microbial challenge. A gain-of-function approach for miR-142-3p revealed a down-regulation of N-Wasp expression accompanied by a decrease of mycobacteria intake, while a loss-of-function approach yielded the reciprocal increase of the phagocytosis process. Equally important, we show Mtb induces the early expression of miR-142-3p and partially down-regulates N-Wasp protein levels in both the murine J774A.1 cell line and primary human Mφs. As proof of principle, the partial siRNA-mediated knock down of N-Wasp resulted in a decrease of Mtb intake by human Mφs, reflected in lower levels of colony-forming units (CFU) counts over time. We therefore propose the modulation of miRNAs as a novel strategy in mycobacterial infection to control factors involved in actin filament assembly and other early events of phagolysosome biogenesis.
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Affiliation(s)
- Paulo Bettencourt
- Centro de Patogénese Molecular, Faculdade de Farmácia, Unidade dos Retrovírus e Infecções Associadas e Instituto de Medicina Molecular, Universidade de Lisboa Lisboa, Portugal
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78
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Dong H, Lei J, Ding L, Wen Y, Ju H, Zhang X. MicroRNA: Function, Detection, and Bioanalysis. Chem Rev 2013; 113:6207-33. [PMID: 23697835 DOI: 10.1021/cr300362f] [Citation(s) in RCA: 833] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Haifeng Dong
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P. R. China
| | - Jianping Lei
- State Key Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Lin Ding
- State Key Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Yongqiang Wen
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P. R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P. R. China
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79
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Chan YT, Lin YC, Lin RJ, Kuo HH, Thang WC, Chiu KP, Yu AL. Concordant and discordant regulation of target genes by miR-31 and its isoforms. PLoS One 2013; 8:e58169. [PMID: 23472152 PMCID: PMC3589381 DOI: 10.1371/journal.pone.0058169] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/30/2013] [Indexed: 01/19/2023] Open
Abstract
It has been shown that imprecise cleavage of a primary or precursor RNA by Drosha or Dicer, respectively, may yield a group of microRNA (miRNA) variants designated as "isomiR". Variations in the relative abundance of isoforms for a given miRNA among different species and different cell types beg the question whether these isomiRs might regulate target genes differentially. We compared the capacity of three miR-31 isoforms (miR-31-H, miR-31-P, and miR-31-M), which differ only slightly in their 5'- and/or 3'-end sequences, to regulate several known targets and a predicted target, Dicer. Notably, we found isomiR-31s displayed concordant and discordant regulation of 6 known target genes. Furthermore, we validated a predicted target gene, Dicer, to be a novel target of miR-31 but only miR-31-P could directly repress Dicer expression in both MCF-7 breast cancer cells and A549 lung cancer cells, resulting in their enhanced sensitivity to cisplatin, a known attribute of Dicer knockdown. This was further supported by reporter assay using full length 3'-untranslated region (UTR) of Dicer. Our findings not only revealed Dicer to be a direct target of miR-31, but also demonstrated that isomiRs displayed similar and disparate regulation of target genes in cell-based systems. Coupled with the variations in the distribution of isomiRs among different cells or conditions, our findings support the possibility of fine-tuning gene expression by miRNAs.
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Affiliation(s)
- Yu-Tzu Chan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - You-Chin Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Ruey-Jen Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Huan-Hsien Kuo
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Alice L. Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Department of Pediatrics/Hematology-Oncology, University of California San Diego Medical Center, San Diego, California, United States of America
- * E-mail:
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80
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Starega-Roslan J, Krzyzosiak WJ. Analysis of microRNA length variety generated by recombinant human Dicer. Methods Mol Biol 2013; 936:21-34. [PMID: 23007496 DOI: 10.1007/978-1-62703-083-0_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
miRNAs are a large subgroup of noncoding regulatory RNAs, which vary in length within the 20-25 nt range and show substantial length diversity and heterogeneity. To analyze the latter phenomenon, we recently developed high-resolution northern blotting and employed this method to investigate cleavages generated by recombinant human Dicer in the synthetic miRNA precursors. We paid special care to visualize clearly the cleavages generated by the individual RNase III domains of Dicer. We have compared the results of northern blotting with the results of standard analysis with the use of end-labeled RNA and visualization of Dicer cleavage products by autoradiography. The point-by-point steps of substrate preparation, recombinant Dicer cleavage assay, and northern blotting are described in this manuscript.
