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RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
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RNA secondary structure profiling in zebrafish reveals unique regulatory features
Kriti Kaushik1,2, Ambily Sivadas3,2, Shamsudheen Karuthedath Vellarikkal1,2
1Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.
BMC Genomics
|February 17, 2018
Summary
This study maps zebrafish RNA secondary structures at single nucleotide resolution using Parallel Analysis of RNA Structure (PARS). Findings reveal structural features in coding and non-coding RNAs, impacting gene regulation.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- RNA molecules play crucial roles in gene regulation.
- These regulatory functions are linked to RNA's complex secondary and tertiary structures.
Purpose of the Study:
- To create a comprehensive transcriptome-wide RNA secondary structure map for zebrafish.
- To analyze RNA structural features and their relationship with gene function and regulation.
Main Methods:
- Utilized Parallel Analysis of RNA Structure (PARS) for high-resolution RNA structure mapping.
- Analyzed secondary structures across coding and non-coding RNAs in the zebrafish transcriptome.
Main Results:
- Documented single nucleotide pairing probabilities for over 54,000 zebrafish transcripts.
- Identified distinct structural signatures at translation start/stop sites, coding regions (codon periodicity), and splice sites.
- Observed higher structural signals in 3' Untranslated Regions (UTRs) compared to coding sequences and 5' UTRs.
- Explored secondary structures in long non-coding RNAs to infer molecular functions.
Conclusions:
- Presented the first PARS-based transcriptome-wide RNA secondary structure map of zebrafish.
- The map provides single nucleotide precision for RNA pairing probabilities.
- Findings facilitate further research into zebrafish RNA structural elements and their influence on gene expression.
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