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Sen P, Aziz R, Deka RC, Feil EJ, Ray SK, Satapathy SS. Stem Region of tRNA Genes Favors Transition Substitution Towards Keto Bases in Bacteria. J Mol Evol 2022; 90:114-123. [PMID: 35084523 DOI: 10.1007/s00239-021-10045-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/21/2021] [Indexed: 11/25/2022]
Abstract
Transversion and transition mutations have variable effects on the stability of RNA secondary structure considering that the former destabilizes the double helix geometry to a greater extent by introducing purine:purine (R:R) or pyrimidine:pyrimidine (Y:Y) base pairs. Therefore, transversion frequency is likely to be lower than that of transition in the secondary structure regions of RNA genes. Here, we performed an analysis of transition and transversion frequencies in tRNA genes defined well with secondary structure and compared with the intergenic regions in five bacterial species namely Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Staphylococcus aureus and Streptococcus pneumoniae using a large genome sequence data set. In general, the transversion frequency was observed to be lower than that of transition in both tRNA genes and intergenic regions. The transition to transversion ratio was observed to be greater in tRNA genes than that in the intergenic regions in all the five bacteria that we studied. Interestingly, the intraspecies base substitution analysis in tRNA genes revealed that non-compensatory substitutions were more frequent than compensatory substitutions in the stem region. Further, transition to transversion ratio in the loop region was observed to be significantly lesser than that among the non-compensatory substitutions in the stem region. This indicated that the transversion is more deleterious than transition in the stem regions. In addition, substitutions from amino bases (A/C) to keto bases (G/T) were also observed to be more than the reverse substitutions in the stem region. Substitution from amino bases to keto bases are likely to facilitate the stable G:U pairing unlike the reverse substitution that facilitates the unstable A:C pairing in the stem region of tRNA. This work provides additional support that the secondary structure of tRNA molecule is what drives the different substitutions in its gene sequence.
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Affiliation(s)
- Piyali Sen
- Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur, Assam, 784028, India
| | - Ruksana Aziz
- Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur, Assam, 784028, India
| | - Ramesh C Deka
- Chemical Sciences, Tezpur University, Napaam, Tezpur, Assam, 784028, India
- Center for Multidisciplinary Research, Tezpur University, Napaam, Tezpur, Assam, 784028, India
| | - Edward J Feil
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, BA2 7AY, UK.
| | - Suvendra Kumar Ray
- Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur, Assam, 784028, India.
- Center for Multidisciplinary Research, Tezpur University, Napaam, Tezpur, Assam, 784028, India.
| | - Siddhartha Sankar Satapathy
- Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur, Assam, 784028, India.
- Center for Multidisciplinary Research, Tezpur University, Napaam, Tezpur, Assam, 784028, India.
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Chen D, Chen S, Zhao C, Yan J, Ma Z, Zhao X, Wang Z, Wang X, Wang H. Screening and functional identification of antioxidant microRNA-size sRNAs from Spirulina platensis using high-throughput sequencing. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:973-983. [PMID: 34112312 DOI: 10.1071/fp20405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
MiRNA-size small RNAs, abbreviated as sRNAs, are increasingly being discovered as research progresses and omics technologies development in prokaryotes. However, there is a paucity of data concerning whether or not sRNAs exist in cyanobacteria and regulate the resistance to oxidative stress. In this investigation, small RNA libraries were constructed from the control, 50-nM and 100-nM H2O2 treatments of Spirulina platensis. By high-throughput sequencing, 23 candidate sRNAs showed significantly differential expression under oxidative stress, among which eight sRNAs were identified with the similar expression patterns as the sequencing results by real-time qPCR. By nucleic acid hybridisation, the corresponding expression changes also demonstrated that sequencing results of sRNAs were feasible and credible. By bioinformatics prediction and structure identification, 43 target genes were predicted for 8 sRNAs in plant miRNA database, among which 29 were annotated into the genome and related metabolic pathways of S. platensis. By COG functional classification and KEGG pathway analysis, 31 target genes were predicted to be directly or indirectly involved in the defence mechanism of H2O2 stress. Thirteen target genes displayed reversely changing patterns compared with those of their sRNAs under H2O2 treatment. These findings provide compelling evidence that these sRNAs in S. platensis play a crucial role in oxidative stress responses, and thus provide a theoretical reference for improving the stress-triggering physiological regulation.
