The mouse genome: experimental examination of gene predictions and transcriptional start sites

Dike, S., Balija, V. S., Nascimento, L. U., Xuan, Z. Y., Ou, J., Zutavern, T., Palmer, L. E., Hannon, G. J., Zhang, M. Q., McCombie, W. R. (December 2004) The mouse genome: experimental examination of gene predictions and transcriptional start sites. Genome Res, 14 (12). pp. 2424-9. ISSN 1088-9051 (Print)

[thumbnail of Paper]
PDF (Paper)
Hannon et al Genome Research 2004.pdf - Published Version

Download (210kB) | Preview
DOI: 10.1101/gr.3158304


The completion of the mouse and other mammalian genome sequences will provide necessary, but not sufficient, knowledge for an understanding of much of mouse biology at the molecular level. As a requisite next step in this process, the genes in mouse and their structure must be elucidated. In particular, knowledge of the transcriptional start site of these genes will be necessary for further study of their regulatory regions. To assess the current state of mouse genome annotation to support this activity, we identified several hundred gene predictions in mouse with varying levels of supporting evidence and tested them using RACE-PCR. Modifications were made to the procedure allowing pooling of RNA samples, resulting in a scaleable procedure. The results illustrate potential errors or omissions in the current 5' end annotations in 58% of the genes detected. In testing experimentally unsupported gene predictions, we were able to identify 58 that are not usually annotated as genes but produced spliced transcripts (approximately 25% success rate). In addition, in many genes we were able to detect novel exons not predicted by any gene prediction algorithms. In 19.8% of the genes detected in this study, multiple transcript species were observed. These data show an urgent need to provide direct experimental validation of gene annotations. Moreover, these results show that direct validation using RACE-PCR can be an important component of genome-wide validation. This approach can be a useful tool in the ongoing efforts to increase the quality of gene annotations, especially transcriptional start sites, in complex genomes.

Item Type: Paper
Uncontrolled Keywords: Animals Base Sequence CpG Islands genetics DNA Primers DNA Complementary genetics Exons genetics Genes genetics Genome Mice genetics Molecular Sequence Data Open Reading Frames genetics Polymerase Chain Reaction methods Sequence Analysis DNA Transcription Initiation Site
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > CpG islands
CSHL Authors:
Communities: CSHL labs > Hannon lab
CSHL labs > McCombie lab
CSHL labs > Zhang lab
Depositing User: CSHL Librarian
Date: December 2004
Date Deposited: 09 Feb 2012 17:41
Last Modified: 06 Nov 2017 17:22
PMCID: PMC534666
Related URLs:

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving