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Shen Y, Tian F, Tu J, Li R, Chen Z, Bai Y, Ge Q, Lu Z. Construction and optimization of an efficient breathing-based isothermal emulsion amplification method. Anal Chim Acta 2017; 973:43-50. [PMID: 28502426 DOI: 10.1016/j.aca.2017.03.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/20/2017] [Accepted: 03/26/2017] [Indexed: 11/25/2022]
Abstract
The reaction temperature is one of the main factors that affect the stability of emulsion PCR (emPCR). Focusing on this point, we applied the "DNA breathing" mechanism in BEAMing (Bead, Emulsion, Amplification, and Magnetic) and proposed a more stable emulsion amplification method. Compared to the conventional emPCR, this method provided excellent results. Firstly, more stable emulsion system resulted in higher percentage of single-molecular amplifications (73.17%). Secondly, an ordinary temperature-controlling device was enough. Our outcome showed that the reaction temperature of this method was not strict so that the ordinary temperature-controlling device was enough for it (the heat block sets vs. the PCR instrument: 13.140 ± 0.110 vs. 13.008 ± 0.039, P = 0.120). Thirdly, the single-biotinylated emP1 coated streptavidin beads were stable enough to be used for this method (the control temperature vs. the reaction temperature: 2967.91 ± 409.045 vs. 3026.22 ± 442.129, P = 0.334), which could replace the double-biotinylated emP1 coated beads and was benefit for saving cost. In conclusion, the method presented here with stable emulsion system, simplified temperature-controlling device, and decreased investment would be a highly streamlined and inexpensive option for future single-molecular amplification based researches.
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Affiliation(s)
- Yanting Shen
- Research Center for Learning Science, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096, PR China.
| | - Fei Tian
- Research Center for Learning Science, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096, PR China.
| | - Jing Tu
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096, PR China.
| | - Rui Li
- Research Center for Learning Science, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096, PR China.
| | - Zhenzhu Chen
- Research Center for Learning Science, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096, PR China.
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096, PR China.
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096, PR China.
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096, PR China.
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2
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Liang T, Yu J, Liu C, Guo L. IsomiR expression patterns in canonical and Dicer‑independent microRNAs. Mol Med Rep 2017; 15:1071-1078. [PMID: 28098889 PMCID: PMC5367367 DOI: 10.3892/mmr.2017.6117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 11/11/2016] [Indexed: 11/23/2022] Open
Abstract
Multiple microRNA (miRNA) variants, known as isomiRs, are extensively distributed in miRNA loci and predominantly derive from the alternative cleavage of Drosha/Dicer and 3′addition events. The present study aimed to investigate the expression patterns of multiple isomiRs in typical miRNA and Dicer-independent miRNA loci by conducting evolutionary and expression analysis using public datasets. Although different miRNA maturation processes exist, multiple isomiRs can be detected by similar expression distributions. However, isomiR expression in Dicer-independent miRNA loci tends to be at a moderate level, particularly for random distribution in the ends that are split by Dicer in the typical miRNA loci. Compared with the mature miRNA locus (dominant miRNA locus), the non-dominant miRNA locus indicates an expression distribution similar to that of the Dicer-independent miRNA locus. These results increase the understanding of multiple isomiRs in the progression of diseases.
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Affiliation(s)
- Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Jiafeng Yu
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong 253023, P.R. China
| | - Chang Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Li Guo
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu 210023, P.R. China
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3
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Guo L, Yu J, Liang T, Zou Q. miR-isomiRExp: a web-server for the analysis of expression of miRNA at the miRNA/isomiR levels. Sci Rep 2016; 6:23700. [PMID: 27009551 PMCID: PMC4806314 DOI: 10.1038/srep23700] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/09/2016] [Indexed: 12/22/2022] Open
Abstract
MicroRNA (miRNA) locus has been found that can generate a series of varied isomiR sequences. Most studies always focus on determining miRNA level, however, the canonical miRNA sequence is only a specific member in the multiple isomiRs. Some studies have shown that isomiR sequences play versatile roles in biological progress, and the analysis and research should be simultaneously performed at the miRNA/isomiR levels. Based on the biological characteristics of miRNA and isomiR, we developed miR-isomiRExp to analyze expression pattern of miRNA at the miRNA/isomiR levels, provide insights into tracking miRNA/isomiR maturation and processing mechanisms, and reveal functional characteristics of miRNA/isomiR. Simultaneously, we also performed expression analysis of specific human diseases using public small RNA sequencing datasets based on the analysis platform, which may help in surveying the potential deregulated miRNA/isomiR expression profiles, especially sequence and function-related isomiRs for further interaction analysis and study. The miR-isomiRExp platform provides miRNA/isomiR expression patterns and more information to study deregulated miRNA loci and detailed isomiR sequences. This comprehensive analysis will enrich experimental miRNA studies. miR-isomiRExp is available at http://server.malab.cn/miRisomiRExp/.
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Affiliation(s)
- Li Guo
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Jiafeng Yu
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, China
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Quan Zou
- School of Computer Science and Technology, Tianjin University, Tianjin, 300072, China
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4
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Liang T, Yang C, Li P, Liu C, Guo L. Genetic analysis of loop sequences in the let-7 gene family reveal a relationship between loop evolution and multiple isomiRs. PLoS One 2014; 9:e113042. [PMID: 25397967 PMCID: PMC4232593 DOI: 10.1371/journal.pone.0113042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 10/11/2014] [Indexed: 11/18/2022] Open
Abstract
While mature miRNAs have been widely studied, the terminal loop sequences are rarely examined despite regulating both primary and mature miRNA functions. Herein, we attempted to understand the evolutionary pattern of loop sequences by analyzing loops in the let-7 gene family. Compared to the stable miRNA length distributions seen in most metazoans, higher metazoan species exhibit a longer length distribution. Examination of these loop sequence length distributions, in addition to phylogenetic tree construction, implicated loop sequences as the main evolutionary drivers in miRNA genes. Moreover, loops from relevant clustered miRNA gene families showed varying length distributions and higher levels of nucleotide divergence, even between homologous pre-miRNA loops. Furthermore, we found that specific nucleotides were dominantly distributed in the 5' and 3' terminal loop ends, which may contribute to the relatively precise cleavage that leads to a stable isomiR expression profile. Overall, this study provides further insight into miRNA processing and maturation and further enriches our understanding of miRNA biogenesis.
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Affiliation(s)
- Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Chen Yang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Ping Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Chang Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Li Guo
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
- * E-mail:
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5
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Liang T, Yu J, Liu C, Guo L. An exploration of evolution, maturation, expression and function relationships in mir-23 ∼ 27 ∼ 24 cluster. PLoS One 2014; 9:e106223. [PMID: 25157521 PMCID: PMC4144971 DOI: 10.1371/journal.pone.0106223] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/29/2014] [Indexed: 12/21/2022] Open
Abstract
The study aims to explore the potential relationships of evolution, maturation, expression and function between homologous/clustered miRNAs. mir-23∼27∼24 gene cluster, including the two gene clusters (mir-23a and mir-23b) and the three miRNA gene families (mir-23, mir-27 and mir-24), was typically selected as an example. These related miRNAs show similar evolutionary patterns and various expression patterns. Most of them show consistent isomiR expression pattern, and the “switching” phenomenon can be found between different abundant isomiR species. These findings suggest that these sequence or location related miRNAs show the similar miRNA processing and maturation processes, and the robust selection of the most dominant isomiR exists in specific tissues. Functional analysis show that these miRNAs show similar distributions of enriched gene categories, suggesting the close functional prelateships via direct or indirect coordinate regulation in biological processes. The study reveals the close evolutionary, expression and functional relationships between related homologous/clustered miRNAs, which will further enrich miRNA studies and understand direct or indirect interactions between miRNAs.
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Affiliation(s)
- Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China
| | - JiaFeng Yu
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong, China
| | - Chang Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Li Guo
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- * E-mail:
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6
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Guo L, Zhao Y, Yang S, Zhang H, Chen F. A genome-wide screen for non-template nucleotides and isomiR repertoires in miRNAs indicates dynamic and versatile microRNAome. Mol Biol Rep 2014; 41:6649-58. [PMID: 24993117 DOI: 10.1007/s11033-014-3548-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/20/2014] [Indexed: 11/30/2022]
Abstract
miRNA variants (termed isomiRs) have been reported as potential functional molecules that may affect miRNA stability or target selection. The aims of the present study were to comprehensively survey and characterize non-template nucleotides (NTNs) and isomiR repertoires in miRNAs. Over 50 % of the NTNs were located in the 3' ends (also termed 3' additions), followed by the 5' ends and adjacent positions to 5' and 3' ends. The similar distributions of NTNs and isomiR repertoires might be detected between homologous or clustered miRNAs. miRNA might be stably expressed based on the typical analysis, but its isomiRs might be strongly up- or down-regulated. IsomiRs with novel seed sequences were mainly derived from "seed shifting" events in 5' isomiRs, NTNs in 5' ends or in seed sequences. IsomiRs from a miRNA locus or homologous miRNA loci maybe have the same seed sequences, but they would have various enrichment levels and 3' ends. Interestingly, isomiR species with novel seed sequences via NTNs in the seed region were always stably expressed. These novel seed sequences could lead to novel functional roles through driving the potential novel target mRNAs. Integrated predicted target mRNAs and further microarray validation showed that these isomiRs have versatile biological roles. Collectively, multiple isomiR products and miRNA maturation processes provide opportunities to perform versatile roles in the regulatory network, which further enriches and complicates the regulation of biological processes.
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Affiliation(s)
- Li Guo
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China,
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7
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Guo L, Zhao Y, Yang S, Zhang H, Chen F. An integrated analysis of miRNA, lncRNA, and mRNA expression profiles. BIOMED RESEARCH INTERNATIONAL 2014; 2014:345605. [PMID: 25045664 PMCID: PMC4086520 DOI: 10.1155/2014/345605] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/24/2014] [Accepted: 04/25/2014] [Indexed: 11/17/2022]
Abstract
Increasing amounts of evidence indicate that noncoding RNAs (ncRNAs) have important roles in various biological processes. Here, miRNA, lncRNA, and mRNA expression profiles were analyzed in human HepG2 and L02 cells using high-throughput technologies. An integrative method was developed to identify possible functional relationships between different RNA molecules. The dominant deregulated miRNAs were prone to be downregulated in tumor cells, and the most abnormal mRNAs and lncRNAs were always upregulated. However, the genome-wide analysis of differentially expressed RNA species did not show significant bias between up- and downregulated populations. miRNA-mRNA interaction was performed based on their regulatory relationships, and miRNA-lncRNA and mRNA-lncRNA interactions were thoroughly surveyed and identified based on their locational distributions and sequence correlations. Aberrantly expressed miRNAs were further analyzed based on their multiple isomiRs. IsomiR repertoires and expression patterns were varied across miRNA loci. Several specific miRNA loci showed differences between tumor and normal cells, especially with respect to abnormally expressed miRNA species. These findings suggest that isomiR repertoires and expression patterns might contribute to tumorigenesis through different biological roles. Systematic and integrative analysis of different RNA molecules with potential cross-talk may make great contributions to the unveiling of the complex mechanisms underlying tumorigenesis.