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Affiliation(s)
- Dechao Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215004, China
| | - Shuya Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215004, China
| | - Chenxi Zhao
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215004, China
| | - Jin Yan
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215004, China
| | - Zelong Ma
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215004, China
| | - Xiaokai Zhao
- School of Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Zhenfeng Wang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215004, China; and School of Life Science, Wenzhou Medical University, Wenzhou 325035, China; and Corresponding authors. ;
| | - Xuedong Wang
- School of Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Huili Wang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215004, China; and Corresponding authors. ;
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3
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Gangemi CMA, Alaimo S, Pulvirenti A, García-Viñuales S, Milardi D, Falanga AP, Fragalà ME, Oliviero G, Piccialli G, Borbone N, Ferro A, D'Urso A, Croce CM, Purrello R. Endogenous and artificial miRNAs explore a rich variety of conformations: a potential relationship between secondary structure and biological functionality. Sci Rep 2020; 10:453. [PMID: 31949213 PMCID: PMC6965629 DOI: 10.1038/s41598-019-57289-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/23/2019] [Indexed: 12/22/2022] Open
Abstract
Mature microRNAs are short non-coding RNA sequences which upon incorporation into the RISC ribonucleoprotein complex, play a crucial role in regulation of gene expression. However, miRNAs can exist within the cell also as free molecules fulfilling their biological activity. Therefore, it is emerging that in addition to sequence even the structure adopted by mature miRNAs might play an important role to reach the target. Indeed, we analysed by several spectroscopic techniques the secondary structures of two artificial miRNAs selected by computational tool (miR-Synth) as best candidates to silence c-MET and EGFR genes and of two endogenous miRNAs (miR-15a and miR-15b) having the same seed region, but different biological activity. Our results demonstrate that both endogenous and artificial miRNAs can arrange in several 3D-structures which affect their activity and selectivity toward the targets.
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Affiliation(s)
- C M A Gangemi
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - S Alaimo
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy c/o Department of Mathematics and Computer Science, Viale A. Doria 6, 95125, Catania, Italy
| | - A Pulvirenti
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy c/o Department of Mathematics and Computer Science, Viale A. Doria 6, 95125, Catania, Italy
| | | | - D Milardi
- Istituto di Cristallografia CNR, Via P. Gaifami 9, 95126, Catania, Italy
| | - A P Falanga
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131, Napoli, Italy
| | - M E Fragalà
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - G Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131, Napoli, Italy
| | - G Piccialli
- Department of Pharmacy, University of Naples Federico II, D. Montesano 49, 80131, Napoli, Italy
| | - N Borbone
- Department of Pharmacy, University of Naples Federico II, D. Montesano 49, 80131, Napoli, Italy
| | - A Ferro
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy c/o Department of Mathematics and Computer Science, Viale A. Doria 6, 95125, Catania, Italy.
| | - A D'Urso
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - C M Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - R Purrello
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125, Catania, Italy.