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Affiliation(s)
- Julia Starega-Roslan
- Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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81
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Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs. Cell 2012; 151:521-32. [PMID: 23063654 DOI: 10.1016/j.cell.2012.09.022] [Citation(s) in RCA: 228] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 06/26/2012] [Accepted: 08/15/2012] [Indexed: 11/23/2022]
Abstract
RNase III Drosha initiates microRNA (miRNA) maturation by cleaving a primary miRNA transcript and releasing a pre-miRNA with a 2 nt 3' overhang. Dicer recognizes the 2 nt 3' overhang structure to selectively process pre-miRNAs. Here, we find that, unlike prototypic pre-miRNAs (group I), group II pre-miRNAs acquire a shorter (1 nt) 3' overhang from Drosha processing and therefore require a 3'-end mono-uridylation for Dicer processing. The majority of let-7 and miR-105 belong to group II. We identify TUT7/ZCCHC6, TUT4/ZCCHC11, and TUT2/PAPD4/GLD2 as the terminal uridylyl transferases responsible for pre-miRNA mono-uridylation. The TUTs act specifically on dsRNAs with a 1 nt 3' overhang, thereby creating a 2 nt 3' overhang. Depletion of TUTs reduces let-7 levels and disrupts let-7 function. Although the let-7 suppressor, Lin28, induces inhibitory oligo-uridylation in embryonic stem cells, mono-uridylation occurs in somatic cells lacking Lin28 to promote let-7 biogenesis. Our study reveals functional duality of uridylation and introduces TUT7/4/2 as components of the miRNA biogenesis pathway.
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82
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Montag J, Brameier M, Schmädicke AC, Gilch S, Schätzl HM, Motzkus D. A genome-wide survey for prion-regulated miRNAs associated with cholesterol homeostasis. BMC Genomics 2012; 13:486. [PMID: 22985096 PMCID: PMC3477035 DOI: 10.1186/1471-2164-13-486] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 09/10/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Prion diseases are neurodegenerative diseases that are characterized by the conversion of the cellular prion protein (PrPc) into a pathogenic isoform (PrPSc). It is known that neurodegeneration is often accompanied by the disturbance of cholesterol homeostasis. We have recently identified a set of genes that were upregulated after prion infection of N2a neuronal cells (Bach et al., 2009). RESULTS We have now used ultra-deep sequencing technology to profile all microRNAs (miRNA) that could be associated with this effect in these N2a cells. Using stringent filters and normalization strategies we identified a small set of miRNAs that were up- or downregulated upon prion infection. Using bioinformatic tools we predicted whether the downregulated miRNAs could target mRNAs that have been previously identified to enhance cholesterol synthesis in these cells. Application of this joint profiling approach revealed that nine miRNAs potentially target cholesterol-related genes. Four of those miRNAs are localized in a miRNA-dense cluster on the mouse X-chromosome. Among these, twofold downregulation of mmu-miR-351 and mmu-miR-542-5p was confirmed by qRT-PCR. The same miRNAs were predicted as putative regulators of the sterol regulatory element-binding factor 2 (Srebf2), the low-density lipoprotein receptor (Ldlr) or the IPP isomerase. CONCLUSIONS The results demonstrate that joined profiling by ultra-deep sequencing is highly valuable to identify candidate miRNAs involved in prion-induced dysregulation of cholesterol homeostasis.
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Affiliation(s)
- Judith Montag
- German Primate Center, Unit of Infection Models, Kellnerweg, 4, 37077, Göttingen, Germany
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83
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Deep sequencing reveals small RNA characterization of invasive micropapillary carcinomas of the breast. Breast Cancer Res Treat 2012; 136:77-87. [PMID: 22976804 DOI: 10.1007/s10549-012-2166-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 07/10/2012] [Indexed: 12/14/2022]
Abstract
Invasive micropapillary carcinoma (IMPC) is an uncommon histological type of breast cancer. IMPC has a special growth pattern and a more aggressive behavior than invasive ductal carcinomas of no special types (IDC-NSTs). microRNAs are a large class of non-coding RNAs involved in the regulation of various biological processes. Here, we analyzed the small RNA transcriptomes of five formalin-fixed paraffin-embedded (FFPE) pure IMPC samples and five FFPE IDC-NSTs samples by means of next-generation sequencing, generating a total of >170,000,000 clean reads. In an unsupervised cluster analysis, differently expressed miRNAs generated a tree with clear distinction between IMPC and IDC-NSTs classes. Paired fresh-frozen and FFPE specimens showed very similar miRNA expression profiles. By means of RT-qPCR, we further investigated miRNA expression in more IMPC (n = 22) and IDC-NSTs (n = 24) FFPE samples and found let-7b, miR-30c, miR-148a, miR-181a, miR-181a*, and miR-181b were significantly differently expressed between the two groups. We also elucidated several features of miRNA in these breast cancer tissues including 5' variability, miRNA editing, and 3' untemplated addition. Our findings will lead to further understanding of the invasive potency of IMPC and gain an insight into the diversity and complexity of small RNA molecules in breast cancer tissues.
