scholarly journals FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds

2019 ◽  
Author(s):  
Andrew M. Watkins ◽  
Rhiju Das
Keyword(s):  
Experimental Data ◽  
De Novo ◽  
Accurate Prediction ◽  
Human Intervention ◽  
Fragment Assembly ◽  
3D Structures ◽  
Rna Molecules ◽  
Fragment Libraries ◽  
Large Model

SummaryMethods to predict RNA 3D structures from sequence are needed to understand the exploding number of RNA molecules being discovered across biology. As assessed during community-wide RNA-Puzzles trials, Rosetta’s Fragment Assembly of RNA with Full-Atom Refinement (FARFAR) enables accurate prediction of complex folds, but it remains unclear how much human intervention and experimental guidance is needed to achieve this performance. Here, we present FARFAR2, a protocol integrating recent innovations with updated RNA fragment libraries and helix modeling. In 16 of 21 RNA-Puzzles revisited without experimental data or expert intervention, FARFAR2 recovers structures that are more accurate than the original models submitted by our group and other participants during the RNA-Puzzles trials. In five prospective tests, pre-registered FARFAR2 models for riboswitches and adenovirus VA-I achieved 3–8 Å RMSD accuracies. Finally, we present a server and three large model archives (FARFAR2-Classics, FARFAR2-Motifs, and FARFAR2-Puzzles) to guide future applications and advances.

scholarly journals Induction of Promoter DNA Methylation Upon High-Pressure Spraying of Double-Stranded RNA in Plants

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 789
Author(s):  
Athanasios Dalakouras ◽  
Ioannis Ganopoulos
Keyword(s):  
High Pressure ◽  
De Novo ◽  
Epigenetic Changes ◽  
Double Stranded Rna ◽  
Rna Molecules ◽  
Promoter Sequences ◽  
Promoter Dna Methylation ◽  
Promoter Dna ◽  
First Time ◽  
De Novo Methylation

Exogenous application of RNA molecules is a potent method to trigger RNA interference (RNAi) in plants in a transgene-free manner. So far, all exogenous RNAi (exo-RNAi) applications have aimed to trigger mRNA degradation of a given target. However, the issue of concomitant epigenetic changes was never addressed. Here, we report for the first time that high-pressure spraying of dsRNAs can trigger de novo methylation of promoter sequences in plants.

Combining theoretical and experimental data to decipher CFTR 3D structures and functions

2018 ◽  
Vol 75 (20) ◽  
pp. 3829-3855 ◽  
Author(s):  
Brice Hoffmann ◽  
Ahmad Elbahnsi ◽  
Pierre Lehn ◽  
Jean-Luc Décout ◽  
Fabio Pietrucci ◽  
...  
Keyword(s):  
Experimental Data ◽  
3D Structures

scholarly journals Lyapunov Exponent-Based Study of Chaotic Mechanical Behavior of Concrete under Compression

2019 ◽  
Vol 2019 ◽  
pp. 1-12
Author(s):  
Yuhu Quan ◽  
Xu Yang
Keyword(s):  
Experimental Data ◽  
Lyapunov Exponent ◽  
Evolution Equation ◽  
Mechanical Behavior ◽  
Chaos Theory ◽  
Human Intervention

Chaos theory is advantageous in achieving a deeper understanding of the nonlinearity and randomness of concrete behavior. In this study, the experimental data of concrete under compression were examined and discussed using Lyapunov exponent. According to the value of the Lyapunov exponent, which was larger than 0, it could be quantitatively demonstrated that measured and fitted data exhibited chaotic features. Besides, the mechanical behavior of concrete could be predicted by deducing its evolution equation. Furthermore, the evolution and trends of the Lyapunov exponent indicated that the series with human intervention showed a stronger chaotic property, which led to the result that this kind of series might be more difficult to predict.

