Specific expression of long noncoding RNAs in the mouse brain
Open accessAbstract
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.
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SOX2-OT is a heavily spliced, evolutionarily conserved lncRNA with predominant brain expression and is a hub of these oligodendrocyte modules.
“SOX2-OT is a heavily spliced, evolutionarily-conserved lncRNA exhibiting predominant brain expression and a hub of these oligodendrocyte modules, without previous mechanistic links to myelination (75, 76).”
From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [76]
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- Authors
- Mercer, T. R., Dinger, M. E., Sunkin, S. M., Mehler, M. F., & Mattick, J. S.
- Affiliations
- Australian Research Council (AU)
- Allen Institute for Brain Science (US)
- Albert Einstein College of Medicine (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2008-01-15
- Volume
- 105
- Issue
- 2
- Pages
- 716-721
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC2206602
- OpenAlex
- W2121828161
- Cited by
- 1,103
- References
- 64
- Citations by year
- 2026: 6 · 2025: 26 · 2024: 35 · 2023: 29 · 2022: 42 · 2021: 70 · 2020: 71 · 2019: 64 · 2018: 81 · 2017: 84 · 2016: 84 · 2015: 97 · 2014: 79 · 2013: 101 · 2012: 67
- FWCI
- 18.79
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- RIKEN
- National Institute of Neurological Disorders and Stroke (R01NS038902)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- long non-coding RNA, mouse brain, brain regional expression, cell types, antisense transcription, imprinted loci, intergenic transcripts, Allen Brain Atlas, transcriptome
- MeSH terms
- Animals, Brain, Gene Expression Regulation, Humans, Introns, Nucleic Acid Conformation, Transcription, Genetic, Genome, RNA, Complementary, Genomic Imprinting, Gene Expression Profiling, RNA, Untranslated, Genomics, Mice, Rats
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