Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
- PMID: 20436462
- PMCID: PMC2868100
- DOI: 10.1038/nbt.1633
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
Erratum in
- Nat Biotechnol. 2010 Jul;28(7):756
Abstract
Massively parallel cDNA sequencing (RNA-Seq) provides an unbiased way to study a transcriptome, including both coding and noncoding genes. Until now, most RNA-Seq studies have depended crucially on existing annotations and thus focused on expression levels and variation in known transcripts. Here, we present Scripture, a method to reconstruct the transcriptome of a mammalian cell using only RNA-Seq reads and the genome sequence. We applied it to mouse embryonic stem cells, neuronal precursor cells and lung fibroblasts to accurately reconstruct the full-length gene structures for most known expressed genes. We identified substantial variation in protein coding genes, including thousands of novel 5' start sites, 3' ends and internal coding exons. We then determined the gene structures of more than a thousand large intergenic noncoding RNA (lincRNA) and antisense loci. Our results open the way to direct experimental manipulation of thousands of noncoding RNAs and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes.
Figures
Comment in
-
Advancing RNA-Seq analysis.Nat Biotechnol. 2010 May;28(5):421-3. doi: 10.1038/nbt0510-421. Nat Biotechnol. 2010. PMID: 20458303 No abstract available.
Similar articles
-
Systematic identification of long intergenic non-coding RNAs expressed in bovine oocytes.Reprod Biol Endocrinol. 2020 Feb 21;18(1):13. doi: 10.1186/s12958-020-00573-4. Reprod Biol Endocrinol. 2020. PMID: 32085734 Free PMC article.
-
Identification of transcribed protein coding sequence remnants within lincRNAs.Nucleic Acids Res. 2018 Sep 28;46(17):8720-8729. doi: 10.1093/nar/gky608. Nucleic Acids Res. 2018. PMID: 29986053 Free PMC article.
-
Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression.BMC Genomics. 2017 May 2;18(1):340. doi: 10.1186/s12864-017-3720-8. BMC Genomics. 2017. PMID: 28464849 Free PMC article.
-
Characterizing and annotating the genome using RNA-seq data.Sci China Life Sci. 2017 Feb;60(2):116-125. doi: 10.1007/s11427-015-0349-4. Epub 2016 Jun 13. Sci China Life Sci. 2017. PMID: 27294835 Review.
-
RNA-Seq: a revolutionary tool for transcriptomics.Nat Rev Genet. 2009 Jan;10(1):57-63. doi: 10.1038/nrg2484. Nat Rev Genet. 2009. PMID: 19015660 Free PMC article. Review.
Cited by
-
RNA-Seq Analysis Unraveling Novel Genes and Pathways Influencing Corneal Wound Healing.Invest Ophthalmol Vis Sci. 2024 Sep 3;65(11):13. doi: 10.1167/iovs.65.11.13. Invest Ophthalmol Vis Sci. 2024. PMID: 39240550 Free PMC article.
-
RNaseH-based ribodepletion of total planarian RNA improves detection of longer and non-polyadenylated transcripts.bioRxiv [Preprint]. 2024 Jul 21:2024.07.20.604429. doi: 10.1101/2024.07.20.604429. bioRxiv. 2024. PMID: 39071286 Free PMC article. Preprint.
-
Potential Intersections between lncRNA, Vascular Cognitive Impairment, and Immunization Strategies: Insights and Future Directions.Vaccines (Basel). 2024 Feb 28;12(3):251. doi: 10.3390/vaccines12030251. Vaccines (Basel). 2024. PMID: 38543885 Free PMC article. Review.
-
The role of non-protein-coding RNAs in ischemic acute kidney injury.Front Immunol. 2024 Feb 8;15:1230742. doi: 10.3389/fimmu.2024.1230742. eCollection 2024. Front Immunol. 2024. PMID: 38390339 Free PMC article. Review.
-
Interaction between lncRNAs and RNA-binding proteins (RBPs) influences DNA damage response in cancer chemoresistance.Mol Biol Rep. 2024 Feb 17;51(1):308. doi: 10.1007/s11033-024-09288-w. Mol Biol Rep. 2024. PMID: 38366290 Review.
References
-
- Carninci P, et al. The transcriptional landscape of the mammalian genome. Science. 2005;309:1559–1563. - PubMed
-
- Kapranov P, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (New York, NY) 2007;316:1484–1488. 1138341 [pii] 10.1126/science.1138341. - PubMed
-
- Bertone P, et al. Global identification of human transcribed sequences with genome tiling arrays. Science (New York, NY) 2004;306:2242–2246. 1103388 [pii] 10.1126/science.1103388. - PubMed
Publication types
MeSH terms
Substances
Associated data
- Actions
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources