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Embarc-Buh A, Francisco-Velilla R, Garcia-Martin JA, Abellan S, Ramajo J, Martinez-Salas E. Gemin5-dependent RNA association with polysomes enables selective translation of ribosomal and histone mRNAs. Cell Mol Life Sci 2022; 79:490. [PMID: 35987821 PMCID: PMC9392717 DOI: 10.1007/s00018-022-04519-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 11/03/2022]
Abstract
AbstractSelective translation allows to orchestrate the expression of specific proteins in response to different signals through the concerted action of cis-acting elements and RNA-binding proteins (RBPs). Gemin5 is a ubiquitous RBP involved in snRNP assembly. In addition, Gemin5 regulates translation of different mRNAs through apparently opposite mechanisms of action. Here, we investigated the differential function of Gemin5 in translation by identifying at a genome-wide scale the mRNAs associated with polysomes. Among the mRNAs showing Gemin5-dependent enrichment in polysomal fractions, we identified a selective enhancement of specific transcripts. Comparison of the targets previously identified by CLIP methodologies with the polysome-associated transcripts revealed that only a fraction of the targets was enriched in polysomes. Two different subsets of these mRNAs carry unique cis-acting regulatory elements, the 5’ terminal oligopyrimidine tracts (5’TOP) and the histone stem-loop (hSL) structure at the 3’ end, respectively, encoding ribosomal proteins and histones. RNA-immunoprecipitation (RIP) showed that ribosomal and histone mRNAs coprecipitate with Gemin5. Furthermore, disruption of the TOP motif impaired Gemin5-RNA interaction, and functional analysis showed that Gemin5 stimulates translation of mRNA reporters bearing an intact TOP motif. Likewise, Gemin5 enhanced hSL-dependent mRNA translation. Thus, Gemin5 promotes polysome association of only a subset of its targets, and as a consequence, it favors translation of the ribosomal and the histone mRNAs. Together, the results presented here unveil Gemin5 as a novel translation regulator of mRNA subsets encoding proteins involved in fundamental cellular processes.
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Minuesa G, Alsina C, Garcia-Martin JA, Oliveros JC, Dotu I. Correction to 'MoiRNAiFold: a novel tool for complex in silico RNA design'. Nucleic Acids Res 2021; 50:1198. [PMID: 34935977 PMCID: PMC8789039 DOI: 10.1093/nar/gkab1284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Gerard Minuesa
- Moirai Biodesign, c/ Baldiri Reixach s/n, Parc Científic de Barcelona (PCB), 08028 Barcelona, Spain
| | - Cristina Alsina
- Moirai Biodesign, c/ Baldiri Reixach s/n, Parc Científic de Barcelona (PCB), 08028 Barcelona, Spain
| | - Juan Antonio Garcia-Martin
- Bioinformatics for Genomics and Proteomics. National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain.,Grupo Interdisciplinar de Sistemas Complejos (GISC), Universidad Carlos III de Madrid, 28911 Madrid, Spain
| | - Juan Carlos Oliveros
- Bioinformatics for Genomics and Proteomics. National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain
| | - Ivan Dotu
- Moirai Biodesign, c/ Baldiri Reixach s/n, Parc Científic de Barcelona (PCB), 08028 Barcelona, Spain
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Minuesa G, Alsina C, Garcia-Martin JA, Oliveros J, Dotu I. MoiRNAiFold: a novel tool for complex in silico RNA design. Nucleic Acids Res 2021; 49:4934-4943. [PMID: 33956139 PMCID: PMC8136780 DOI: 10.1093/nar/gkab331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/09/2021] [Accepted: 04/21/2021] [Indexed: 12/23/2022] Open
Abstract
Novel tools for in silico design of RNA constructs such as riboregulators are required in order to reduce time and cost to production for the development of diagnostic and therapeutic advances. Here, we present MoiRNAiFold, a versatile and user-friendly tool for de novo synthetic RNA design. MoiRNAiFold is based on Constraint Programming and it includes novel variable types, heuristics and restart strategies for Large Neighborhood Search. Moreover, this software can handle dozens of design constraints and quality measures and improves features for RNA regulation control of gene expression, such as Translation Efficiency calculation. We demonstrate that MoiRNAiFold outperforms any previous software in benchmarking structural RNA puzzles from EteRNA. Importantly, with regard to biologically relevant RNA designs, we focus on RNA riboregulators, demonstrating that the designed RNA sequences are functional both in vitro and in vivo. Overall, we have generated a powerful tool for de novo complex RNA design that we make freely available as a web server (https://moiraibiodesign.com/design/).
