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 not contain an 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-mRNA 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.[Supplemental material is available online at www.genome.org. The microarray data from this study have been submitted to the Gene Expression Omnibus under accession nos. GSD275 and GSE3098.] In recent years there have been increasing reports of functional non-protein-coding RNAs (ncRNAs) that are involved or implicated in developmental, tissue-specific, and disease processes, including X-chromosome dosage compensation, germ cell development and embryogenesis, neural and immune cell development, kidney and testis development, B-cell neoplasia, lung cancer, prostate cancer, cartilage-hair hypoplasia, spinocerebellar ataxia type 8, DiGeorge syndrome, autism, and schizophrenia (see Pang et al. 2005). Many putative ncRNAs are alternatively spliced and/or polyadenylated (Sutherland et al. 1996;Tam et al. 1997;Bussemakers et al. 1999;Raho et al. 2000;Charlier et al. 2001;Wolf et al. 2001). Smaller ncRNAs, termed microRNAs, have also been shown to be involved in developmental processes in both plants and animals, as well as implicated in disease (Carrington and Ambros 2003;Mattick and Makunin 2005). Recent evidence suggests that these microRNAs are derived from the introns of capped and polyadenylated protein-coding transcripts as well as the exons and introns of non-protein-coding transcripts, many of which are derived from "intergenic" regions (Cai et al. 2004;Rodriguez et al. 2004;Seitz et al. 2004;Mattick and Makunin 2005;Ying and Lin 2005). In addition, many complex genetic phenomena, including cosuppression, imprinting, methylation, and gene silencing (see Mattick...

We established a medium-scale real-time RT-PCR system focusing on transcription factors and applied it to their expression profiles in the adult mouse 11 brain regions (http:// genome.gsc.riken.jp/qRT-PCR/). Almost 90% of the examined genes showed significant expression in at least one region. We successfully extracted 179 region-specific genes by clustering analysis. Interestingly, the transcription factors involved in the development of the pituitary were still expressed in the adult pituitary, suggesting that they also play important roles in maintenance of the pituitary. These results provide unique molecular markers that may account for the molecular basis of the unique functions of specific brain regions.

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