StructureFold: Genome-wide RNA secondary structure mapping and reconstruction in vivo

Yin Tang, Emil Bouvier, Chun Kit Kwok, Yiliang Ding, Anton Nekrutenko, Philip C. Bevilacqua, Sarah M. Assmann

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

Motivation: RNAs fold into complex structures that are integral to the diverse mechanisms underlying RNA regulation of gene expression. Recent development of transcriptome-wide RNA structure profiling through the application of structure-probing enzymes or chemicals combined with high-throughput sequencing has opened a new field that greatly expands the amount of in vitro and in vivo RNA structural information available. The resultant datasets provide the opportunity to investigate RNA structural information on a global scale. However, the analysis of high-throughput RNA structure profiling data requires considerable computational effort and expertise. Results: We present a new platform, StructureFold, that provides an integrated computational solution designed specifically for large-scale RNA structure mapping and reconstruction across any transcriptome. StructureFold automates the processing and analysis of raw high-throughput RNA structure profiling data, allowing the seamless incorporation of wet-bench structural information from chemical probes and/or ribonucleases to restrain RNA secondary structure prediction via the RNAstructure and ViennaRNA package algorithms. StructureFold performs reads mapping and alignment, normalization and reactivity derivation, and RNA structure prediction in a single user-friendly web interface or via local installation. The variation in transcript abundance and length that prevails in living cells and consequently causes variation in the counts of structure-probing events between transcripts is accounted for. Accordingly, StructureFold is applicable to RNA structural profiling data obtained in vivo as well as to in vitro or in silico datasets. StructureFold is deployed via the Galaxy platform. Availability and Implementation: StructureFold is freely available as a component of Galaxy available at: https://usegalaxy.org/.

Original languageEnglish (US)
Pages (from-to)2668-2675
Number of pages8
JournalBioinformatics
Volume31
Issue number16
DOIs
StatePublished - Jan 19 2015

Fingerprint

RNA Secondary Structure
RNA
Genome
Profiling
Genes
High Throughput
Structure Prediction
Galaxies
Event Structures
Reactivity
Expertise
Throughput
Complex Structure
Sequencing
Expand
Normalization
Gene Expression
Transcriptome
Count
Enzymes

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Medicine(all)
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

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abstract = "Motivation: RNAs fold into complex structures that are integral to the diverse mechanisms underlying RNA regulation of gene expression. Recent development of transcriptome-wide RNA structure profiling through the application of structure-probing enzymes or chemicals combined with high-throughput sequencing has opened a new field that greatly expands the amount of in vitro and in vivo RNA structural information available. The resultant datasets provide the opportunity to investigate RNA structural information on a global scale. However, the analysis of high-throughput RNA structure profiling data requires considerable computational effort and expertise. Results: We present a new platform, StructureFold, that provides an integrated computational solution designed specifically for large-scale RNA structure mapping and reconstruction across any transcriptome. StructureFold automates the processing and analysis of raw high-throughput RNA structure profiling data, allowing the seamless incorporation of wet-bench structural information from chemical probes and/or ribonucleases to restrain RNA secondary structure prediction via the RNAstructure and ViennaRNA package algorithms. StructureFold performs reads mapping and alignment, normalization and reactivity derivation, and RNA structure prediction in a single user-friendly web interface or via local installation. The variation in transcript abundance and length that prevails in living cells and consequently causes variation in the counts of structure-probing events between transcripts is accounted for. Accordingly, StructureFold is applicable to RNA structural profiling data obtained in vivo as well as to in vitro or in silico datasets. StructureFold is deployed via the Galaxy platform. Availability and Implementation: StructureFold is freely available as a component of Galaxy available at: https://usegalaxy.org/.",
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StructureFold : Genome-wide RNA secondary structure mapping and reconstruction in vivo. / Tang, Yin; Bouvier, Emil; Kwok, Chun Kit; Ding, Yiliang; Nekrutenko, Anton; Bevilacqua, Philip C.; Assmann, Sarah M.

In: Bioinformatics, Vol. 31, No. 16, 19.01.2015, p. 2668-2675.

Research output: Contribution to journalArticle

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T1 - StructureFold

T2 - Genome-wide RNA secondary structure mapping and reconstruction in vivo

AU - Tang, Yin

AU - Bouvier, Emil

AU - Kwok, Chun Kit

AU - Ding, Yiliang

AU - Nekrutenko, Anton

AU - Bevilacqua, Philip C.

AU - Assmann, Sarah M.

PY - 2015/1/19

Y1 - 2015/1/19

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