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Affiliation(s)
- Li Guo
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yang Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Sheng Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Hui Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Feng Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
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8
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A challenge for miRNA: multiple isomiRs in miRNAomics. Gene 2014; 544:1-7. [PMID: 24768184 DOI: 10.1016/j.gene.2014.04.039] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 04/11/2014] [Accepted: 04/18/2014] [Indexed: 11/22/2022]
Abstract
Accumulating evidence suggests that a single microRNA (miRNA) locus can generate a series of sequences during miRNA maturation process. These multiple sequences, called miRNA variants, or isomiRs, have different lengths and different 5' and 3' ends. Some of these isomiRs are detected as varied nucleotides and 3' additional non-template nucleotides. As physiological miRNA isoforms, they have drawn attention for possible regulatory biological roles. The present work mainly reviews miRNA/isomiR biogenesis, isomiR expression patterns, and functional and evolutionary implications, especially between isomiRs from homologous and clustered miRNA loci. The phenomenon of multiple isomiRs and their biological roles indicates that analysis performed at the miRNA and isomiR levels should be included in miRNA studies. This may enrich and complicate miRNA biogenesis and coding-non-coding RNA regulatory networks.
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9
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Guo L, Zhao Y, Zhang H, Yang S, Chen F. Close association between paralogous multiple isomiRs and paralogous/orthologues miRNA sequences implicates dominant sequence selection across various animal species. Gene 2013; 527:624-9. [PMID: 23856130 DOI: 10.1016/j.gene.2013.06.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/25/2013] [Accepted: 06/27/2013] [Indexed: 10/26/2022]
Abstract
MicroRNAs (miRNAs) are crucial negative regulators of gene expression at the post-transcriptional level. Next-generation sequencing technologies have identified a series of miRNA variants (named isomiRs). In this study, paralogous isomiR assemblies (from the miRNA locus) were systematically analyzed based on data acquired from deep sequencing data sets. Evolutionary analysis of paralogous (members in miRNA gene family in a specific species) and orthologues (across different animal species) miRNAs was also performed. The sequence diversity of paralogous isomiRs was found to be similar to the diversity of paralogous and orthologues miRNAs. Additionally, both isomiRs and paralogous/orthologues miRNAs were implicated in 5' and 3' ends (especially 3' ends), nucleotide substitutions, and insertions and deletions. Generally, multiple isomiRs can be produced from a single miRNA locus, but most of them had lower enrichment levels, and only several dominant isomiR sequences were detected. These dominant isomiR groups were always stable, and one of them would be selected as the most abundant miRNA sequence in specific animal species. Some isomiRs might be consistent to miRNA sequences in some species but not the other. Homologous miRNAs were often detected in similar isomiR repertoires, and showed similar expression patterns, while dominant isomiRs showed complex evolutionary patterns from miRNA sequences across the animal kingdom. These results indicate that the phenomenon of multiple isomiRs is not a random event, but rather the result of evolutionary pressures. The existence of multiple isomiRs enables different species to express advantageous sequences in different environments. Thus, dominant sequences emerge in response to functional and evolutionary pressures, allowing an organism to adapt to complex intra- and extra-cellular events.
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Affiliation(s)
- Li Guo
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, 210029, China.
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Plé H, Landry P, Benham A, Coarfa C, Gunaratne PH, Provost P. The repertoire and features of human platelet microRNAs. PLoS One 2012; 7:e50746. [PMID: 23226537 PMCID: PMC3514217 DOI: 10.1371/journal.pone.0050746] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 10/24/2012] [Indexed: 12/21/2022] Open
Abstract
Playing a central role in the maintenance of hemostasis as well as in thrombotic disorders, platelets contain a relatively diverse messenger RNA (mRNA) transcriptome as well as functional mRNA-regulatory microRNAs, suggesting that platelet mRNAs may be regulated by microRNAs. Here, we elucidated the complete repertoire and features of human platelet microRNAs by high-throughput sequencing. More than 492 different mature microRNAs were detected in human platelets, whereas the list of known human microRNAs was expanded further by the discovery of 40 novel microRNA sequences. As in nucleated cells, platelet microRNAs bear signs of post-transcriptional modifications, mainly terminal adenylation and uridylation. In vitro enzymatic assays demonstrated the ability of human platelets to uridylate microRNAs, which correlated with the presence of the uridyltransferase enzyme TUT4. We also detected numerous microRNA isoforms (isomiRs) resulting from imprecise Drosha and/or Dicer processing, in some cases more frequently than the reference microRNA sequence, including 5′ shifted isomiRs with redirected mRNA targeting abilities. This study unveils the existence of a relatively diverse and complex microRNA repertoire in human platelets, and represents a mandatory step towards elucidating the intraplatelet and extraplatelet role, function and importance of platelet microRNAs.
