scholarly journals Cross-linked RNA Secondary Structure Analysis using Network Techniques

2019 ◽  
Author(s):  
Irena Fischer-Hwang ◽  
Zhipeng Lu ◽  
James Zou ◽  
Tsachy Weissman
Keyword(s):  
Network Analysis ◽  
Secondary Structure ◽  
Structure Analysis ◽  
Rna Secondary Structure ◽  
Secondary Structures ◽  
Rna Structures ◽  
Secondary Structure Analysis ◽  
Automated Method ◽  
Analysis Package ◽  
Generation Sequencing

AbstractNext generation sequencing and biochemical cross-linking methods have been combined into powerful tools to probe RNA secondary structure. One such method, known as PARIS, has been used to produce near base-pair maps of long-range and alternative RNA structures in living cells. However, the procedure for generating these maps typically relies on laborious manual analysis. We developed an automated method for producing RNA secondary structure maps using network analysis techniques. We produced an analysis pipeline, dubbed cross-linked RNA secondary structure analysis using network techniques (CRSSANT), which automates the grouping of gapped RNA sequencing reads produced using the PARIS assay, and tests the validity of secondary structures implied by the groups. We validated the clusters and secondary structures produced by CRSSANT using manually-produced grouping maps and known secondary structures. We implemented CRSSANT in Python using the network analysis package NetworkX and RNA folding software package ViennaRNA. CRSSANT is fast and efficient, and is available as Python source code at https://github.com/ihwang/CRSSANT.

scholarly journals Chemogenomics driven discovery of endogenous polyketide anti-infective compounds from endosymbiotic Emericella variecolor CLB38 and their RNA secondary structure analysis

PLoS ONE ◽  
2017 ◽  
Vol 12 (2) ◽  
pp. e0172848 ◽  
Author(s):  
H. C. Yashavantha Rao ◽  
Devaraju Rakshith ◽  
Ballagere Puttaraju Harini ◽  
Doddahosuru Mahadevappa Gurudatt ◽  
Sreedharamurthy Satish
Keyword(s):  
Secondary Structure ◽  
Structure Analysis ◽  
Rna Secondary Structure ◽  
Secondary Structure Analysis ◽  
Emericella Variecolor

scholarly journals RNAStructViz: Graphical base pairing analysis

2021 ◽  
Author(s):  
Maxie Dion Schmidt ◽  
Anna Kirkpatrick ◽  
Christine Heitsch
Keyword(s):  
Secondary Structure ◽  
Structure Analysis ◽  
Rna Secondary Structure ◽  
Central Feature ◽  
Style File ◽  
Base Pairing ◽  
Circular Arc ◽  
Secondary Structure Analysis ◽  
Graphical Tool ◽  
Similarities And Differences

AbstractSummaryWe present a new graphical tool for RNA secondary structure analysis. The central feature is the ability to visually compare/contrast up to three base pairing configurations for a given sequence in a compact, standardized circular arc diagram layout. This is complemented by a built-in CT-style file viewer and radial layout substructure viewer which are directly linked to the arc diagram window via the zoom selection tool. Additional functionality includes the computation of some numerical information, and the ability to export images and data for later use. This tool should be of use to researchers seeking to better understand similarities and differences between structural alternatives for an RNA sequence.Availability and implementationhttps://github.com/gtDMMB/RNAStructViz/wikiAuthor [email protected], [email protected], and [email protected]

scholarly journals In Vivo and In Vitro Genome-Wide Profiling of RNA Secondary Structures Reveals Key Regulatory Features in Plasmodium falciparum

2021 ◽  
Vol 11 ◽  
Author(s):  
Yanwei Qi ◽  
Yuhong Zhang ◽  
Guixing Zheng ◽  
Bingxia Chen ◽  
Mengxin Zhang ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Structure ◽  
Rna Secondary Structure ◽  
Secondary Structures ◽  
Rna Structures ◽  
Trophozoite Stage ◽  
Rna Secondary Structures ◽  
Biological Programme

It is widely accepted that the structure of RNA plays important roles in a number of biological processes, such as polyadenylation, splicing, and catalytic functions. Dynamic changes in RNA structure are able to regulate the gene expression programme and can be used as a highly specific and subtle mechanism for governing cellular processes. However, the nature of most RNA secondary structures in Plasmodium falciparum has not been determined. To investigate the genome-wide RNA secondary structural features at single-nucleotide resolution in P. falciparum, we applied a novel high-throughput method utilizing the chemical modification of RNA structures to characterize these structures. Structural data from parasites are in close agreement with the known 18S ribosomal RNA secondary structures of P. falciparum and can help to predict the in vivo RNA secondary structure of a total of 3,396 transcripts in the ring-stage and trophozoite-stage developmental cycles. By parallel analysis of RNA structures in vivo and in vitro during the Plasmodium parasite ring-stage and trophozoite-stage intraerythrocytic developmental cycles, we identified some key regulatory features. Recent studies have established that the RNA structure is a ubiquitous and fundamental regulator of gene expression. Our study indicate that there is a critical connection between RNA secondary structure and mRNA abundance during the complex biological programme of P. falciparum. This work presents a useful framework and important results, which may facilitate further research investigating the interactions between RNA secondary structure and the complex biological programme in P. falciparum. The RNA secondary structure characterized in this study has potential applications and important implications regarding the identification of RNA structural elements, which are important for parasite infection and elucidating host-parasite interactions and parasites in the environment.

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