Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

By Y. Okazaki, M. Furuno, T. Kasukawa, J. Adachi, Hidemasa Bono, S. Kondo, I. Nikaido, N. Osato, R. Saito, H. Suzuki and 127 more. Nature, 2002

1,597 citations recorded by the source corpus.

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 ‘transcriptional units’, contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense–antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fd6a0fab6f4447da5738a4f9540d7f1d811e8815

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In Molecular Biology

Citations in the corpus

Long Noncoding RNAs: Past, Present, and Future (2013, background): “Although lncRNAs are found across many taxa, and many crucial discoveries have been made in plants, fungi, and invertebrates (Gelbart and Kuroda 2009; Au et al. 2011), we largely limit our discussion to mammalian examples, with occasional reference to lncRNAs of other taxa.”
RNA Sequencing and Analysis (2015, neutral): “As a functional class, lncRNAs were first described in mice during the largescale sequencing of cDNA libraries (Okazaki et al. 2002).”
Cloning of adiponectin receptors that mediate antidiabetic metabolic effects (2003, background): “Here we report the cloning of complementary DNAs encoding adiponectin receptors 1 and 2 (AdipoR1 and AdipoR2) by expression clonin”
lincRNAs: Genomics, Evolution, and Mechanisms (2013, neutral): “Members of an initial lincRNA catalog in mouse (Okazaki et al., 2002) were poorly conserved when evaluated using mouse-rat and mouse-human genome alignments (Wang et al., 2004).”
Function of alternative splicing. (2005, neutral): “Approximately 75% of alternative splicing events occur in the translated regions of mRNAs and will affect the protein-coding region (Okazaki et al., 2002; Zavolan et al., 2003).”
Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences (2003, neutral): “indicated that there are many thousands of ncRNA transcripts in mammals [16].”
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs (2014, background): “LncRNAs were first described as a class in conjunction with early large-scale sequencing libraries of cDNA clones (29).”
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. (2007, methodology): “We used the stringent sets of putative ncRNAs from the mouse (Mus musculus) FANTOM2 (4280 transcripts) (Okazaki et al. 2002; Numata et al. 2003; Pang et al. 2005) and FANTOM3 projects (2886 transcripts) (Carninci et al. 2005; ftp://fantom.gsc.riken.jp/ FANTOM3/noncoding/README.txt).”
Identification of conserved regulatory elements by comparative genome analysis (2003, methodology): “In addition 50,821 mouse cDNAs from the RIKEN project [44] were mapped to the mouse genome assembly using the client/server version of BLAT [45] with default settings.”
Is prokaryotic complexity limited by accelerated growth inregulatory overhead? (2003, background): “It is evident that prokaryotes have never reached the size and complexity of multicellular eukaryotes, whose genomes contain 14000-50000 individually regulated protein-coding genes [23-26], that are subject to alternative splicing to produce many more isoforms, in addition to large numbers of noncod”
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004, neutral): “Analysis of the H-Inv cDNA dataset revealed that 6.5% of the transcripts are possibly non-protein-coding, although the number is much smaller than that estimated in mice (Okazaki et al. 2002).”