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4
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Functional Prediction of Candidate MicroRNAs for CRC Management Using in Silico Approach. Int J Mol Sci 2019; 20:ijms20205190. [PMID: 31635135 PMCID: PMC6834124 DOI: 10.3390/ijms20205190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/13/2019] [Accepted: 09/14/2019] [Indexed: 02/07/2023] Open
Abstract
Approximately 30–50% of malignant growths can be prevented by avoiding risk factors and implementing evidence-based strategies. Colorectal cancer (CRC) accounted for the second most common cancer and the third most common cause of cancer death worldwide. This cancer subtype can be reduced by early detection and patients’ management. In this study, the functional roles of the identified microRNAs were determined using an in silico pipeline. Five microRNAs identified using an in silico approach alongside their seven target genes from our previous study were used as datasets in this study. Furthermore, the secondary structure and the thermodynamic energies of the microRNAs were revealed by Mfold algorithm. The triplex binding ability of the oligonucleotide with the target promoters were analyzed by Trident. Finally, evolutionary stage-specific somatic events and co-expression analysis of the target genes in CRC were analyzed by SEECancer and GeneMANIA plugin in Cytoscape. Four of the five microRNAs have the potential to form more than one secondary structure. The ranges of the observed/expected ratio of CpG dinucleotides of these genes range from 0.60 to 1.22. Three of the candidate microRNA were capable of forming multiple triplexes along with three of the target mRNAs. Four of the total targets were involved in either early or metastatic stage-specific events while three other genes were either a product of antecedent or subsequent events of the four genes implicated in CRC. The secondary structure of the candidate microRNAs can be used to explain the different degrees of genetic regulation in CRC due to their conformational role to modulate target interaction. Furthermore, due to the regulation of important genes in the CRC pathway and the enrichment of the microRNA with triplex binding sites, they may be a useful diagnostic biomarker for the disease subtype.
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López JA, Granados-López AJ. Future directions of extracellular vesicle-associated miRNAs in metastasis. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:115. [PMID: 28361080 DOI: 10.21037/atm.2017.01.26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Numerous studies have demonstrated the dynamic cell-to-cell communication mediated by extracellular vesicles (EV) in cancer cell survival and metastasis development. EV content includes proteins, lipids, DNA, and RNA like microRNAs. Non-protein coding microRNAs play a very active role in almost all cellular processes targeting mRNAs for silencing. Different miRNA profiles have been found in different cancer types, and clarification of miRNAs packed in EV from different types of cancers will allow the understanding of metastasis and the application of miRNAs as biomolecules in diagnostic, prognostic and therapeutic approaches to fight cancer. The profound review of Dhondt et al., 2016, provides a wide view of EV miRNAs involved in various steps of the metastasis process to illustrate how the cancer cell interaction with the near and long distance microenvironment allows metastasis. These studies will surely conduce to additional patient studies to prove the relevance of EV miRNAs in metastasis in vivo. It remains to be elucidated how the tumoral cell sorts the miRNAs for secretion to send a message, and to well recognize the type of EV performing this message delivering. It will be very useful to identify whether miRNAs are delivered with post-transcriptional modifications since this is an important feature for miRNAs activity and stability.
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Affiliation(s)
- Jesús Adrián López
- Laboratorio de microRNAs, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico; Doctorado en Ciencias Básicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | - Angelica Judith Granados-López
- Laboratorio de microRNAs, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico; Doctorado en Ciencias Básicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
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6
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Intracellular and extracellular microRNA: An update on localization and biological role. ACTA ACUST UNITED AC 2016; 51:33-49. [PMID: 27396686 DOI: 10.1016/j.proghi.2016.06.001] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/24/2016] [Accepted: 06/24/2016] [Indexed: 12/12/2022]
Abstract
MicroRNA (miRNA) is a class of small non-coding RNAs which mediate post-transcriptional gene silencing (PTGS) by sequence-specific inhibition of target mRNAs translation and/or lowering their half-lives in the cytoplasm. Together with their binding partners, Argonaute (AGO) proteins, miRNAs form cores of RNA-induced silencing complexes (RISC). Despite a substantial progress in understanding RISC structure, until recently little was known about its localization in the cell. This review is aimed to provide an overview of the emerging picture of miRNA and RISC localization and function both in the intracellular space and outside of the cell. In contrast to the common assumption that PTGS occurs in the cytoplasm, it was found to operate mainly on the membranes of the endoplasmic reticulum (ER). Besides ER membranes miRNAs were found in all main cellular compartments including nucleus, nucleolus and mitochondria where they regulate various processes including transcription, translation, alternative splicing and DNA repair. Moreover, a certain pool of miRNAs may not be associated with RISC and carry completely different functions. Finally, the discovery of cell-free miRNAs in all biological fluids suggests that miRNAs might also act as signaling molecules outside the cell, and may be utilized as biomarkers for a variety of diseases. In this review we discuss miRNA secretion mechanisms and possible pathways of cell-cell communication via miRNA-containing exosomes in vivo.
