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mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex

Nature Neuroscience volume 16, pages 499–506 (2013)Cite this article

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Abstract

The complexity of the adult brain is a result of both developmental processes and experience-dependent circuit formation. One way to look at the differences between embryonic and adult brain is to examine gene expression. Previous studies have used microarrays to address this in a global manner. However, the transcriptome is more complex than gene expression levels alone, as alternative splicing and RNA editing generate a diverse set of mature transcripts. Here we report a high-resolution transcriptome data set of mouse cerebral cortex at embryonic and adult stages using RNA sequencing (RNA-Seq). We found many differences in gene expression, splicing and RNA editing between embryonic and adult cerebral cortex. Each data set was validated technically and biologically, and in each case we found our RNA-Seq observations to have predictive validity. We provide this data set and analysis as a resource for understanding gene expression in the embryonic and adult cerebral cortex.

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Figure 1: Gene expression.
Figure 2: Alternative exon utilization.
Figure 3: A-to-I RNA editing.

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Gene Expression Omnibus

Referenced accessions

NCBI Reference Sequence

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Acknowledgements

The authors would like to thank E. Lindquist for excellent technical assistance. We would also like to thank M. Do for assistance with cloning experiments. This research was supported in part by the Intramural Research Program of the US National Institutes of Health, National Institute on Aging (project AG000947) and by the Swedish Research Council and Swedish Brain Power.

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Authors and Affiliations

  1. Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA

    Allissa A Dillman, David N Hauser, Melissa K McCoy, Iakov N Rudenko & Mark R Cookson

  2. Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden

    Allissa A Dillman & Dagmar Galter

  3. Department of Neuroscience, Brown University/National Institutes of Health Graduate Partnership Program, Brown University, Providence, Rhode Island, USA

    David N Hauser

  4. Computational Biology Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA

    J Raphael Gibbs

  5. Reta Lila Weston Laboratories and Department of Molecular Neuroscience, University College London Institute of Neurology, London, UK

    J Raphael Gibbs

  6. Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA

    Michael A Nalls

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  1. Allissa A Dillman
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Contributions

A.A.D. performed the RNA-Seq experiments and analyzed the data. J.R.G. and M.A.N. provided additional analytical approaches. D.N.H., M.K.M. and I.N.R. performed mouse dissections and contributed additional validation results. M.R.C. and D.G. supervised the project. M.R.C. and A.A.D. wrote the paper with contributions from all authors.

Corresponding author

Correspondence to Mark R Cookson.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–13, Supplementary Tables 1 and 5–7 (PDF 2934 kb)

Supplementary Table 2

Gene expression in the embryonic and adult mouse cerebral cortex. (CSV format) (XLS 711 kb)

Supplementary Table 3

Alternate exon usage in the embryonic and adult mouse cerebral cortex. (CSV format) (XLS 130 kb)

Supplementary Table 4

Adenosine-to-inosine RNA editing in the embryonic and adult mouse cerebral cortex. (CSV format) (XLS 44 kb)

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Dillman, A., Hauser, D., Gibbs, J. et al. mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex. Nat Neurosci 16, 499–506 (2013). https://doi.org/10.1038/nn.3332

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