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Affiliation(s)
- Gerard Minuesa
- Moirai Biodesign, c/ Baldiri Reixach s/n, Parc Científic de Barcelona (PCB), 08028 Barcelona, Spain
| | - Cristina Alsina
- Moirai Biodesign, c/ Baldiri Reixach s/n, Parc Científic de Barcelona (PCB), 08028 Barcelona, Spain
| | - Juan Antonio Garcia-Martin
- Bioinformatics for Genomics and Proteomics. National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Universidad Carlos III de Madrid, 28911 Madrid, Spain
| | - Juan Carlos Oliveros
- Bioinformatics for Genomics and Proteomics. National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain
| | - Ivan Dotu
- Moirai Biodesign, c/ Baldiri Reixach s/n, Parc Científic de Barcelona (PCB), 08028 Barcelona, Spain
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Garcia-Martin JA, Chavarría M, de Lorenzo V, Pazos F. Concomitant prediction of environmental fate and toxicity of chemical compounds. Biol Methods Protoc 2020; 5:bpaa025. [PMID: 33376807 PMCID: PMC7750720 DOI: 10.1093/biomethods/bpaa025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 01/15/2023] Open
Abstract
The environmental fate of many functional molecules that are produced on a large scale as precursors or as additives to specialty goods (plastics, fibers, construction materials, etc.), let alone those synthesized by the pharmaceutical industry, is generally unknown. Assessing their environmental fate is crucial when taking decisions on the manufacturing, handling, usage, and release of these substances, as is the evaluation of their toxicity in humans and other higher organisms. While this data are often hard to come by, the experimental data already available on the biodegradability and toxicity of many unusual compounds (including genuinely xenobiotic molecules) make it possible to develop machine learning systems to predict these features. As such, we have created a predictor of the "risk" associated with the use and release of any chemical. This new system merges computational methods to predict biodegradability with others that assess biological toxicity. The combined platform, named BiodegPred (https://sysbiol.cnb.csic.es/BiodegPred/), provides an informed prognosis of the chance a given molecule can eventually be catabolized in the biosphere, as well as of its eventual toxicity, all available through a simple web interface. While the platform described does not give much information about specific degradation kinetics or particular biodegradation pathways, BiodegPred has been instrumental in anticipating the probable behavior of a large number of new molecules (e.g. antiviral compounds) for which no biodegradation data previously existed.