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7
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Rolle K, Piwecka M, Belter A, Wawrzyniak D, Jeleniewicz J, Barciszewska MZ, Barciszewski J. The Sequence and Structure Determine the Function of Mature Human miRNAs. PLoS One 2016; 11:e0151246. [PMID: 27031951 PMCID: PMC4816427 DOI: 10.1371/journal.pone.0151246] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/15/2016] [Indexed: 12/31/2022] Open
Abstract
Micro RNAs (miRNAs) (19–25 nucleotides in length) belong to the group of non-coding RNAs are the most abundant group of posttranscriptional regulators in multicellular organisms. They affect a gene expression by binding of fully or partially complementary sequences to the 3’-UTR of target mRNA. Furthermore, miRNAs present a mechanism by which genes with diverse functions on multiple pathways can be simultaneously regulated at the post-transcriptional level. However, little is known about the specific pathways through which miRNAs with specific sequence or structural motifs regulate the cellular processes. In this paper we showed the broad and deep characteristics of mature miRNAs according to their sequence and structural motifs. We investigated a distinct group of miRNAs characterized by the presence of specific sequence motifs, such as UGUGU, GU-repeats and purine/pyrimidine contents. Using computational function and pathway analysis of their targeted genes, we were able to observe the relevance of sequence and the type of targeted mRNAs. As the consequence of the sequence analysis we finally provide the comprehensive description of pathways, biological processes and proteins associated with the distinct group of characterized miRNAs. Here, we found that the specific group of miRNAs with UGUGU can activate the targets associated to the interferon induction pathway or pathways prominently observed during carcinogenesis. GU-rich miRNAs are prone to regulate mostly processes in neurogenesis, whereas purine/pyrimidine rich miRNAs could be involved rather in transport and/or degradation of RNAs. Additionally, we have also analyzed the simple sequence repeats (SSRs). Their variation within mature miRNAs might be critical for normal miRNA regular activity. Expansion or contraction of SSRs in mature miRNA might directly affect its mRNA interaction or even change the function of that distinct miRNA. Our results prove that due to the specific sequence features, these molecules can also be involved in well-defined cellular processes depending on their sequence contents. The pathway mapping and theoretical gene target identification allowed us to create a biological framework to show the relevance of the specific miRNAs in regulation the distinct type of targets.
