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Wang N, Jiang Y, Nie K, Li D, Liu H, Wang J, Huang C, Li C. Toehold-mediated strand displacement reaction-propelled cascade DNAzyme amplifier for microRNA let-7a detection. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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2
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Schorr AL, Mangone M. miRNA-Based Regulation of Alternative RNA Splicing in Metazoans. Int J Mol Sci 2021; 22:ijms222111618. [PMID: 34769047 PMCID: PMC8584187 DOI: 10.3390/ijms222111618] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022] Open
Abstract
Alternative RNA splicing is an important regulatory process used by genes to increase their diversity. This process is mainly executed by specific classes of RNA binding proteins that act in a dosage-dependent manner to include or exclude selected exons in the final transcripts. While these processes are tightly regulated in cells and tissues, little is known on how the dosage of these factors is achieved and maintained. Several recent studies have suggested that alternative RNA splicing may be in part modulated by microRNAs (miRNAs), which are short, non-coding RNAs (~22 nt in length) that inhibit translation of specific mRNA transcripts. As evidenced in tissues and in diseases, such as cancer and neurological disorders, the dysregulation of miRNA pathways disrupts downstream alternative RNA splicing events by altering the dosage of splicing factors involved in RNA splicing. This attractive model suggests that miRNAs can not only influence the dosage of gene expression at the post-transcriptional level but also indirectly interfere in pre-mRNA splicing at the co-transcriptional level. The purpose of this review is to compile and analyze recent studies on miRNAs modulating alternative RNA splicing factors, and how these events contribute to transcript rearrangements in tissue development and disease.
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Affiliation(s)
- Anna L. Schorr
- Molecular and Cellular Biology Graduate Program, School of Life Sciences, 427 East Tyler Mall, Tempe, AZ 85287, USA;
| | - Marco Mangone
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave., Tempe, AZ 85287, USA
- Correspondence: ; Tel.: +1-480-965-7957
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3
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Subirana JA, Messeguer X. DNA Satellites Are Transcribed as Part of the Non-Coding Genome in Eukaryotes and Bacteria. Genes (Basel) 2021; 12:genes12111651. [PMID: 34828257 PMCID: PMC8625621 DOI: 10.3390/genes12111651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/16/2021] [Accepted: 10/17/2021] [Indexed: 12/01/2022] Open
Abstract
It has been shown in recent years that many repeated sequences in the genome are expressed as RNA transcripts, although the role of such RNAs is poorly understood. Some isolated and tandem repeats (satellites) have been found to be transcribed, such as mammalian Alu sequences and telomeric/centromeric satellites in different species. However, there is no detailed study on the eventual transcription of the interspersed satellites found in many species. Therefore, we decided to study for the first time the transcription of the abundant DNA satellites in the bacterium Bacillus coagulans and in the nematode Caenorhabditis elegans. We have updated the data for C. elegans satellites using the latest version of the genome. We analyzed the transcription of satellites in both species in available RNA-seq results and found that they are widely transcribed. Our demonstration that satellite RNAs are transcribed adds a new family of non-coding RNAs. This is a field that requires further investigation and will provide a deeper understanding of gene expression and control.
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4
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Stellwagen NC. Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations. Electrophoresis 2021; 43:309-326. [PMID: 34510492 DOI: 10.1002/elps.202100176] [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: 06/11/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 11/08/2022]
Abstract
This review describes the results obtained by using free-solution capillary electrophoresis to probe the electrostatic and hydrodynamic properties of DNA in solutions containing various monovalent cations. In brief, we found that the mobilities of double-stranded DNAs (dsDNAs) increase with increasing molecular weight before leveling off and becoming constant at molecular weights ≥400 bp. The mobilities of single-stranded DNAs (ssDNAs) go through a maximum at ∼10-20 nucleotides before decreasing and becoming constant for oligomers larger than ∼30-50 bases. The mobilities of both ss- and dsDNAs increase linearly with the logarithm of increasing charge per unit length and decrease linearly with the logarithm of increasing ionic strength. Surprisingly, ss- and dsDNA mobilities level off and become nearly constant at ionic strengths ≥0.6 M. The thermal stabilities of dsDNAs decrease linearly with increasing solution viscosity. The diffusion coefficients of dsDNA are modulated by the diffusion coefficients of their counterions because of electrostatic DNA-cation coupling interactions. Finally, the anomalously slow mobilities observed for A-tract-containing DNAs can be attributed both to differences in shape and to the preferential localization of small cations in the A-tract minor groove. Since many of these results are mirrored in other polyion-counterion systems, free-solution electrophoresis can be viewed as a reporter of the electrostatics and hydrodynamics of highly charged polyions. New results describing the mobilities of dsDNA analogues of a microRNA-messenger RNA complex are also presented.