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84
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Song FJ, Chen KX. Single-nucleotide polymorphisms among microRNA: big effects on cancer. CHINESE JOURNAL OF CANCER 2012; 30:381-91. [PMID: 21627860 PMCID: PMC4013412 DOI: 10.5732/cjc.011.10142] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the transcriptional or posttranscriptional level. Many miRNAs are found to play a significant role in cancer development either as tumor suppressor genes or as oncogenes. Examination of tumor-specific miRNA expression profiles in diverse cancers has revealed widespread deregulation of these molecules, whose loss and overexpression respectively have diagnostic and prognostic significance. Genetic variations, mostly single-nucleotide polymorphisms (SNPs) within miRNA sequences or their target sites, have been found to be associated with many kinds of cancers. In this review, we summarize the current knowledge of miRNAs including their biogenesis and role in cancer development, and finally, how SNPs among miRNAs affect miRNA biogenesis and contribute to cancer.
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Affiliation(s)
- Feng-Ju Song
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Hospital and Institute, Tianjin 300060, People's Republic of China
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85
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Neilsen CT, Goodall GJ, Bracken CP. IsomiRs--the overlooked repertoire in the dynamic microRNAome. Trends Genet 2012; 28:544-9. [PMID: 22883467 DOI: 10.1016/j.tig.2012.07.005] [Citation(s) in RCA: 343] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/09/2012] [Accepted: 07/12/2012] [Indexed: 12/13/2022]
Abstract
The development of deep sequencing has enabled the identification of novel microRNAs (miRNAs), leading to a growing appreciation for the fact that individual miRNAs can be heterogeneous in length and/or sequence. These variants, termed isomiRs, can be expressed in a cell-specific manner, and numerous recent studies suggest that at least some isomiRs may affect target selection, miRNA stability, or loading into the RNA-induced silencing complex (RISC). Reports indicating differential functionality for isomiRs are currently confined to several specific variants, and although isomiRs are common, their broader biological significance is yet to be fully resolved. Here we review the growing body of evidence suggesting that isomiRs have functional differences, of which at least some appear biologically relevant, and caution researchers to take miRNA isoforms into consideration in their experiments.
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Affiliation(s)
- Corine T Neilsen
- Centre for Cancer Biology, SA Pathology, Frome Road, Adelaide, South Australia, 5000, Australia
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86
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Sibley CR, Seow Y, Curtis H, Weinberg MS, Wood MJA. Silencing of Parkinson's disease-associated genes with artificial mirtron mimics of miR-1224. Nucleic Acids Res 2012; 40:9863-75. [PMID: 22848108 PMCID: PMC3479180 DOI: 10.1093/nar/gks712] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mirtrons are a recently described category of microRNA (miRNA) relying on splicing rather than processing by the microprocessor complex to generate pre-miRNA precursors of the RNA interference (RNAi) pathway. Their discovery and subsequent verification provides important information about a distinct class of miRNA and inherent advantages that could be exploited to silence genes of interest. These include micro-processor-independent biogenesis, pol-II-dependent transcription, accurate species generation and the delivery of multiple artificial mirtrons as introns within a single host transcript. Here we determined the sequence motifs required for correct processing of the mmu-miR-1224 mirtron and incorporated these into artificial mirtrons targeting Parkinson's disease-associated LRRK2 and α-synuclein genes. By incorporating these rules associated with processing and splicing, artificial mirtrons could be designed and made to silence complementary targets either at the mRNA or protein level. We further demonstrate with a LRRK2 targeting artificial mirtron that neuronal-specific silencing can be directed under the control of the human synapsin promoter. Finally, multiple mirtrons were co-delivered within a single host transcript, an eGFP reporter, to allow simultaneous targeting of two or more targets in a combinatorial approach. Thus, the unique characteristics of artificial mirtrons make this an attractive approach for future RNAi applications.
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Affiliation(s)
- Christopher R Sibley
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
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87
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Seow Y, Sibley CR, Wood MJ. Artificial mirtron-mediated gene knockdown: functional DMPK silencing in mammalian cells. RNA (NEW YORK, N.Y.) 2012; 18:1328-1337. [PMID: 22647847 PMCID: PMC3383964 DOI: 10.1261/rna.030601.111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 05/04/2012] [Indexed: 06/01/2023]
Abstract
Mirtrons are introns that form pre-miRNA hairpins after splicing to produce RNA interference (RNAi) effectors distinct from Drosha-dependent intronic miRNAs. Here we present a design algorithm for artificial mirtrons and demonstrate, for the first time, efficient gene knockdown of myotonic dystrophy protein kinase (DMPK) target sequences in Renilla luciferase 3' UTR and subsequently pathogenic DMPK mRNA, causative of Type I myotonic dystrophy, using artificial mirtrons cloned as eGFP introns. Deep sequencing of artificial mirtrons suggests that functional mature transcripts corresponding to the designed sequence were produced in high abundance. They were further shown to be splicing-dependent, Drosha-independent, and partially dependent on exportin-5, resulting in the precise generation of pre-miRNAs. In a murine myoblast line containing a pathogenic copy of human DMPK with more than 500 CUG repeats, the DMPK artificial mirtron corrected DM1-associated splicing abnormalities of the Serca-1 mRNA, demonstrating the therapeutic potential of mirtron-mediated RNAi. Thus, further development and exploitation of the unique properties of mirtrons will benefit future research and therapeutic RNAi applications as an alternative to conventional RNAi strategies.
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Affiliation(s)
- Yiqi Seow
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
- Molecular Engineering Laboratory, Science and Engineering Institutes, Singapore 138668
| | - Christopher R. Sibley
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Matthew J.A. Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
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88
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Curtis HJ, Sibley CR, Wood MJA. Mirtrons, an emerging class of atypical miRNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:617-32. [PMID: 22733569 DOI: 10.1002/wrna.1122] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Post-transcriptional gene silencing (PTGS) via RNA interference (RNAi) is a vital gene regulatory mechanism for fine-tuning gene expression. RNAi effectors termed microRNAs (miRNAs) are implicated in various aspects of animal development and normal physiological function, while dysregulation has been linked to several pathologies. Several atypical miRNA biogenesis pathways have been identified, yet in most cases the reasons for their emergence remain unclear. One of these atypical pathways is the mirtron pathway, where short introns are excised by splicing to generate intermediates of the RNAi pathway, with no cleavage by the microprocessor. Closely related pathways involving tailed-mirtron and simtron biogenesis have also been described. There is extensive evidence that mirtrons function as miRNAs, and while some are evolutionarily conserved across similar species, others appear to have emerged relatively recently. In addition, through exploitation of the potent and sequence-specific silencing capabilities of RNAi, synthetic mirtrons may have potential for overcoming certain therapeutic challenges.
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Affiliation(s)
- Helen J Curtis
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
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89
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Chugh P, Dittmer DP. Potential pitfalls in microRNA profiling. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:601-16. [PMID: 22566380 DOI: 10.1002/wrna.1120] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that post-transcriptionally influence a wide range of cellular processes such as the host response to viral infection, innate immunity, cell cycle progression, migration, and apoptosis through the inhibition of target mRNA translation. Owing to the growing number of miRNAs and identification of their functional roles, miRNA profiling of many different sample types has become more expansive, especially with relevance to disease signatures. In this review, we address some of the advantages and potential pitfalls of the currently available methods for miRNA expression profiling. Some of the topics discussed include isomiRNAs, comparison of different profiling platforms, normalization strategies, and issues with regard to sample preparation and experimental analyses.