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Affiliation(s)
- Juan Antonio Garcia-Martin
- Bioinformatics for Genomics and Proteomics, National Centre for Biotechnology (CNB-CSIC), 28049 Madrid, Spain
| | - Max Chavarría
- Escuela de Química/CIPRONA Universidad de Costa Rica, 11501-2060 San José, Costa Rica
| | - Victor de Lorenzo
- Department of Systems Biology, National Centre for Biotechnology (CNB-CSIC), 28049 Madrid, Spain
| | - Florencio Pazos
- Department of Systems Biology, National Centre for Biotechnology (CNB-CSIC), 28049 Madrid, Spain
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Abstract
Background Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement). Results We describe a unique computational tool, RNAsampleCDS, designed to compute the number of RNA sequences that code two (or more) peptides p,q in overlapping reading frames, that are identical (or have BLOSUM/PAM similarity that exceeds a user-specified value) to the input peptides p,q. RNAsampleCDS then samples a user-specified number of messenger RNAs that code such peptides; alternatively, RNAsampleCDS can exactly compute the position-specific scoring matrix and codon usage bias for all such RNA sequences. Our software allows the user to stipulate overlapping coding requirements for all 6 possible reading frames simultaneously, even allowing IUPAC constraints on RNA sequences and fixing GC-content. We generalize the notion of codon preference index (CPI) to overlapping reading frames, and use RNAsampleCDS to generate control sequences required in the computation of CPI. Moreover, by applying RNAsampleCDS, we are able to quantify the extent to which the overlapping coding requirement in HIV-1 [resp. HCV] contribute to the formation of the stem-loop [resp. double stem-loop] secondary structure known as the frameshift stimulating signal. Using our software, we confirm that certain experimentally determined deleterious HCV mutations occur in positions for which our software RNAsampleCDS and RNAiFold both indicate a single possible nucleotide. We generalize the notion of codon preference index (CPI) to overlapping coding regions, and use RNAsampleCDS to generate control sequences required in the computation of CPI for the Gag-Pol overlapping coding region of HIV-1. These applications show that RNAsampleCDS constitutes a unique tool in the software arsenal now available to evolutionary biologists. Conclusion Source code for the programs and additional data are available at http://bioinformatics.bc.edu/clotelab/RNAsampleCDS/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1389-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amir H Bayegan
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill MA, 02467, USA
| | | | - Peter Clote
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill MA, 02467, USA.
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Garcia-Martin JA, Bayegan AH, Dotu I, Clote P. RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory. BMC Bioinformatics 2016; 17:424. [PMID: 27756204 PMCID: PMC5069997 DOI: 10.1186/s12859-016-1280-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/26/2016] [Indexed: 12/01/2022] Open
Abstract
Background RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s0, i.e. whose minimum free energy secondary structure is identical to the target s0. Here we consider the ensemble of all RNA sequences that have low free energy with respect to a given target s0. Results We introduce the program RNAdualPF, which computes the dual partition functionZ∗, defined as the sum of Boltzmann factors exp(−E(a,s0)/RT) of all RNA nucleotide sequences a compatible with target structure s0. Using RNAdualPF, we efficiently sample RNA sequences that approximately fold into s0, where additionally the user can specify IUPAC sequence constraints at certain positions, and whether to include dangles (energy terms for stacked, single-stranded nucleotides). Moreover, since we also compute the dual partition functionZ∗(k) over all sequences having GC-content k, the user can require that all sampled sequences have a precise, specified GC-content. Using Z∗, we compute the dual expected energy 〈E∗〉, and use it to show that natural RNAs from the Rfam 12.0 database have higher minimum free energy than expected, thus suggesting that functional RNAs are under evolutionary pressure to be only marginally thermodynamically stable. We show that C. elegans precursor microRNA (pre-miRNA) is significantly non-robust with respect to mutations, by comparing the robustness of each wild type pre-miRNA sequence with 2000 [resp. 500] sequences of the same GC-content generated by RNAdualPF, which approximately [resp. exactly] fold into the wild type target structure. We confirm and strengthen earlier findings that precursor microRNAs and bacterial small noncoding RNAs display plasticity, a measure of structural diversity. Conclusion We describe RNAdualPF, which rapidly computes the dual partition functionZ∗ and samples sequences having low energy with respect to a target structure, allowing sequence constraints and specified GC-content. Using different inverse folding software, another group had earlier shown that pre-miRNA is mutationally robust, even controlling for compositional bias. Our opposite conclusion suggests a cautionary note that computationally based insights into molecular evolution may heavily depend on the software used. C/C++-software for RNAdualPF is available at http://bioinformatics.bc.edu/clotelab/RNAdualPF. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1280-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Antonio Garcia-Martin
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, 02467, MA, USA.,Present Address: Systems Biology Program Centro Nacional de Biotecnología Consejo Superior de Investigaciones Científicas (CSIC) C/ Darwin 3, Madrid, 28049, Spain
| | - Amir H Bayegan
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, 02467, MA, USA
| | - Ivan Dotu
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader, 88, Barcelona, Spain
| | - Peter Clote
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, 02467, MA, USA.
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Garcia-Martin JA, Dotu I, Fernandez-Chamorro J, Lozano G, Ramajo J, Martinez-Salas E, Clote P. RNAiFold2T: Constraint Programming design of thermo-IRES switches. Bioinformatics 2016; 32:i360-i368. [PMID: 27307638 PMCID: PMC4908349 DOI: 10.1093/bioinformatics/btw265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
MOTIVATION RNA thermometers (RNATs) are cis-regulatory elements that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting potential resource in synthetic biology, where engineered RNATs could prove to be useful tools in biosensors and conditional gene regulation. RESULTS Solving the 2-temperature inverse folding problem is critical for RNAT engineering. Here we introduce RNAiFold2T, the first Constraint Programming (CP) and Large Neighborhood Search (LNS) algorithms to solve this problem. Benchmarking tests of RNAiFold2T against existent programs (adaptive walk and genetic algorithm) inverse folding show that our software generates two orders of magnitude more solutions, thus allowing ample exploration of the space of solutions. Subsequently, solutions can be prioritized by computing various measures, including probability of target structure in the ensemble, melting temperature, etc. Using this strategy, we rationally designed two thermosensor internal ribosome entry site (thermo-IRES) elements, whose normalized cap-independent translation efficiency is approximately 50% greater at 42 °C than 30 °C, when tested in reticulocyte lysates. Translation efficiency is lower than that of the wild-type IRES element, which on the other hand is fully resistant to temperature shift-up. This appears to be the first purely computational design of functional RNA thermoswitches, and certainly the first purely computational design of functional thermo-IRES elements. AVAILABILITY RNAiFold2T is publicly available as part of the new release RNAiFold3.0 at https://github.com/clotelab/RNAiFold and http://bioinformatics.bc.edu/clotelab/RNAiFold, which latter has a web server as well. The software is written in C ++ and uses OR-Tools CP search engine. CONTACT clote@bc.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Ivan Dotu
- Department of Experimental and Health Sciences, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra. Dr. Aiguader 88, Barcelona, Spain
| | - Javier Fernandez-Chamorro
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, 28049 Madrid, Spain
| | - Gloria Lozano
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, 28049 Madrid, Spain
| | - Jorge Ramajo
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, 28049 Madrid, Spain
| | - Encarnacion Martinez-Salas
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, 28049 Madrid, Spain
| | - Peter Clote
- Biology Department, Boston College, Chestnut Hill, MA 02467, USA
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Abstract
Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner’99 and Turner’04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs.
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Affiliation(s)
| | - Peter Clote
- Department of Biology, Boston College, Chestnut Hill, MA 02467, United States of America
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Garcia-Martin JA, Dotu I, Clote P. RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules. Nucleic Acids Res 2015; 43:W513-21. [PMID: 26019176 PMCID: PMC4489274 DOI: 10.1093/nar/gkv460] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 04/27/2015] [Indexed: 12/25/2022] Open
Abstract
Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead of heuristic methods. For that reason, RNAiFold can generate all sequences that fold into the target structure or determine that there is no solution. RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now defunct COMET language to C++. The new code properly extends the capabilities of its predecessor by providing a user-friendly pipeline to design synthetic constructs having the functionality of given Rfam families. In addition, the new software supports amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; moreover, structure compatibility/incompatibility constraints have been expanded. With these features, RNAiFold 2.0 allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules. Availability: the web server, source code and linux binaries are publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold2.0.