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5
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Lynn NS, Špringer T, Slabý J, Špačková B, Gráfová M, Ermini ML, Homola J. Analyte transport to micro- and nano-plasmonic structures. LAB ON A CHIP 2019; 19:4117-4127. [PMID: 31740906 DOI: 10.1039/c9lc00699k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The study of optical affinity biosensors based on plasmonic nanostructures has received significant attention in recent years. The sensing surfaces of these biosensors have complex architectures, often composed of localized regions of high sensitivity (electromagnetic hot spots) dispersed along a dielectric substrate having little to no sensitivity. Under conditions such that the sensitive regions are selectively functionalized and the remaining regions passivated, the rate of analyte capture (and thus the sensing performance) will have a strong dependence on the nanoplasmonic architecture. Outside of a few recent studies, there has been little discussion on how changes to a nanoplasmonic architecture will affect the rate of analyte transport. We recently proposed an analytical model to predict transport to such complex architectures; however, those results were based on numerical simulation and to date, have only been partially verified. In this study we measure the characteristics of analyte transport across a wide range of plasmonic structures, varying both in the composition of their base plasmonic element (microwires, nanodisks, and nanorods) and the packing density of such elements. We functionalized each structure with nucleic acid-based bioreceptors, where for each structure we used analyte/receptor sequences as to maintain a Damköhler number close to unity. This method allows to extract both kinetic (in the form of association and dissociation constants) and analyte transport parameters (in the form of a mass transfer coefficient) from sensorgrams taken from each substrate. We show that, despite having large differences in optical characteristics, measured rates of analyte transport for all plasmonic structures match very well to predictions using our previously proposed model. These results highlight that, along with optical characteristics, analyte transport plays a large role in the overall sensing performance of a nanoplasmonic biosensor.
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Affiliation(s)
- N Scott Lynn
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, 182 51 Prague, Czech Republic.
| | - Tomáš Špringer
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, 182 51 Prague, Czech Republic.
| | - Jiří Slabý
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, 182 51 Prague, Czech Republic.
| | - Barbora Špačková
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, 182 51 Prague, Czech Republic.
| | - Michaela Gráfová
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, 182 51 Prague, Czech Republic.
| | - Maria Laura Ermini
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, 182 51 Prague, Czech Republic.
| | - Jiří Homola
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, 182 51 Prague, Czech Republic.
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6
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Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs. Genetics 2018; 209:651-673. [PMID: 29967059 PMCID: PMC6028246 DOI: 10.1534/genetics.118.300291] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are small, noncoding RNAs that regulate gene expression at the post-transcriptional level in essentially all aspects of Caenorhabditis elegans biology. More than 140 genes that encode microRNAs in C. elegans regulate development, behavior, metabolism, and responses to physiological and environmental changes. Genetic analysis of C. elegans microRNA genes continues to enhance our fundamental understanding of how microRNAs are integrated into broader gene regulatory networks to control diverse biological processes, including growth, cell division, cell fate determination, behavior, longevity, and stress responses. As many of these microRNA sequences and the related processing machinery are conserved over nearly a billion years of animal phylogeny, the assignment of their functions via worm genetics may inform the functions of their orthologs in other animals, including humans. In vivo investigations are especially important for microRNAs because in silico extrapolation of their functions using mRNA target prediction programs can easily assign microRNAs to incorrect genetic pathways. At this mezzanine level of microRNA bioinformatic sophistication, genetic analysis continues to be the gold standard for pathway assignments.