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Affiliation(s)
- Pauline Chugh
- Department of Microbiology, UNC-Chapel Hill, Chapel Hill, NC, USA
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90
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Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. Cell Host Microbe 2012; 10:515-26. [PMID: 22100165 DOI: 10.1016/j.chom.2011.09.012] [Citation(s) in RCA: 244] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 07/26/2011] [Accepted: 09/26/2011] [Indexed: 12/11/2022]
Abstract
Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus (KSHV) and frequently also harbors Epstein-Barr virus (EBV). The expression of KSHV- and EBV-encoded microRNAs (miRNAs) in PELs suggests a role for these miRNAs in latency and lymphomagenesis. Using PAR-CLIP, a technology which allows the direct and transcriptome-wide identification of miRNA targets, we delineate the target sites for all viral and cellular miRNAs expressed in PEL cell lines. The resulting data set revealed that KSHV miRNAs directly target more than 2000 cellular mRNAs, including many involved in pathways relevant to KSHV pathogenesis. Moreover, 58% of these mRNAs are also targeted by EBV miRNAs, via distinct binding sites. In addition to a known viral analog of cellular miR-155, we show that KSHV encodes a viral miRNA that mimics cellular miR-142-3p function. In summary, this study identifies an extensive list of KSHV miRNA targets, which are likely to influence viral replication and pathogenesis.
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91
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Voellenkle C, van Rooij J, Guffanti A, Brini E, Fasanaro P, Isaia E, Croft L, David M, Capogrossi MC, Moles A, Felsani A, Martelli F. Deep-sequencing of endothelial cells exposed to hypoxia reveals the complexity of known and novel microRNAs. RNA (NEW YORK, N.Y.) 2012; 18:472-84. [PMID: 22282338 PMCID: PMC3285935 DOI: 10.1261/rna.027615.111] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 12/07/2011] [Indexed: 05/24/2023]
Abstract
In order to understand the role of microRNAs (miRNAs) in vascular physiopathology, we took advantage of deep-sequencing techniques to accurately and comprehensively profile the entire miRNA population expressed by endothelial cells exposed to hypoxia. SOLiD sequencing of small RNAs derived from human umbilical vein endothelial cells (HUVECs) exposed to 1% O₂ or normoxia for 24 h yielded more than 22 million reads per library. A customized bioinformatic pipeline identified more than 400 annotated microRNA/microRNA* species with a broad abundance range: miR-21 and miR-126 totaled almost 40% of all miRNAs. A complex repertoire of isomiRs was found, displaying also 5' variations, potentially affecting target recognition. High-stringency bioinformatic analysis identified microRNA candidates, whose predicted pre-miRNAs folded into a stable hairpin. Validation of a subset by qPCR identified 18 high-confidence novel miRNAs as detectable in independent HUVEC cultures and associated to the RISC complex. The expression of two novel miRNAs was significantly down-modulated by hypoxia, while miR-210 was significantly induced. Gene ontology analysis of their predicted targets revealed a significant association to hypoxia-inducible factor signaling, cardiovascular diseases, and cancer. Overexpression of the novel miRNAs in hypoxic endothelial cells affected cell growth and confirmed the biological relevance of their down-modulation. In conclusion, deep-sequencing accurately profiled known, variant, and novel microRNAs expressed by endothelial cells in normoxia and hypoxia.
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Affiliation(s)
- Christine Voellenkle
- Laboratorio di Cardiologia Molecolare, IRCCS-Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Jeroen van Rooij
- Laboratorio di Cardiologia Molecolare, IRCCS-Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | | | | | - Pasquale Fasanaro
- Laboratorio di Patologia Vascolare, Istituto Dermopatico dell'Immacolata-IRCCS, 00167 Rome, Italy
| | - Eleonora Isaia
- Laboratorio di Cardiologia Molecolare, IRCCS-Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Larry Croft
- Institute for Molecular Bioscience, University of Queensland, 4072 Brisbane, Australia
| | - Matei David
- Computational Biology Laboratory, University of Toronto, M5S 3G4 Toronto, Canada
| | - Maurizio C. Capogrossi
- Laboratorio di Patologia Vascolare, Istituto Dermopatico dell'Immacolata-IRCCS, 00167 Rome, Italy
| | - Anna Moles
- Genomnia srl, Lainate, 20020 Milan, Italy
| | | | - Fabio Martelli
- Laboratorio di Patologia Vascolare, Istituto Dermopatico dell'Immacolata-IRCCS, 00167 Rome, Italy
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92
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A potential regulatory role for intronic microRNA-338-3p for its host gene encoding apoptosis-associated tyrosine kinase. PLoS One 2012; 7:e31022. [PMID: 22363537 PMCID: PMC3281898 DOI: 10.1371/journal.pone.0031022] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/31/2011] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are important gene regulators that are abundantly expressed in both the developing and adult mammalian brain. These non-coding gene transcripts are involved in post-transcriptional regulatory processes by binding to specific target mRNAs. Approximately one third of known miRNA genes are located within intronic regions of protein coding and non-coding regions, and previous studies have suggested a role for intronic miRNAs as negative feedback regulators of their host genes. In the present study, we monitored the dynamic gene expression changes of the intronic miR-338-3p and miR-338-5p and their host gene Apoptosis-associated Tyrosine Kinase (AATK) during the maturation of rat hippocampal neurons. This revealed an uncorrelated expression pattern of mature miR-338 strands with their host gene. Sequence analysis of the 3′ untranslated region (UTR) of rat AATK mRNA revealed the presence of two putative binding sites for miR-338-3p. Thus, miR-338-3p may have the capacity to modulate AATK mRNA levels in neurons. Transfection of miR-338-3p mimics into rat B35 neuroblastoma cells resulted in a significant decrease of AATK mRNA levels, while the transfection of synthetic miR-338-5p mimics did not alter AATK levels. Our results point to a possible molecular mechanism by which miR-338-3p participates in the regulation of its host gene by modulating the levels of AATK mRNA, a kinase which plays a role during differentiation, apoptosis and possibly in neuronal degeneration.
