DOI: 10.1101/gr.6036807. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs

Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs

10.1101/gr.6036807

Crossref journal-article

Cold Spring Harbor Laboratory

Genome Research (246)

Abstract

Long transcripts that do not encode protein have only rarely been the subject of experimental scrutiny. Presumably, this is owing to the current lack of evidence of their functionality, thereby leaving an impression that, instead, they represent “transcriptional noise.” Here, we describe an analysis of 3122 long and full-length, noncoding RNAs (“macroRNAs”) from the mouse, and compare their sequences and their promoters with orthologous sequence from human and from rat. We considered three independent signatures of purifying selection related to substitutions, sequence insertions and deletions, and splicing. We find that the evolution of the set of noncoding RNAs is not consistent with neutralist explanations. Rather, our results indicate that purifying selection has acted on the macroRNAs’ promoters, primary sequence, and consensus splice site motifs. Promoters have experienced the greatest elimination of nucleotide substitutions, insertions, and deletions. The proportion of conserved sequence (4.1%–5.5%) in these macroRNAs is comparable to the density of exons within protein-coding transcripts (5.2%). These macroRNAs, taken together, thus possess the imprint of purifying selection, thereby indicating their functionality. Our findings should now provide an incentive for the experimental investigation of these macroRNAs’ functions.

Bibliography

Ponjavic, J., Ponting, C. P., & Lunter, G. (2007). Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Research, 17(5), 556â565.

Authors 3

Jasmina Ponjavic (first)
Chris P. Ponting (additional)
Gerton Lunter (additional)

References 58 Referenced 609

Dates

Type	When
Created	18 years, 5 months ago (March 26, 2007, 9:04 p.m.)
Deposited	3 years, 9 months ago (Nov. 18, 2021, 2:48 p.m.)
Indexed	14 hours, 58 minutes ago (Sept. 3, 2025, 6:20 a.m.)
Issued	18 years, 5 months ago (March 26, 2007)
Published	18 years, 5 months ago (March 26, 2007)
Published Online	18 years, 5 months ago (March 26, 2007)
Published Print	18 years, 4 months ago (May 1, 2007)

Funders 0

None

BibTeX

@article{Ponjavic_2007, title={Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs}, volume={17}, ISSN={1088-9051}, url={http://dx.doi.org/10.1101/gr.6036807}, DOI={10.1101/gr.6036807}, number={5}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Ponjavic, Jasmina and Ponting, Chris P. and Lunter, Gerton}, year={2007}, month=mar, pages={556–565} }

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  "abstract": "<jats:p>Long transcripts that do not encode protein have only rarely been the subject of experimental scrutiny. Presumably, this is owing to the current lack of evidence of their functionality, thereby leaving an impression that, instead, they represent \u201ctranscriptional noise.\u201d Here, we describe an analysis of 3122 long and full-length, noncoding RNAs (\u201cmacroRNAs\u201d) from the mouse, and compare their sequences and their promoters with orthologous sequence from human and from rat. We considered three independent signatures of purifying selection related to substitutions, sequence insertions and deletions, and splicing. We find that the evolution of the set of noncoding RNAs is not consistent with neutralist explanations. Rather, our results indicate that purifying selection has acted on the macroRNAs\u2019 promoters, primary sequence, and consensus splice site motifs. Promoters have experienced the greatest elimination of nucleotide substitutions, insertions, and deletions. The proportion of conserved sequence (4.1%\u20135.5%) in these macroRNAs is comparable to the density of exons within protein-coding transcripts (5.2%). These macroRNAs, taken together, thus possess the imprint of purifying selection, thereby indicating their functionality. Our findings should now provide an incentive for the experimental investigation of these macroRNAs\u2019 functions.</jats:p>",
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