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Ren H, Xu Y, Wang Q, Jiang J, Wudumuli, Hui L, Zhang Q, Zhang X, Wang E, Sun L, Qiu X. E3 ubiquitin ligase tripartite motif-containing 71 promotes the proliferation of non-small cell lung cancer through the inhibitor of kappaB-α/nuclear factor kappaB pathway. Oncotarget 2017. [PMID: 29541383 PMCID: PMC5834285 DOI: 10.18632/oncotarget.19075] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Tripartite motif-containing (TRIM) 71 belongs to the TRIM protein family. Many studies have shown that TRIM71 plays conserved roles in stem cell proliferation, differentiation, and embryonic development; however, the relationship between TRIM71 and tumorigenesis is not clear. In this study, we demonstrate that TRIM71 expression in non-small cell lung cancer (NSCLC) is associated with tumor size, lymph node metastasis, TNM stage, and poor prognosis. We found that TRIM71 was highly expressed in NSCLC cell lines compared with that in human normal bronchial epithelial cells. Moreover, by altering the expression of TRIM71 in selected cell lines, we found that TRIM71 promoted the proliferation of NSCLC cells through activation of the inhibitor of kappaB/nuclear factor kappaB pathway. These results suggested that TRIM71 plays a role in promoting the development of NSCLC.
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Affiliation(s)
- Hongjiu Ren
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
| | - Yitong Xu
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
| | - Qiongzi Wang
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
| | - Jun Jiang
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
| | - Wudumuli
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
| | - Linping Hui
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China.,Fouth Affiliated Hospital, China Medical University, Shenyang, China
| | - Qingfu Zhang
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
| | - Xiupeng Zhang
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
| | - Enhua Wang
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
| | - Limei Sun
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
| | - Xueshan Qiu
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
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8
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Kotagama K, Babb CS, Wolter JM, Murphy RP, Mangone M. A human 3'UTR clone collection to study post-transcriptional gene regulation. BMC Genomics 2015; 16:1036. [PMID: 26645212 PMCID: PMC4673713 DOI: 10.1186/s12864-015-2238-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/24/2015] [Indexed: 11/16/2022] Open
Abstract
Background 3′untranslated regions (3′UTRs) are poorly understood portions of eukaryotic mRNAs essential for post-transcriptional gene regulation. Sequence elements in 3′UTRs can be target sites for regulatory molecules such as RNA binding proteins and microRNAs (miRNAs), and these interactions can exert significant control on gene networks. However, many such interactions remain uncharacterized due to a lack of high-throughput (HT) tools to study 3′UTR biology. HT cloning efforts such as the human ORFeome exemplify the potential benefits of genomic repositories for studying human disease, especially in relation to the discovery of biomarkers and targets for therapeutic agents. Currently there are no publicly available human 3′UTR libraries. To address this we have prepared the first version of the human 3′UTRome (h3′UTRome v1) library. The h3′UTRome is produced to a single high quality standard using the same recombinational cloning technology used for the human ORFeome, enabling universal operating methods and high throughput experimentation. The library is thoroughly sequenced and annotated with simple online access to information, and made publically available through gene repositories at low cost to all scientists with minimal restriction. Results The first release of the h3′UTRome library comprises 1,461 human 3′UTRs cloned into Gateway® entry vectors, ready for downstream analyses. It contains 3′UTRs for 985 transcription factors, 156 kinases, 171 RNA binding proteins, and 186 other genes involved in gene regulation and in disease. We demonstrate the feasibility of the h3′UTRome library by screening a panel of 87 3′UTRs for targeting by two miRNAs: let-7c, which is implicated in tumorigenesis, and miR-221, which is implicated in atherosclerosis and heart disease. The panel is enriched with genes involved in the RAS signaling pathway, putative novel targets for the two miRNAs, as well as genes implicated in tumorigenesis and heart disease. Conclusions The h3′UTRome v1 library is a modular resource that can be utilized for high-throughput screens to identify regulatory interactions between trans-acting factors and 3′UTRs, Importantly, the library can be customized based on the specifications of the researcher, allowing the systematic study of human 3′UTR biology. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2238-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kasuen Kotagama
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA.
| | - Cody S Babb
- Virginia G. Piper Center For Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, AZ, USA.
| | - Justin M Wolter
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA.
| | - Ronan P Murphy
- School of Health & Human Performance, Dublin City University, Dublin, Ireland.
| | - Marco Mangone
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA. .,Virginia G. Piper Center For Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, AZ, USA.
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9
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Nowakowski M, Saxena S, Stanek J, Żerko S, Koźmiński W. Applications of high dimensionality experiments to biomolecular NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 90-91:49-73. [PMID: 26592945 DOI: 10.1016/j.pnmrs.2015.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 07/03/2015] [Accepted: 07/03/2015] [Indexed: 05/23/2023]
Abstract
High dimensionality NMR experiments facilitate resonance assignment and precise determination of spectral parameters such as coupling constants. Sparse non-uniform sampling enables acquisition of experiments of high dimensionality with high resolution in acceptable time. In this review we present and compare some significant applications of NMR experiments of dimensionality higher than three in the field of biomolecular studies in solution.
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Affiliation(s)
- Michał Nowakowski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Saurabh Saxena
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Jan Stanek
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Szymon Żerko
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Wiktor Koźmiński
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland.
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10
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Zhang H, Artiles KL, Fire AZ. Functional relevance of "seed" and "non-seed" sequences in microRNA-mediated promotion of C. elegans developmental progression. RNA (NEW YORK, N.Y.) 2015; 21:1980-1992. [PMID: 26385508 PMCID: PMC4604436 DOI: 10.1261/rna.053793.115] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 08/05/2015] [Indexed: 06/05/2023]
Abstract
The founding heterochronic microRNAs, lin-4 and let-7, together with their validated targets and well-characterized phenotypes in C. elegans, offer an opportunity to test functionality of microRNAs in a developmental context. In this study, we defined sequence requirements at the microRNA level for these two microRNAs, evaluating lin-4 and let-7 mutant microRNAs for their ability to support temporal development under conditions where the wild-type lin-4 and let-7 gene products are absent. For lin-4, we found a strong requirement for seed sequences, with function drastically affected by several central mutations in the seed sequence, while rescue was retained by a set of mutations peripheral to the seed. let-7 rescuing activity was retained to a surprising degree by a variety of central seed mutations, while several non-seed mutant effects support potential noncanonical contributions to let-7 function. Taken together, this work illustrates both the functional partnership between seed and non-seed sequences in mediating C. elegans temporal development and a diversity among microRNA effectors in the contributions of seed and non-seed regions to activity.
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Affiliation(s)
- Huibin Zhang
- Stanford University School of Medicine, Stanford, California 94305, USA
| | - Karen L Artiles
- Stanford University School of Medicine, Stanford, California 94305, USA
| | - Andrew Z Fire
- Stanford University School of Medicine, Stanford, California 94305, USA
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11
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Saxena S, Stanek J, Cevec M, Plavec J, Koźmiński W. High resolution 4D HPCH experiment for sequential assignment of (13)C-labeled RNAs via phosphodiester backbone. JOURNAL OF BIOMOLECULAR NMR 2015; 63:291-298. [PMID: 26409925 PMCID: PMC4642592 DOI: 10.1007/s10858-015-9989-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 09/20/2015] [Indexed: 06/05/2023]
Abstract
The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of (1)H and (13)C chemical shifts, especially of C4'/H4'. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4'-H4' correlations are resolved along the (1)H3'-(31)P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional (31)P and (1)H3' dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic (13)C-labeling with evolution of C4' carbons. Band selective (13)C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4'-C3' and C4'-C5' homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop.
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Affiliation(s)
- Saurabh Saxena
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02089, Warsaw, Poland
| | - Jan Stanek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02089, Warsaw, Poland
| | - Mirko Cevec
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, 1000, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02089, Warsaw, Poland.
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Abstract
Chronic myelogenous leukemia (CML) is a myeloproliferative neoplasm that is frequently characterized by the constitutive expression of the oncogenic protein BCR-ABL tyrosine kinase. Tyrosine kinase inhibitors (TKIs) targeting breakpoint cluster region-ABL are the first-line therapy for most CML patients and have drastically improved the prognosis of CML. However, some CML patients are unresponsive to TKI treatment, and a notable proportion of initially responsive patients develop drug resistance. Several molecular pathways have been correlated with resistance to TKI treatment, however, the exact mechanism of developing drug resistance remains ambiguous. Recently, microRNAs (miRNAs) have been implicated in the progression of CML and the development of resistance to TKI treatment based on their important regulatory function in cell homeostasis, and the deregulation observed in the initiation and progression of many leukemia subtypes. In this review, we summarize some of the major discoveries regarding miRNAs in CML, and their relevance as biomarkers for diagnosis, disease progression, and drug sensitivity.
