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Improving mRNA 5′ coding sequence determination in the mouse genome

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Abstract

The incomplete determination of the mRNA 5′ end sequence may lead to the incorrect assignment of the first AUG codon and to errors in the prediction of the encoded protein product. Due to the significance of the mouse as a model organism in biomedical research, we performed a systematic identification of coding regions at the 5′ end of all known mouse mRNAs, using an automated expressed sequence tag (EST)-based approach which we have previously described. By parsing almost 4 million BLAT alignments we found 351 mouse loci, out of 20,221 analyzed, in which an extension of the mRNA 5′ coding region was identified. Proof-of-concept confirmation was obtained by in vitro cloning and sequencing for Apc2 and Mknk2 cDNAs. We also generated a list of 16,330 mouse mRNAs where the presence of an in-frame stop codon upstream of the known start codon indicates completeness of the coding sequence at 5′ end in the current form. Systematic searches in the main mouse genome databases and genome browsers showed that 82 % of our results are original and have not been identified by their annotation pipelines. Moreover, the same information is not easily derivable from RNA-Seq data, due to short sequence length and laboriousness in building full-length transcript structures. In conclusion, our results improve the determination of full-length 5′ coding sequences and might be useful in order to reduce errors when studying mouse gene structure and function in biomedical research.

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Acknowledgments

This work was funded by “RFO” Grants from Alma Mater Studiorum—University of Bologna to P.S. and L.V. M.C.’s fellowship is supported by a generous donation made by Illumia, Bologna, Italy. The 5′_ORF_Extender software was executed on the Apple Mac Pro “Multiprocessor Server” available at the Center for Research in Molecular Genetics “Fondazione CARISBO”, Bologna, and funded by “Fondazione CARISBO”. We are grateful to Gabriella Mattei and Michela Bonaguro for their excellent technical assistance with cDNA sequencing. We are grateful to Danielle Mitzman for her expert revision of the manuscript.

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Authors and Affiliations

  1. Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy

    Allison Piovesan, Maria Caracausi, Maria Chiara Pelleri, Lorenza Vitale, Silvia Martini, Chiara Bassani, Annalisa Gurioli & Pierluigi Strippoli

  2. Department for Life Quality Studies, University of Bologna, C.so d’Augusto 237, 47921, Rimini, RN, Italy

    Raffaella Casadei

  3. Dipartimento di Biotecnologie Mediche e Medicina Traslazionale (BioMeTra), Università degli Studi di Milano, Via Viotti 3/5, 20133, Milan, Italy

    Giulia Soldà

Authors
  1. Allison Piovesan
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  2. Maria Caracausi
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  3. Maria Chiara Pelleri
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  4. Lorenza Vitale
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  5. Silvia Martini
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  6. Chiara Bassani
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  7. Annalisa Gurioli
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  8. Raffaella Casadei
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  9. Giulia Soldà
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  10. Pierluigi Strippoli
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Corresponding author

Correspondence to Pierluigi Strippoli.

Additional information

Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers KF481611 and KF612275.

Allison Piovesan and Maria Caracausi contributed equally to the work.

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Piovesan, A., Caracausi, M., Pelleri, M.C. et al. Improving mRNA 5′ coding sequence determination in the mouse genome. Mamm Genome 25, 149–159 (2014). https://doi.org/10.1007/s00335-013-9498-3

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  • DOI: https://doi.org/10.1007/s00335-013-9498-3

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