Viroid-induced DNA methylation in plants

2013 ◽  
Vol 4 (6) ◽  
pp. 557-565 ◽  
Author(s):  
Athanasios Dalakouras ◽  
Elena Dadami ◽  
Michael Wassenegger
Keyword(s):  
Dna Methylation ◽  
Small Rnas ◽  
Rna Silencing ◽  
De Novo ◽  
Rna Degradation ◽  
Double Stranded Rna ◽  
Methyl Group ◽  
Rna Molecules ◽  
Cumulative Data

AbstractIn eukaryotes, DNA methylation refers to the addition of a methyl group to the fifth atom in the six-atom ring of cytosine residues. At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). RdDM was first discovered in viroid-infected plants. Viroids are pathogenic circular, non-coding, single-stranded RNA molecules. Members of the Pospiviroidae family replicate in the nucleus through double-stranded RNA intermediates, attracting the host RNA silencing machinery. The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. Here, we provide an overview of the cumulative data on the field of viroid-induced RdDM and discuss three possible scenarios concerning the mechanistic details of its establishment.

Polyadenylate-containing RNA in dormant and germinating Botryodiplodia theobromae pycnidiospores

1979 ◽  
Vol 25 (3) ◽  
pp. 375-379 ◽  
Author(s):  
James L. Van Etten ◽  
Carroll D. Rawn
Keyword(s):  
Germ Tube ◽  
De Novo ◽  
Segment Length ◽  
Botryodiplodia Theobromae ◽  
Rna Molecules ◽  
Polyuridylic Acid ◽  
Tube Emergence ◽  
Dormant Spore ◽  
Average Size

Hybridization of [3H]polyuridylic acid to RNA isolated from Botryodiplodia theobromae pycnidiospores yielded an estimate of about 6.25 × 105 polyadenylate-containing RNA (poly A(+) RNA) molecules per dormant spore. The number increased about fourfold by the time of germ tube emergence at 3 h. The average size of this presumed mRNA was about 4.1 × 105 daltons (1275 nucleotides), with an average polyadenylate segment length of 26 nucleotides. Neither of these values changed significantly during germination. The earliest detectable (first 30 min of germination) de novo synthesized mRNA's were rapidly incorporated into polyribosomes. This newly synthesized, presumably functional, mRNA was composed of both poly A(+) RNA and polyadenylate-lacking RNA. The average sizesof the two polyribosomal mRNA subpopulations and the total poly A(+) RNA population were identical.

scholarly journals Revealing the host antiviral protein ZAP-S as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting

2021 ◽  
Author(s):  
Matthias Michael Zimmer ◽  
Anuja Nitin Kibe ◽  
Ulfert Rand ◽  
Lukas Pekarek ◽  
Luca Cicin-Sain ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Specific Inhibitor ◽  
Antiviral Protein ◽  
Ribosomal Frameshifting ◽  
Reading Frame ◽  
Rna Molecules ◽  
Cellular Factors ◽  
Infected Cells

Programmed ribosomal frameshifting (PRF) is a fundamental gene expression event in many viruses including SARS-CoV-2, which allows production of essential structural and replicative enzymes from an alternative reading frame. Despite the importance of PRF for the viral life cycle, it is still largely unknown how and to what extent cellular factors alter mechanical properties of frameshifting RNA molecules and thereby impact virulence. This prompted us to comprehensively dissect the interplay between the host proteome and the SARS-CoV-2 frameshift element. Here, we reveal that zinc-finger antiviral protein (ZAP-S) is a direct and specific regulator of PRF in SARS-CoV-2 infected cells. ZAP-S overexpression strongly impairs frameshifting and viral replication. Using in vitro ensemble and single-molecule techniques, we further demonstrate that ZAP-S directly interacts with the SARS-CoV-2 RNA and ribosomes and interferes with the folding of the frameshift RNA. Together these data illuminate ZAP-S as de novo host-encoded specific inhibitor of SARS-CoV-2 frameshifting and expand our understanding of RNA-based gene regulation.

scholarly journals OMGene: Mutual improvement of gene models through optimisation of evolutionary conservation

2017 ◽  
Author(s):  
Michael P. Dunne ◽  
Steven Kelly
Keyword(s):  
Experimental Data ◽  
De Novo ◽  
Gene Prediction ◽  
Expression Profiles ◽  
Accurate Determination ◽  
Subcellular Localisation ◽  
Rna Seq ◽  
Gene Model ◽  
Specific Expression ◽  
Gene Models