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93
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Cloonan N, Wani S, Xu Q, Gu J, Lea K, Heater S, Barbacioru C, Steptoe AL, Martin HC, Nourbakhsh E, Krishnan K, Gardiner B, Wang X, Nones K, Steen JA, Matigian NA, Wood DL, Kassahn KS, Waddell N, Shepherd J, Lee C, Ichikawa J, McKernan K, Bramlett K, Kuersten S, Grimmond SM. MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biol 2011; 12:R126. [PMID: 22208850 PMCID: PMC3334621 DOI: 10.1186/gb-2011-12-12-r126] [Citation(s) in RCA: 270] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 09/21/2011] [Accepted: 12/30/2011] [Indexed: 12/15/2022] Open
Abstract
Background Variants of microRNAs (miRNAs), called isomiRs, are commonly reported in deep-sequencing studies; however, the functional significance of these variants remains controversial. Observational studies show that isomiR patterns are non-random, hinting that these molecules could be regulated and therefore functional, although no conclusive biological role has been demonstrated for these molecules. Results To assess the biological relevance of isomiRs, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline called miRNA-MATE to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. A large proportion of isomiRs potentially derive from AGO2 cleavage independent of Dicer. We isolated polyribosome-associated mRNA, captured the mRNA-bound miRNAs, and found that isomiRs and canonical miRNAs are equally associated with translational machinery. Finally, we transfected cells with biotinylated RNA duplexes encoding isomiRs or their canonical counterparts and directly assayed their mRNA targets. These studies allow us to experimentally determine genome-wide mRNA targets, and these experiments showed substantial overlap in functional mRNA networks suppressed by both canonical miRNAs and their isomiRs. Conclusions Together, these results find isomiRs to be biologically relevant and functionally cooperative partners of canonical miRNAs that act coordinately to target pathways of functionally related genes. This work exposes the complexity of the miRNA-transcriptome, and helps explain a major miRNA paradox: how specific regulation of biological processes can occur when the specificity of miRNA targeting is mediated by only 6 to 11 nucleotides.
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Affiliation(s)
- Nicole Cloonan
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.
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94
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Wu H, Ma H, Ye C, Ramirez D, Chen S, Montoya J, Shankar P, Wang XA, Manjunath N. Improved siRNA/shRNA functionality by mismatched duplex. PLoS One 2011; 6:e28580. [PMID: 22174840 PMCID: PMC3235145 DOI: 10.1371/journal.pone.0028580] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 11/10/2011] [Indexed: 11/26/2022] Open
Abstract
siRNA (small interfering RNA) and shRNA (small hairpin RNA) are powerful and commonly used tools in biomedical research. Currently, siRNAs are generally designed as two 21 nt strands of RNA that include a 19 nt completely complementary part and a 2 nt overhang. However, since the si/shRNAs use the endogenous miRNA machinery for gene silencing and the miRNAs are generally 22 nt in length and contain multiple internal mismatches, we tested if the functionality can be increased by designing the si/shRNAs to mimic a miRNA structure. We systematically investigated the effect of single or multiple mismatches introduced in the passenger strand at different positions on siRNA functionality. Mismatches at certain positions could significantly increase the functionality of siRNAs and also, in some cases decreased the unwanted passenger strand functionality. The same strategy could also be used to design shRNAs. Finally, we showed that both si and miRNA structured oligos (siRNA with or without mismatches in the passenger strand) can repress targets in all individual Ago containing cells, suggesting that the Ago proteins do not differentiate between si/miRNA-based structure for silencing activity.
