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BIOLOGICAL SCIENCES / NEUROSCIENCE
Specific expression of long noncoding RNAs in the mouse brain
*Australian Research Council (ARC) Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD 4072, Australia; Allen Institute for Brain Science, Seattle, WA 98103; and Institute for Brain Disorders and Neural Regeneration, Departments of Neurology, Neuroscience and Psychiatry, and Behavioral Sciences, Einstein Cancer Center and Rose F. Kennedy Center for Research in Mental Retardation and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, New York, NY 10461
Edited by Huda Y. Zoghbi, Baylor College of Medicine, Houston, TX, and approved November 21, 2007 (received for review July 17, 2007)
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.
genomics | neuroscience | transcriptomics | imprinting | subcellular
Author contributions: T.R.M. and M.E.D. contributed equally to this work; T.R.M. and M.E.D. designed research; T.R.M. and M.E.D. performed research; M.E.D. and S.M.S. contributed new reagents/analytic tools; T.R.M., M.E.D., S.M.S., and M.F.M. analyzed data; and T.R.M., M.E.D., and J.S.M. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
This article contains supporting information online at www.pnas.org/cgi/content/full/0706729105/DC1.
To whom correspondence should be addressed. E-mail: j.mattick{at}imb.uq.edu.au
© 2008 by The National Academy of Sciences of the USA
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