The DOI matches its Crossref record; 71 of the 71 references it cites were found in a registry or an index.
Genome-wide analysis of long noncoding RNA stability
Open accessAbstract
Transcriptomic analyses have identified tens of thousands of intergenic, intronic, and cis-antisense long noncoding RNAs (lncRNAs) that are expressed from mammalian genomes. Despite progress in functional characterization, little is known about the post-transcriptional regulation of lncRNAs and their half-lives. Although many are easily detectable by a variety of techniques, it has been assumed that lncRNAs are generally unstable, but this has not been examined genome-wide. Utilizing a custom noncoding RNA array, we determined the half-lives of ∼800 lncRNAs and ∼12,000 mRNAs in the mouse Neuro-2a cell line. We find only a minority of lncRNAs are unstable. LncRNA half-lives vary over a wide range, comparable to, although on average less than, that of mRNAs, suggestive of complex metabolism and widespread functionality. Combining half-lives with comprehensive lncRNA annotations identified hundreds of unstable (half-life < 2 h) intergenic, cis-antisense, and intronic lncRNAs, as well as lncRNAs showing extreme stability (half-life > 16 h). Analysis of lncRNA features revealed that intergenic and cis-antisense RNAs are more stable than those derived from introns, as are spliced lncRNAs compared to unspliced (single exon) transcripts. Subcellular localization of lncRNAs indicated widespread trafficking to different cellular locations, with nuclear-localized lncRNAs more likely to be unstable. Surprisingly, one of the least stable lncRNAs is the well-characterized paraspeckle RNA Neat1, suggesting Neat1 instability contributes to the dynamic nature of this subnuclear domain. We have created an online interactive resource (http://stability.matticklab.com) that allows easy navigation of lncRNA and mRNA stability profiles and provides a comprehensive annotation of ∼7200 mouse lncRNAs.
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“Although actinomycin D treatment can stabilize transcripts globally, the rank order of transcript stabilities appears relatively unchanged (Rabani et al. 2011; Schwanhausser et al. 2011), supporting the validity of our conclusions regarding lncRNA stability.”
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Research works printed but not linked: 2
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- 10.1093/bioinformatics/btr209 · doi:10.1093/bioinformatics/btr209 · Paper page
Cited by
Long non-coding RNAs: definitions, functions, challenges and recommendations
Mattick, J. S., Amaral, P. P., Carninci, P., Carpenter, S., Chang, H. Y., Chen, L.-L., Chen, R., Dean, C., Dinger, M. E., Fitzgerald, K. A., et al. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00566-8 · Cited by 2,356
Self-citationEndogenous microRNA sponges: evidence and controversy
Thomson, D. W., & Dinger, M. E. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.20 · Cited by 2,185
Self-citationLong noncoding RNAs: past, present, and future
Kung, J. T. Y., Colognori, D., & Lee, J. T. (2013) · Genetics · doi:10.1534/genetics.112.146704 · Cited by 1,874
LNCcation: lncRNA localization and function
Bridges, M. C., Daulagala, A. C., & Kourtidis, A. (2021) · Journal of Cell Biology · doi:10.1083/jcb.202009045 · Cited by 1,556
Morris, K. V., & Mattick, J. S. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3722 · Cited by 1,371
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Metadata
- Authors
- Clark, M. B., Johnston, R. L., Inostroza-Ponta, M., Fox, A. H., Fortini, E., Moscato, P., Dinger, M. E., & Mattick, J. S.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2012-03-09
- Volume
- 22
- Issue
- 5
- Pages
- 885-898
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2136550485
- Cited by
- 593
- References
- 71
- Type
- posted content
- Language
- en
- Open access
- bronze
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