Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

Ravasi, T., Suzuki, H., Pang, K. C., Katayama, S., Furuno, M., Okunishi, R., Fukuda, S., Ru, K., Frith, M., Gongora, M., Grimmond, S., Hume, D. A., Hayashizaki, Y. and Mattick, J. S. (2006) Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Research, 16 1: 11-19. doi:10.1101/gr.4200206

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Author Ravasi, T.
Suzuki, H.
Pang, K. C.
Katayama, S.
Furuno, M.
Okunishi, R.
Fukuda, S.
Ru, K.
Frith, M.
Gongora, M.
Grimmond, S.
Hume, D. A.
Hayashizaki, Y.
Mattick, J. S.
Title Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
Publication date 2006-01
Year available 2005
Sub-type Article (original research)
DOI 10.1101/gr.4200206
Open Access Status File (Publisher version)
Volume 16
Issue 1
Start page 11
End page 19
Total pages 9
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Lab Press
Collection year 2006
Language eng
Abstract Recent large-scale analyses of mainly full-length cDNA libraries generated from a variety of mouse tissues indicated that almost half of all representative cloned sequences did flat contain ail apparent protein-coding sequence, and were putatively derived from non-protein-coding RNA (ncRNA) genes. However, many of these clones were singletons and the majority were unspliced, raising the possibility that they may be derived from genomic DNA or unprocessed pre-rnRNA contamination during library construction, or alternatively represent nonspecific transcriptional noise. Here we Show, using reverse transcriptase-dependent PCR, microarray, and Northern blot analyses, that many of these clones were derived from genuine transcripts Of unknown function whose expression appears to be regulated. The ncRNA transcripts have larger exons and fewer introns than protein-coding transcripts. Analysis of the genomic landscape around these sequences indicates that some cDNA clones were produced not from terminal poly(A) tracts but internal priming sites within longer transcripts, only a minority of which is encompassed by known genes. A significant proportion of these transcripts exhibit tissue-specific expression patterns, as well as dynamic changes in their expression in macrophages following lipopolysaccharide Stimulation. Taken together, the data provide strong support for the conclusion that ncRNAs are an important, regulated component of the mammalian transcriptome.
Keyword Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Genetics & Heredity
Drosophila Bithorax Complex
Intergenic Transcription
Dna Methylation
Imprinted Genes
Candidate Gene
Tiling Arrays
Fission Yeast
Q-Index Code C1
Institutional Status UQ

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Created: Wed, 15 Aug 2007, 08:44:33 EST