Specific expression of long noncoding RNAs in the mouse brain.

@article{citeulike:2229597, 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.}, address = {Australian Research Council (ARC) Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD 4072, Australia;}, author = {Mercer, Tim R R. and Dinger, Marcel E E. and Sunkin, Susan M M. and Mehler, Mark F F. and Mattick, John S S. }, citeulike-article-id = {2229597}, doi = {10.1073/pnas.0706729105}, issn = {1091-6490}, journal = {Proc Natl Acad Sci U S A}, keywords = {bioinformatics, brain, expression, mice, ncrna, rna}, month = {January}, posted-at = {2008-01-17 02:01:31}, priority = {2}, title = {Specific expression of long noncoding RNAs in the mouse brain.}, url = {http://dx.doi.org/10.1073/pnas.0706729105}, year = {2008} }

TY - JOUR ID - citeulike:2229597 L3 - citeulike-article-id:2229597 TI - Specific expression of long noncoding RNAs in the mouse brain. JF - Proc Natl Acad Sci U S A AD - Australian Research Council (ARC) Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD 4072, Australia; SN - 1091-6490 N2 - 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. KW - bioinformatics KW - brain KW - expression KW - mice KW - ncrna KW - rna AU - Mercer, Tim R AU - Dinger, Marcel E AU - Sunkin, Susan M AU - Mehler, Mark F AU - Mattick, John S PY - 2008/01/09/ UR - http://dx.doi.org/10.1073/pnas.0706729105 ER -