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Affiliation(s)
- Katarzyna Rolle
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
- * E-mail: (JB); (KR)
| | - Monika Piwecka
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Agnieszka Belter
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Dariusz Wawrzyniak
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Jaroslaw Jeleniewicz
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Miroslawa Z. Barciszewska
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
- * E-mail: (JB); (KR)
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8
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Belter A, Gudanis D, Rolle K, Piwecka M, Gdaniec Z, Naskręt-Barciszewska MZ, Barciszewski J. Mature miRNAs form secondary structure, which suggests their function beyond RISC. PLoS One 2014; 9:e113848. [PMID: 25423301 PMCID: PMC4244182 DOI: 10.1371/journal.pone.0113848] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/30/2014] [Indexed: 12/11/2022] Open
Abstract
The generally accepted model of the miRNA-guided RNA down-regulation suggests that mature miRNA targets mRNA in a nucleotide sequence-specific manner. However, we have shown that the nucleotide sequence of miRNA is not the only determinant of miRNA specificity. Using specific nucleases, T1, V1 and S1 as well as NMR, UV/Vis and CD spectroscopies, we found that miR-21, miR-93 and miR-296 can adopt hairpin and/or homoduplex structures. The secondary structure of those miRNAs in solution is a function of RNA concentration and ionic conditions. Additionally, we have shown that a formation of miRNA hairpin is facilitated by cellular environment.Looking for functional consequences of this observation, we have perceived that structure of these miRNAs resemble RNA aptamers, short oligonucleotides forming a stable 3D structures with a high affinity and specificity for their targets. We compared structures of anti-tenascin C (anti-Tn-C) aptamers, which inhibit brain tumor glioblastoma multiforme (GBM, WHO IV) and selected miRNA. A strong overexpression of miR-21, miR-93 as well Tn-C in GBM may imply some connections between them. The structural similarity of these miRNA hairpins and anti-Tn-C aptamers indicates that miRNAs may function also beyond RISC and are even more sophisticated regulators, that it was previously expected. We think that the knowledge of the miRNA structure may give a new insight into miRNA-dependent gene regulation mechanism and be a step forward in the understanding their function and involvement in cancerogenesis. This may improve design process of anti-miRNA therapeutics.
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Affiliation(s)
- Agnieszka Belter
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Dorota Gudanis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Katarzyna Rolle
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Monika Piwecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | | | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
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9
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Tan Gana NH, Victoriano AFB, Okamoto T. Evaluation of online miRNA resources for biomedical applications. Genes Cells 2011; 17:11-27. [PMID: 22077698 DOI: 10.1111/j.1365-2443.2011.01564.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
MicroRNAs (miRNAs) are endogenous single-stranded, 22-nt (nucleotide) RNAs which complement mRNA to initiate post-transcriptional regulation. This review presents updates and evaluations of the public domain resources available for miRNA identification and target prediction toward their utilization in the biomedical research approach. This study discusses the basic principles of miRNA computational studies based on the nature and mechanism of action of miRNAs. Furthermore, we have explored fifty-nine current online miRNA tools that can be categorized into three classes in this paper: (i) miRNA identification; (ii) miRNA target prediction; and (iii) specialized miRNA tools.
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Affiliation(s)
- Neil H Tan Gana
- Department of Molecular and Cell Biology, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya City 467-8601, Japan
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Ragan C, Zuker M, Ragan MA. Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations. PLoS Comput Biol 2011; 7:e1001090. [PMID: 21390282 PMCID: PMC3044769 DOI: 10.1371/journal.pcbi.1001090] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 01/20/2011] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) suppress gene expression by forming a duplex with a target messenger RNA (mRNA), blocking translation or initiating cleavage. Computational approaches have proven valuable for predicting which mRNAs can be targeted by a given miRNA, but currently available prediction methods do not address the extent of duplex formation under physiological conditions. Some miRNAs can at low concentrations bind to target mRNAs, whereas others are unlikely to bind within a physiologically relevant concentration range. Here we present a novel approach in which we find potential target sites on mRNA that minimize the calculated free energy of duplex formation, compute the free energy change involved in unfolding these sites, and use these energies to estimate the extent of duplex formation at specified initial concentrations of both species. We compare our predictions to experimentally confirmed miRNA-mRNA interactions (and non-interactions) in Drosophila melanogaster and in human. Although our method does not predict whether the targeted mRNA is degraded and/or its translation to protein inhibited, our quantitative estimates generally track experimentally supported results, indicating that this approach can be used to predict whether an interaction occurs at specified concentrations. Our approach offers a more-quantitative understanding of post-translational regulation in different cell types, tissues, and developmental conditions.
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Affiliation(s)
- Chikako Ragan
- ARC Centre of Excellence in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Michael Zuker
- Rensselaer Polytechnic Institute, Troy, New York, United States of America
| | - Mark A. Ragan
- ARC Centre of Excellence in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- * E-mail:
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