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Affiliation(s)
| | - Ivan Dotu
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute); C/Dr. Aiguader 88, Barcelona E-08003, Spain
| | - Peter Clote
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
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Dotu I, Garcia-Martin JA, Slinger BL, Mechery V, Meyer MM, Clote P. Complete RNA inverse folding: computational design of functional hammerhead ribozymes. Nucleic Acids Res 2014; 42:11752-62. [PMID: 25209235 PMCID: PMC4191386 DOI: 10.1093/nar/gku740] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold, which can determine all RNA sequences whose minimum free energy secondary structure is a user-specified target structure. Using RNAiFold, we design ten cis-cleaving hammerhead ribozymes, all of which are shown to be functional by a cleavage assay. We additionally use RNAiFold to design a functional cis-cleaving hammerhead as a modular unit of a synthetic larger RNA. Analysis of kinetics on this small set of hammerheads suggests that cleavage rate of computationally designed ribozymes may be correlated with positional entropy, ensemble defect, structural flexibility/rigidity and related measures. Artificial ribozymes have been designed in the past either manually or by SELEX (Systematic Evolution of Ligands by Exponential Enrichment); however, this appears to be the first purely computational design and experimental validation of novel functional ribozymes. RNAiFold is available at http://bioinformatics.bc.edu/clotelab/RNAiFold/.
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Affiliation(s)
- Ivan Dotu
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
| | | | - Betty L Slinger
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
| | - Vinodh Mechery
- Hofstra North Shore-LIJ School of Medicine, Hempstead, NY 11549, USA
| | - Michelle M Meyer
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
| | - Peter Clote
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
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Abstract
Synthetic biology and nanotechnology are poised to make revolutionary contributions to the 21st century. In this article, we describe a new web server to support in silico RNA molecular design. Given an input target RNA secondary structure, together with optional constraints, such as requiring GC-content to lie within a certain range, requiring the number of strong (GC), weak (AU) and wobble (GU) base pairs to lie in a certain range, the RNAiFold web server determines one or more RNA sequences, whose minimum free-energy secondary structure is the target structure. RNAiFold provides access to two servers: RNA-CPdesign, which applies constraint programming, and RNA-LNSdesign, which applies the large neighborhood search heuristic; hence, it is suitable for larger input structures. Both servers can also solve the RNA inverse hybridization problem, i.e. given a representation of the desired hybridization structure, RNAiFold returns two sequences, whose minimum free-energy hybridization is the input target structure. The web server is publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold, which provides access to two specialized servers: RNA-CPdesign and RNA-LNSdesign. Source code for the underlying algorithms, implemented in COMET and supported on linux, can be downloaded at the server website.
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Abstract
Synthetic biology is a rapidly emerging discipline with long-term ramifications that range from single-molecule detection within cells to the creation of synthetic genomes and novel life forms. Truly phenomenal results have been obtained by pioneering groups--for instance, the combinatorial synthesis of genetic networks, genome synthesis using BioBricks, and hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment, biomolecular self-assembly pathways, etc. Such work strongly suggests that nanotechnology and synthetic biology together seem poised to constitute the most transformative development of the 21st century. In this paper, we present a Constraint Programming (CP) approach to solve the RNA inverse folding problem. Given a target RNA secondary structure, we determine an RNA sequence which folds into the target structure; i.e. whose minimum free energy structure is the target structure. Our approach represents a step forward in RNA design--we produce the first complete RNA inverse folding approach which allows for the specification of a wide range of design constraints. We also introduce a Large Neighborhood Search approach which allows us to tackle larger instances at the cost of losing completeness, while retaining the advantages of meeting design constraints (motif, GC-content, etc.). Results demonstrate that our software, RNAiFold, performs as well or better than all state-of-the-art approaches; nevertheless, our approach is unique in terms of completeness, flexibility, and the support of various design constraints. The algorithms presented in this paper are publicly available via the interactive webserver http://bioinformatics.bc.edu/clotelab/RNAiFold; additionally, the source code can be downloaded from that site.
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