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Affiliation(s)
- Kasuen Kotagama
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA
| | - Yung Chang
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA.,Center of Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Marco Mangone
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA.,Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
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13
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Strom S, Shiskova E, Hahm Y, Grover N. Thermodynamic examination of 1- to 5-nt purine bulge loops in RNA and DNA constructs. RNA (NEW YORK, N.Y.) 2015; 21:1313-22. [PMID: 26022248 PMCID: PMC4478350 DOI: 10.1261/rna.046631.114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 04/09/2015] [Indexed: 05/24/2023]
Abstract
Bulge loops are common features of RNA structures that are involved in the formation of RNA tertiary structures and are often sites for interactions with proteins and ions. Minimal thermodynamic data currently exist on the bulge size and sequence effects. Using thermal denaturation methods, thermodynamic properties of 1- to 5-nt adenine and guanine bulge loop constructs were examined in 10 mM MgCl(2) or 1 M KCl. The [Formula: see text] loop parameters for 1- to 5-nt purine bulge loops in RNA constructs were between 3.07 and 5.31 kcal/mol in 1 M KCl buffer. In 10 mM magnesium ions, the ΔΔG° values relative to 1 M KCl were 0.47-2.06 kcal/mol more favorable for the RNA bulge loops. The [Formula: see text] loop parameters for 1- to 5-nt purine bulge loops in DNA constructs were between 4.54 and 5.89 kcal/mol. Only 4- and 5-nt guanine constructs showed significant change in stability for the DNA constructs in magnesium ions. A linear correlation is seen between the size of the bulge loop and its stability. New prediction models are proposed for 1- to 5-nt purine bulge loops in RNA and DNA in 1 M KCl. We show that a significant stabilization is seen for small bulge loops in RNA in the presence of magnesium ions. A prediction model is also proposed for 1- to 5-nt purine bulge loop RNA constructs in 10 mM magnesium chloride.
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Affiliation(s)
- Shane Strom
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Evgenia Shiskova
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Yaeeun Hahm
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Neena Grover
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
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14
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Wolter JM, Kotagama K, Babb CS, Mangone M. Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay. J Vis Exp 2015:e52647. [PMID: 26066857 DOI: 10.3791/52647] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Luminescent Identification of Functional Elements in 3'UTRs (3'LIFE) allows the rapid identification of targets of specific miRNAs within an array of hundreds of queried 3'UTRs. Target identification is based on the dual-luciferase assay, which detects binding at the mRNA level by measuring translational output, giving a functional readout of miRNA targeting. 3'LIFE uses non-proprietary buffers and reagents, and publically available reporter libraries, making genome-wide screens feasible and cost-effective. 3'LIFE can be performed either in a standard lab setting or scaled up using liquid handling robots and other high-throughput instrumentation. We illustrate the approach using a dataset of human 3'UTRs cloned in 96-well plates, and two test miRNAs, let-7c and miR-10b. We demonstrate how to perform DNA preparation, transfection, cell culture and luciferase assays in 96-well format, and provide tools for data analysis. In conclusion 3'LIFE is highly reproducible, rapid, systematic, and identifies high confidence targets.
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Affiliation(s)
- Justin M Wolter
- School of Life Sciences, Arizona State University; Biodesign Institute, Arizona State University
| | - Kasuen Kotagama
- School of Life Sciences, Arizona State University; Biodesign Institute, Arizona State University
| | - Cody S Babb
- Biodesign Institute, Arizona State University
| | - Marco Mangone
- School of Life Sciences, Arizona State University; Biodesign Institute, Arizona State University;
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15
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Abstract
![]()
Influenza A is an RNA virus with
a genome of eight negative sense
segments. Segment 7 mRNA contains a 3′ splice site for alternative
splicing to encode the essential M2 protein. On the basis of sequence
alignment and chemical mapping experiments, the secondary structure
surrounding the 3′ splice site has an internal loop, adenine
bulge, and hairpin loop when it is in the hairpin conformation that
exposes the 3′ splice site. We report structural features of
a three-dimensional model of the hairpin derived from nuclear magnetic
resonance spectra and simulated annealing with restrained molecular
dynamics. Additional insight was provided by modeling based on 1H chemical shifts. The internal loop containing the 3′
splice site has a dynamic guanosine and a stable imino (cis Watson–Crick/Watson–Crick) GA pair. The adenine bulge
also appears to be dynamic with the A either stacked in the stem or
forming a base triple with a Watson–Crick GC pair. The hairpin
loop is a GAAA tetraloop closed by an AC pair.