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Affiliation(s)
- Haoquan Wu
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
- * E-mail: (HW); (NM)
| | - Hongming Ma
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Chunting Ye
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Danielle Ramirez
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Shuiping Chen
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Jessica Montoya
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Premlata Shankar
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
| | - Xiaozhong A. Wang
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, United States of America
| | - N. Manjunath
- Center of Excellence in Infectious Disease Research, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, United States of America
- * E-mail: (HW); (NM)
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95
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Cazalla D, Xie M, Steitz JA. A primate herpesvirus uses the integrator complex to generate viral microRNAs. Mol Cell 2011; 43:982-92. [PMID: 21925386 PMCID: PMC3176678 DOI: 10.1016/j.molcel.2011.07.025] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 07/05/2011] [Accepted: 07/28/2011] [Indexed: 11/17/2022]
Abstract
Herpesvirus saimiri (HVS) is a γ-herpesvirus that expresses Sm class U RNAs (HSURs) in latently infected marmoset T cells. By deep sequencing, we identified six HVS microRNAs (miRNAs) that are derived from three hairpin structures located immediately downstream of the 3' end processing signals of three of the HSURs. The viral miRNAs associate with Ago proteins and are biologically active. We confirmed that the expression of the two classes of viral noncoding RNAs is linked by identifying chimeric HSUR-pre-miRNA transcripts. We show that HVS miRNA biogenesis relies on cis-acting elements specifically required for synthesis and processing of Sm class RNAs. Knockdown of protein components in vivo and processing assays in vitro demonstrated that HVS does not utilize the Microprocessor complex that generates most host miRNAs. Instead, the Integrator complex cleaves to generate the 3' end of the HSUR and the pre-miRNA hairpin. Exportin-5 and Dicer are then required to generate mature viral miRNAs.
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Affiliation(s)
- Demián Cazalla
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
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96
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Duan D, Zheng KX, Shen Y, Cao R, Jiang L, Lu Z, Yan X, Li J. Label-free high-throughput microRNA expression profiling from total RNA. Nucleic Acids Res 2011; 39:e154. [PMID: 21976734 PMCID: PMC3239174 DOI: 10.1093/nar/gkr774] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
MicroRNAs (miRNAs) are key biological regulators and promising disease markers whose detection technologies hold great potentials in advancing fundamental research and medical diagnostics. Currently, miRNAs in biological samples have to be labeled before being applied to most high-throughput assays. Although effective, these labeling-based approaches are usually labor-intensive, time-consuming and liable to bias. Besides, the cross-hybridization of co-existing miRNA precursors (pre-miRNAs) is not adequately addressed in most assays that use total RNA as input. Here, we present a hybridization-triggered fluorescence strategy for label-free, microarray-based high-throughput miRNA expression profiling. The total RNA is directly applied to the microarray with a short fluorophore-linked oligonucleotide Universal Tag which can be selectively captured by the target-bound probes via base-stacking effects. This Stacking-Hybridized Universal Tag (SHUT) assay has been successfully used to analyze as little as 100 ng total RNA from human tissues, and found to be highly specific to homogenous miRNAs. Superb discrimination toward single-base mismatch at the 5′ or 3′ end has been demonstrated. Importantly, the pre-miRNAs generated negligible signals, validating the direct use of total RNA.
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Affiliation(s)
- Demin Duan
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, 398 Ruoshui Road, Suzhou, 215123, China
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97
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Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs. Proc Natl Acad Sci U S A 2011; 108:15942-7. [PMID: 21911382 DOI: 10.1073/pnas.1110098108] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
There exists an inverse relationship between the rate of molecular evolution and the level of gene expression. Among the many explanations, the "toxic-error" hypothesis is a most general one, which posits that processing errors may often be toxic to the cells. However, toxic errors that constrain the evolution of highly expressed genes are often difficult to measure. In this study, we test the toxic-error hypothesis by using microRNA (miRNA) genes because their processing errors can be directly measured by deep sequencing. A miRNA gene consists of a small mature product (≈22 nt long) and a "backbone." Our analysis shows that (i) like the mature miRNA, the backbone is highly conserved; (ii) the rate of sequence evolution in the backbone is negatively correlated with expression; and (iii) although conserved between distantly related species, the error rate in miRNA processing is also negatively correlated with the expression level. The observations suggest that, as a miRNA gene becomes more highly (or more ubiquitously) expressed, its sequence evolves toward a structure that minimizes processing errors.