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Affiliation(s)
- Hélène Plé
- Centre hospitalier universitaire de Québec Research Center/Centre hospitalier de l'Université Laval, Quebec, Quebec, Canada, and Faculty of Medicine, Université Laval, Quebec, Quebec, Canada
| | - Patricia Landry
- Centre hospitalier universitaire de Québec Research Center/Centre hospitalier de l'Université Laval, Quebec, Quebec, Canada, and Faculty of Medicine, Université Laval, Quebec, Quebec, Canada
| | - Ashley Benham
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Cristian Coarfa
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Preethi H. Gunaratne
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Patrick Provost
- Centre hospitalier universitaire de Québec Research Center/Centre hospitalier de l'Université Laval, Quebec, Quebec, Canada, and Faculty of Medicine, Université Laval, Quebec, Quebec, Canada
- * E-mail:
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Guo L, Sun B, Wu Q, Yang S, Chen F. miRNA-miRNA interaction implicates for potential mutual regulatory pattern. Gene 2012; 511:187-94. [PMID: 23031806 DOI: 10.1016/j.gene.2012.09.066] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 08/02/2012] [Accepted: 09/12/2012] [Indexed: 10/27/2022]
Abstract
BACKGROUND Natural or endogenous sense/antisense miRNAs, located on sense and antisense strands in the same genomic region, respectively, are detected recently. However, little is known about these miRNA pairs, especially for their distributions in different animal species. We herein present systematic analysis of them in human, mouse and rat miRNAs, and their expression patterns based on deep sequencing datasets. METHODS AND RESULTS The phenomenon of miRNA-miRNA interaction could be detected in different animal species. The common miRNAs pairs were found across species. These miRNA pairs could form miRNA:miRNA duplex with complete complementary structure, and were prone to be located on specific chromosomes. They might be homologous miRNA genes (especially in human), or clustered in a gene cluster (especially in rat), or simultaneously detected in different genomic regions due to multicopy pre-miRNAs. Remarkably, some miRNA pairs, located in different genomic regions, also showed complementarity as well as endogenous sense/antisense miRNAs. Based on published deep sequencing datasets, one member of miRNA pairs always was abundantly expressed, whereas another was quite rare. Rare common target mRNAs of these miRNA pairs were predicted. CONCLUSIONS Interaction between miRNAs and significant expression divergence implied complex potential mutual regulatory pattern in the miRNA world. The study would enrich miRNA regulatory network.
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Affiliation(s)
- Li Guo
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 210029, China.
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12
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Guo L, Li H, Liang T, Lu J, Yang Q, Ge Q, Lu Z. Consistent isomiR expression patterns and 3' addition events in miRNA gene clusters and families implicate functional and evolutionary relationships. Mol Biol Rep 2012; 39:6699-706. [PMID: 22391651 DOI: 10.1007/s11033-012-1493-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 01/24/2012] [Indexed: 01/21/2023]
Abstract
3' addition events in miRNAs are widely detected and may contribute to miRNA stability, but little is known about details of the events in miRNA gene clusters and families. Here, we performed a comprehensive analysis of isomiR expression patterns and 3' additions in miRNA gene clusters and families by analyzing high-throughput sequencing dataset. According to dominant modified isomiRs, miRNA members in many miRNA gene clusters and families showed the same 3' additional non-template nucleotides. Although clustered miRNAs and homologous miRNAs had consistent or inconsistent expression levels, we found many of them showed consistent expression patterns at isomiR levels. These findings revealed similar processing mechanism and 3' modification event of miRNAs in gene clusters and families through miRNA maturation process. The consistent maturation mechanism may contribute to co-regulate biological processes, and may originate from ancestral miRNA genes through complex duplication history.
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Affiliation(s)
- Li Guo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
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