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Affiliation(s)
- Jonathan L Chen
- †Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Scott D Kennedy
- ‡Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | - Douglas H Turner
- †Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.,§Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
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16
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Deng X, Su Y, Wu H, Wu R, Zhang P, Dai Y, Chan TM, Zhao M, Lu Q. The Role of MicroRNAs in Autoimmune Diseases with Skin Involvement. Scand J Immunol 2015; 81:153-65. [PMID: 25430682 DOI: 10.1111/sji.12261] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 11/10/2014] [Indexed: 11/26/2022]
Affiliation(s)
- X. Deng
- Hunan Key Laboratory of Medical Epigenetics; Department of Dermatology; Second Xiangya Hospital; Central South University; Changsha Hunan China
| | - Y. Su
- Hunan Key Laboratory of Medical Epigenetics; Department of Dermatology; Second Xiangya Hospital; Central South University; Changsha Hunan China
| | - H. Wu
- Hunan Key Laboratory of Medical Epigenetics; Department of Dermatology; Second Xiangya Hospital; Central South University; Changsha Hunan China
| | - R. Wu
- Hunan Key Laboratory of Medical Epigenetics; Department of Dermatology; Second Xiangya Hospital; Central South University; Changsha Hunan China
| | - P. Zhang
- Hunan Key Laboratory of Medical Epigenetics; Department of Dermatology; Second Xiangya Hospital; Central South University; Changsha Hunan China
| | - Y. Dai
- Clinical Medical Research Center; The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital); Shenzhen Guangdong China
| | - T.-M. Chan
- Division of Nephrology; Department of Medicine; Queen Mary Hospital; University of Hong Kong; Hong Kong China
| | - M. Zhao
- Hunan Key Laboratory of Medical Epigenetics; Department of Dermatology; Second Xiangya Hospital; Central South University; Changsha Hunan China
| | - Q. Lu
- Hunan Key Laboratory of Medical Epigenetics; Department of Dermatology; Second Xiangya Hospital; Central South University; Changsha Hunan China
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17
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Saxena S, Stanek J, Cevec M, Plavec J, Koźmiński W. C4'/H4' selective, non-uniformly sampled 4D HC(P)CH experiment for sequential assignments of (13)C-labeled RNAs. JOURNAL OF BIOMOLECULAR NMR 2014; 60:91-98. [PMID: 25205465 PMCID: PMC4207962 DOI: 10.1007/s10858-014-9861-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/01/2014] [Indexed: 05/30/2023]
Abstract
A through bond, C4'/H4' selective, "out and stay" type 4D HC(P)CH experiment is introduced which provides sequential connectivity via H4'(i)-C4'(i)-C4'(i-1)-H4'(i-1) correlations. The (31)P dimension (used in the conventional 3D HCP experiment) is replaced with evolution of better dispersed C4' dimension. The experiment fully utilizes (13)C-labeling of RNA by inclusion of two C4' evolution periods. An additional evolution of H4' is included to further enhance peak resolution. Band selective (13)C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the of C4'-C3' and C4'-C5' homonuclear couplings. For reasonable resolution, non-uniform sampling is employed in all indirect dimensions. To reduce sensitivity losses, multiple quantum coherences are preserved during shared-time evolution and coherence transfer delays. In the experiment the intra-nucleotide peaks are suppressed whereas inter-nucleotide peaks are enhanced to reduce the ambiguities. The performance of the experiment is verified on a fully (13)C, (15)N-labeled 34-nt hairpin RNA comprising typical structure elements.