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98
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Dicer recognizes the 5' end of RNA for efficient and accurate processing. Nature 2011; 475:201-5. [PMID: 21753850 DOI: 10.1038/nature10198] [Citation(s) in RCA: 373] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 05/16/2011] [Indexed: 11/09/2022]
Abstract
A hallmark of RNA silencing is a class of approximately 22-nucleotide RNAs that are processed from double-stranded RNA precursors by Dicer. Accurate processing by Dicer is crucial for the functionality of microRNAs (miRNAs). The current model posits that Dicer selects cleavage sites by measuring a set distance from the 3' overhang of the double-stranded RNA terminus. Here we report that human Dicer anchors not only the 3' end but also the 5' end, with the cleavage site determined mainly by the distance (∼22 nucleotides) from the 5' end (5' counting rule). This cleavage requires a 5'-terminal phosphate group. Further, we identify a novel basic motif (5' pocket) in human Dicer that recognizes the 5'-phosphorylated end. The 5' counting rule and the 5' anchoring residues are conserved in Drosophila Dicer-1, but not in Giardia Dicer. Mutations in the 5' pocket reduce processing efficiency and alter cleavage sites in vitro. Consistently, miRNA biogenesis is perturbed in vivo when Dicer-null embryonic stem cells are replenished with the 5'-pocket mutant. Thus, 5'-end recognition by Dicer is important for precise and effective biogenesis of miRNAs. Insights from this study should also afford practical benefits to the design of small hairpin RNAs.
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99
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Potter SS, Brunskill EW, Patterson LT. Microdissection of the gene expression codes driving nephrogenesis. Organogenesis 2011; 6:263-9. [PMID: 21220959 DOI: 10.4161/org.6.4.12682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The kidney represents an excellent model system for learning the principles of organogenesis. It is intermediate in complexity, and employs many commonly used developmental processes. As such, kidney development has been the subject of intensive study, using a variety of techniques, including in situ hybridization, organ culture and gene targeting, revealing many critical genes and pathways. Nevertheless, proper organogenesis requires precise patterns of cell type specific differential gene expression, involving very large numbers of genes. This review is focused on the use of global profiling technologies to create an atlas of gene expression codes driving development of different mammalian kidney compartments. Such an atlas allows one to select a gene of interest, and to determine its expression level in each element of the developing kidney, or to select a structure of interest, such as the renal vesicle, and to examine its complete gene expression state. Novel component specific molecular markers are identified, and the changing waves of gene expression that drive nephrogenesis are defined. As the tools continue to improve for the purification of specific cell types and expression profiling of even individual cells it is possible to predict an atlas of gene expression during kidney development that extends to single cell resolution.
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Affiliation(s)
- S Steven Potter
- Division of Developmental Biology, Children’s Hospital Medical Center, Cincinnati, OH, USA.
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100
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The role of the precursor structure in the biogenesis of microRNA. Cell Mol Life Sci 2011; 68:2859-71. [PMID: 21607569 PMCID: PMC3155042 DOI: 10.1007/s00018-011-0726-2] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/20/2011] [Accepted: 05/03/2011] [Indexed: 12/18/2022]
Abstract
The human genome contains more than 1,000 microRNA (miRNA) genes, which are transcribed mainly by RNA polymerase II. The canonical pathway of miRNA biogenesis includes the nuclear processing of primary transcripts (pri-miRNAs) by the ribonuclease Drosha and further cytoplasmic processing of pre-miRNAs by the ribonuclease Dicer. This review discusses the issue of miRNA end heterogeneity generated primarily by Drosha and Dicer cleavage and focuses on the structural aspects of the Dicer step of miRNA biogenesis. We examine the structures of miRNA precursors, both predicted and experimentally determined, as well as the influence of various motifs that disturb the regularity of pre-miRNA structure on Dicer cleavage specificity. We evaluate the structural determinants of the length diversity of miRNA generated by Dicer from different precursors and highlight the importance of asymmetrical motifs. Finally, we discuss the impact of Dicer protein partners on cleavage efficiency and specificity and propose the contribution of pre-miRNA structural plasticity to the dynamics of the dicing complex.
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