AbstractBackgroundThe accurate determination of the genomic coordinates for a given gene – its gene model – is of vital importance to the utility of its annotation, and the accuracy of bioinformatic analyses derived from it. Currently-available methods of computational gene prediction, while on the whole successful, often disagree on the model for a given predicted gene, with some or all of the variant gene models failing to match the biologically observed structure. Many prediction methods can be bolstered by using experimental data such as RNA-seq and mass spectrometry. However, these resources are not always available, and rarely give a comprehensive portrait of an organism’s transcriptome due to temporal and tissue-specific expression profiles.ResultsOrthology between genes provides evolutionary evidence to guide the construction of gene models. OMGene (Optimise My Gene) aims to optimise gene models in the absence of experimental data by optimising the derived amino acid alignments for gene models within orthogroups. Using RNA-seq data sets from plants and fungi, considering intron/exon junction representation and exon coverage, and assessing the intra-orthogroup consistency of subcellular localisation predictions, we demonstrate the utility of OMGene for improving gene models in annotated genomes.ConclusionsWe show that significant improvements in the accuracy of gene model annotations can be made in both established and de novo annotated genomes by leveraging information from multiple species.

ANGEL2 is a member of the CCR4 family of deadenylases with 2′,3′-cyclic phosphatase activity

Science ◽  
2020 ◽  
Vol 369 (6503) ◽  
pp. 524-530
Author(s):  
Paola H. Pinto ◽  
Alena Kroupova ◽  
Alexander Schleiffer ◽  
Karl Mechtler ◽  
Martin Jinek ◽  
...  
Keyword(s):  
Messenger Rna ◽  
De Novo ◽  
Mrna Splicing ◽  
Rna Molecules ◽  
Unfolded Protein ◽  
Rna Pathways ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Cyclic Phosphates ◽  
Hydrolysis Of

RNA molecules are frequently modified with a terminal 2′,3′-cyclic phosphate group as a result of endonuclease cleavage, exonuclease trimming, or de novo synthesis. During pre-transfer RNA (tRNA) and unconventional messenger RNA (mRNA) splicing, 2′,3′-cyclic phosphates are substrates of the tRNA ligase complex, and their removal is critical for recycling of tRNAs upon ribosome stalling. We identified the predicted deadenylase angel homolog 2 (ANGEL2) as a human phosphatase that converts 2′,3′-cyclic phosphates into 2′,3′-OH nucleotides. We analyzed ANGEL2’s substrate preference, structure, and reaction mechanism. Perturbing ANGEL2 expression affected the efficiency of pre-tRNA processing, X-box–binding protein 1 (XBP1) mRNA splicing during the unfolded protein response, and tRNA nucleotidyltransferase 1 (TRNT1)–mediated CCA addition onto tRNAs. Our results indicate that ANGEL2 is involved in RNA pathways that rely on the ligation or hydrolysis of 2′,3′-cyclic phosphates.

DNA Fragment Assembly Using Quantum-Inspired Genetic Algorithm

2019 ◽  
pp. 80-98 ◽  
Author(s):  
Manisha Rathee ◽  
Kumar Dilip ◽  
Ritu Rathee
Keyword(s):  
Genetic Algorithm ◽  
De Novo ◽  
Combinatorial Optimization Problem ◽  
Swarm Optimization ◽  
Fragment Assembly ◽  
Search Spaces ◽  
Target Dna ◽  
Dna Fragment ◽  
Metaheuristic Techniques ◽  
Dna Fragment Assembly

DNA fragment assembly (DFA) is one of the most important and challenging problems in computational biology. DFA problem involves reconstruction of target DNA from several hundred (or thousands) of sequenced fragments by identifying the proper orientation and order of fragments. DFA problem is proved to be a NP-Hard combinatorial optimization problem. Metaheuristic techniques have the capability to handle large search spaces and therefore are well suited to deal with such problems. In this chapter, quantum-inspired genetic algorithm-based DNA fragment assembly (QGFA) approach has been proposed to perform the de novo assembly of DNA fragments using overlap-layout-consensus approach. To assess the efficacy of QGFA, it has been compared genetic algorithm, particle swarm optimization, and ant colony optimization-based metaheuristic approaches for solving DFA problem. Experimental results show that QGFA performs comparatively better (in terms of overlap score obtained and number of contigs produced) than other approaches considered herein.

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