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Affiliation(s)
- Saurabh Saxena
- Biological and Chemical Research Centre (CENT III), Faculty of Chemistry, University of Warsaw, Pasteura1, 02093 Warsaw, Poland
| | - Jan Stanek
- Biological and Chemical Research Centre (CENT III), Faculty of Chemistry, University of Warsaw, Pasteura1, 02093 Warsaw, Poland
| | - Mirko Cevec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova ulica 19, 1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova ulica 19, 1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Dunajska cesta 156, 1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva cesta 5, 1000 Ljubljana, Slovenia
| | - Wiktor Koźmiński
- Biological and Chemical Research Centre (CENT III), Faculty of Chemistry, University of Warsaw, Pasteura1, 02093 Warsaw, Poland
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18
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Wolter JM, Kotagama K, Pierre-Bez AC, Firago M, Mangone M. 3'LIFE: a functional assay to detect miRNA targets in high-throughput. Nucleic Acids Res 2014; 42:e132. [PMID: 25074381 PMCID: PMC4176154 DOI: 10.1093/nar/gku626] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene output at the post-transcriptional level by targeting degenerate elements primarily in 3'untranslated regions (3'UTRs) of mRNAs. Individual miRNAs can regulate networks of hundreds of genes, yet for the majority of miRNAs few, if any, targets are known. Misexpression of miRNAs is also a major contributor to cancer progression, thus there is a critical need to validate miRNA targets in high-throughput to understand miRNAs' contribution to tumorigenesis. Here we introduce a novel high-throughput assay to detect miRNA targets in 3'UTRs, called Luminescent Identification of Functional Elements in 3'UTRs (3'LIFE). We demonstrate the feasibility of 3'LIFE using a data set of 275 human 3'UTRs and two cancer-relevant miRNAs, let-7c and miR-10b, and compare our results to alternative methods to detect miRNA targets throughout the genome. We identify a large number of novel gene targets for these miRNAs, with only 32% of hits being bioinformatically predicted and 27% directed by non-canonical interactions. Functional analysis of target genes reveals consistent roles for each miRNA as either a tumor suppressor (let-7c) or oncogenic miRNA (miR-10b), and preferentially target multiple genes within regulatory networks, suggesting 3'LIFE is a rapid and sensitive method to detect miRNA targets in high-throughput.
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Affiliation(s)
- Justin M Wolter
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 S. McAllister Dr., Tempe, AZ 85287, USA
| | - Kasuen Kotagama
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA Barrett, The Honors College, Arizona State University, 751 E Lemon Mall, Tempe, AZ 85287, USA
| | - Alexandra C Pierre-Bez
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 S. McAllister Dr., Tempe, AZ 85287, USA
| | - Mari Firago
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA
| | - Marco Mangone
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 S. McAllister Dr., Tempe, AZ 85287, USA Barrett, The Honors College, Arizona State University, 751 E Lemon Mall, Tempe, AZ 85287, USA
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19
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Miao CG, Yang YY, He X, Huang C, Huang Y, Zhang L, Lv XW, Jin Y, Li J. The emerging role of microRNAs in the pathogenesis of systemic lupus erythematosus. Cell Signal 2013; 25:1828-36. [DOI: 10.1016/j.cellsig.2013.05.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/06/2013] [Indexed: 12/31/2022]
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20
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Stanek J, Podbevšek P, Koźmiński W, Plavec J, Cevec M. 4D Non-uniformly sampled C,C-NOESY experiment for sequential assignment of 13C, 15N-labeled RNAs. JOURNAL OF BIOMOLECULAR NMR 2013; 57:1-9. [PMID: 23963723 DOI: 10.1007/s10858-013-9771-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 08/10/2013] [Indexed: 05/16/2023]
Abstract
A 4D (13)C(aromatic),(13)C(ribose)-edited NOESY experiment is introduced to improve sequential assignment of non-coding RNA, often hampered by a limited dispersion of (1)H and (13)C chemical shifts. The (13)C-labeling of RNA is fully utilized by inclusion of two (13)C evolution periods. These dimensions provide enhanced dispersion of resonances in the 4D spectrum. High spectral resolution is obtained using random non-uniform sampling in three indirect dimensions. The autocorrelation peaks are efficiently suppressed using band-selective pulses. Since the dynamic range of observed resonances is significantly decreased, the reconstruction of the 4D spectrum is greatly simplified. The experiment can replace two conventionally sampled 3D NOESY spectra (either ribose-(13)C- or aromatic-(13)C-separated), and remove most ambiguities encountered during sequential walks. The assignment strategy based on a homonuclear and 4D C,C-edited NOESY experiments is proposed and verified on a 34-nt RNA showing typical structure elements.
