Making (anti)sense of non-coding sequence conservation
Open accessAbstract
A substantial fraction of vertebrate mRNAs contain long conserved blocks in their untranslated regions as well as long blocks without silent changes in their protein coding regions. These conserved blocks are largely comprised of unique sequence within the genome, leaving us with an important puzzle regarding their function. A large body of experimental data shows that these regions are associated with regulation of mRNA stability. Combining this information with the rapidly accumulating data on endogenous antisense transcripts, we propose that the conserved sequences form long perfect duplexes with antisense transcripts. The formation of such duplexes may be essential for recognition by post-transcriptional regulatory systems. The conservation may then be explained by selection against the dominant negative effect of allelic divergence.
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Earlier reports have described widespread conservation in 3' UTRs, and some have noted an enrichment for genes for DNA-binding proteins.
“These findings are consistent with earlier reports of widespread conservation in 3Ј UTRs (Duret et al. 1993;Lipman 1997), some of which have noted an enrichment for genes for DNA-binding proteins (Duret et al. 1993).”
From Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005) · cites this paper as Lipman 1997
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Tsai, K.-C., Cansino, V. V., Kohn, D. T., Neve, R. L., & Perrone-Bizzozero, N. I. (1997) · The Journal of Neuroscience · doi:10.1523/jneurosci.17-06-01950.1997 · Cited by 66 · see citing works
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- 5 Li, W. H., Luo, C. and Wu, C. (1985) In MacIntyre, R. J. (ed.) Molecular Evolutionary Genetics . Plenum Press, New York, pp. 1-94.
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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 4,408 · see citing works
Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. (2004) · Cell · doi:10.1016/s0092-8674(04)00127-8 · Cited by 1,095 · see citing works
How do synonymous mutations affect fitness?
Parmley, J. L., & Hurst, L. D. (2007) · BioEssays · doi:10.1002/bies.20592 · Cited by 142 · see citing works
- Authors
- Lipman, D. J.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Lipman, D. J.
- ORCID
- Lipman, D. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1997-09-01
- Volume
- 25
- Issue
- 18
- Pages
- 3580-3583
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC146938
- OpenAlex
- W2170119276
- Cited by
- 85
- References
- 1
- Citations by year
- 2024: 1 · 2016: 1 · 2014: 1 · 2013: 3 · 2012: 1
- FWCI
- 0.38
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- untranslated regions, antisense transcripts, mRNA stability, post-transcriptional regulation, duplex formation, allelic divergence, dominant negative effect, sequence conservation
- MeSH terms
- Animals, Humans, RNA, Messenger, Transcription, Genetic, Oligonucleotides, Antisense, Conserved Sequence
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