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RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
Published on: April 10, 2018
Genome-wide analysis of long noncoding RNA stability
Michael B Clark1, Rebecca L Johnston, Mario Inostroza-Ponta
1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
Genome Research
|March 13, 2012
Summary
Most long noncoding RNAs (lncRNAs) are not unstable, contrary to common assumptions. This study reveals diverse lncRNA half-lives, suggesting complex functions and metabolism across the genome.
Area of Science:
- Genomics
- Molecular Biology
- RNA Biology
Background:
- Tens of thousands of long noncoding RNAs (lncRNAs) are transcribed from mammalian genomes.
- The post-transcriptional regulation and half-lives of lncRNAs remain largely uncharacterized.
- A prevailing assumption is that lncRNAs are generally unstable, lacking genome-wide validation.
Purpose of the Study:
- To determine the genome-wide half-lives of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs).
- To investigate the factors influencing lncRNA stability, including genomic origin, splicing, and subcellular localization.
- To create a resource for exploring lncRNA and mRNA stability profiles.
Main Methods:
- Utilized a custom noncoding RNA array to measure the half-lives of approximately 800 lncRNAs and 12,000 mRNAs in mouse Neuro-2a cells.
- Combined half-life data with comprehensive lncRNA annotations.
- Analyzed lncRNA features such as genomic origin, splicing status, and subcellular localization.
Main Results:
- A minority of lncRNAs are unstable; their half-lives exhibit a wide range, comparable to mRNAs.
- Hundreds of unstable (half-life < 2 hours) and stable (half-life > 16 hours) lncRNAs were identified.
- Intergenic and cis-antisense lncRNAs are more stable than intronic lncRNAs; spliced lncRNAs are more stable than unspliced ones.
- Nuclear-localized lncRNAs are generally less stable.
- The paraspeckle RNA Neat1 was found to be surprisingly unstable.
Conclusions:
- lncRNAs display diverse half-lives, challenging the notion of general instability and indicating widespread functionality.
- lncRNA stability is influenced by genomic location, splicing, and cellular compartment.
- An interactive online resource was developed to provide access to lncRNA and mRNA stability data.
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