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Affiliation(s)
- Jan Stanek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warszawa, Poland
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21
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Nomura Y, Tanaka Y, Fukunaga JI, Fujiwara K, Chiba M, Iibuchi H, Tanaka T, Nakamura Y, Kawai G, Kozu T, Sakamoto T. Solution structure of a DNA mimicking motif of an RNA aptamer against transcription factor AML1 Runt domain. J Biochem 2013; 154:513-9. [PMID: 23997091 DOI: 10.1093/jb/mvt082] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
AML1/RUNX1 is an essential transcription factor involved in the differentiation of hematopoietic cells. AML1 binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. In a previous study, we obtained RNA aptamers against the AML1 Runt domain by systematic evolution of ligands by exponential enrichment and revealed that RNA aptamers exhibit higher affinity for the Runt domain than that for RDE and possess the 5'-GCGMGNN-3' and 5'-N'N'CCAC-3' conserved motif (M: A or C; N and N' form Watson-Crick base pairs) that is important for Runt domain binding. In this study, to understand the structural basis of recognition of the Runt domain by the aptamer motif, the solution structure of a 22-mer RNA was determined using nuclear magnetic resonance. The motif contains the AH(+)-C mismatch and base triple and adopts an unusual backbone structure. Structural analysis of the aptamer motif indicated that the aptamer binds to the Runt domain by mimicking the RDE sequence and structure. Our data should enhance the understanding of the structural basis of DNA mimicry by RNA molecules.
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Affiliation(s)
- Yusuke Nomura
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016; CREST, Japan Science and Technology Agency, Saitama 332-0012; Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601; Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama 362-0806; and Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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22
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Gan HH, Gunsalus KC. Tertiary structure-based analysis of microRNA-target interactions. RNA (NEW YORK, N.Y.) 2013; 19:539-51. [PMID: 23417009 PMCID: PMC3677264 DOI: 10.1261/rna.035691.112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Current computational analysis of microRNA interactions is based largely on primary and secondary structure analysis. Computationally efficient tertiary structure-based methods are needed to enable more realistic modeling of the molecular interactions underlying miRNA-mediated translational repression. We incorporate algorithms for predicting duplex RNA structures, ionic strength effects, duplex entropy and free energy, and docking of duplex-Argonaute protein complexes into a pipeline to model and predict miRNA-target duplex binding energies. To ensure modeling accuracy and computational efficiency, we use an all-atom description of RNA and a continuum description of ionic interactions using the Poisson-Boltzmann equation. Our method predicts the conformations of two constructs of Caenorhabditis elegans let-7 miRNA-target duplexes to an accuracy of ∼3.8 Å root mean square distance of their NMR structures. We also show that the computed duplex formation enthalpies, entropies, and free energies for eight miRNA-target duplexes agree with titration calorimetry data. Analysis of duplex-Argonaute docking shows that structural distortions arising from single-base-pair mismatches in the seed region influence the activity of the complex by destabilizing both duplex hybridization and its association with Argonaute. Collectively, these results demonstrate that tertiary structure-based modeling of miRNA interactions can reveal structural mechanisms not accessible with current secondary structure-based methods.
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Affiliation(s)
- Hin Hark Gan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
- Corresponding authorsE-mail E-mail
| | - Kristin C. Gunsalus
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
- New York University, Abu Dhabi, United Arab Emirates
- Corresponding authorsE-mail E-mail
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23
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Lim GF, Merz GE, McCann MD, Gruskiewicz JM, Serra MJ. Stability of single-nucleotide bulge loops embedded in a GAAA RNA hairpin stem. RNA (NEW YORK, N.Y.) 2012; 18:807-14. [PMID: 22345128 PMCID: PMC3312567 DOI: 10.1261/rna.028308.111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 12/11/2011] [Indexed: 05/24/2023]
Abstract
Forty-six RNA hairpins containing combinations of 3' or 5' bulge loops and a 3' or 5' fluorescein label were optically melted in 1 M NaCl, and the thermodynamic parameters ΔH°, ΔS°, ΔG°(37), and T(M) for each hairpin were determined. The bulge loops were of the group I variety, in which the identity of the bulge is known, and the group II variety, in which the bulged nucleotide is identical to one of its nearest neighbors, leading to ambiguity as to the exact position of the bulge. The fluorescein label at either the 3' end or 5' end of the hairpin did not significantly influence the stability of the hairpin. As observed with bulge loops inserted into a duplex motif, the insertion of a bulge loop into the stem of a hairpin loop was destabilizing. The model developed to predict the influence of bulge loops on the stability of duplex formation was extended to predict the influence of bulge loops on hairpin stability. Specifically, the influence of the bulge is related to the stability of the hairpin stem distal from the hairpin loop.
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Affiliation(s)
- Geoffrey F.S. Lim
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | - Gregory E. Merz
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | - Michael D. McCann
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | | | - Martin J. Serra
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
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24
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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