DOI: 10.1073/pnas.0706729105. Specific expression of long noncoding RNAs in the mouse brain

Specific expression of long noncoding RNAs in the mouse brain

10.1073/pnas.0706729105

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

A major proportion of the mammalian transcriptome comprises long RNAs that have little or no protein-coding capacity (ncRNAs). Only a handful of such transcripts have been examined in detail, and it is unknown whether this class of transcript is generally functional or merely artifact. Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Examination of their genomic context revealed that the ncRNAs were expressed from diverse places including intergenic, intronic, and imprinted loci and that many overlap with, or are transcribed antisense to, protein-coding genes of neurological importance. Comparisons between the expression profiles of ncRNAs and their associated protein-coding genes revealed complex relationships that, in combination with the specific expression profiles exhibited at both regional and subcellular levels, are inconsistent with the notion that they are transcriptional noise or artifacts of chromatin remodeling. Our results show that the majority of ncRNAs are expressed in the brain and provide strong evidence that the majority of processed transcripts with no protein-coding capacity function intrinsically as RNAs.

Bibliography

Mercer, T. R., Dinger, M. E., Sunkin, S. M., Mehler, M. F., & Mattick, J. S. (2008). Specific expression of long noncoding RNAs in the mouse brain. Proceedings of the National Academy of Sciences, 105(2), 716â721.

Authors 5

Tim R. Mercer (first)
Marcel E. Dinger (additional)
Susan M. Sunkin (additional)
Mark F. Mehler (additional)
John S. Mattick (additional)

References 62 Referenced 974

Dates

Type	When
Created	17 years, 7 months ago (Jan. 9, 2008, 9:05 p.m.)
Deposited	3 years, 4 months ago (April 12, 2022, 4:09 p.m.)
Indexed	2 hours, 39 minutes ago (Sept. 4, 2025, 9:14 a.m.)
Issued	17 years, 7 months ago (Jan. 15, 2008)
Published	17 years, 7 months ago (Jan. 15, 2008)
Published Online	17 years, 7 months ago (Jan. 15, 2008)
Published Print	17 years, 7 months ago (Jan. 15, 2008)

Funders 0

None

BibTeX

@article{Mercer_2008, title={Specific expression of long noncoding RNAs in the mouse brain}, volume={105}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.0706729105}, DOI={10.1073/pnas.0706729105}, number={2}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Mercer, Tim R. and Dinger, Marcel E. and Sunkin, Susan M. and Mehler, Mark F. and Mattick, John S.}, year={2008}, month=jan, pages={716–721} }

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