mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex
Open accessAbstract
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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Analysis of a published RNA-Seq dataset showed dynamic expression changes for Rbfox family members between E17 and adult mouse cortex.
“We found that Rbfox family members undergodynamic expression change between E17 and adult mouse cortex, as evaluated from a published RNA-Seq dataset (Dillman et al., 2013).”
From HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism (2014) · cites this paper as Dillman et al., 2013
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890 · see citing works
Differential expression analysis for sequence count data
Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581 · see citing works
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108 · see citing works
Spatio-temporal transcriptome of the human brain
Kang, H. J., Kawasawa, Y. I., Cheng, F., Zhu, Y., Xu, X., Li, M., Sousa, A. M. M., Pletikos, M., Meyer, K. A., Sedmak, G., et al. (2011) · Nature · doi:10.1038/nature10523 · Cited by 2,084 · see citing works
Mouse genomic variation and its effect on phenotypes and gene regulation.
Keane, T. M., Goodstadt, L., Danecek, P., White, M. A., Wong, K., Yalcin, B., Heger, A., Agam, A., Slater, G., Goodson, M., et al. (2011) · Nature · doi:10.1038/nature10413 · Cited by 1,580 · see citing works
Functions and Regulation of RNA Editing by ADAR Deaminases
Nishikura, K. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060208-105251 · Cited by 1,303 · see citing works
Higuchi, M., Maas, S., Single, F. N., Hartner, J., Rozov, A., Burnashev, N., Feldmeyer, D., Sprengel, R., & Seeburg, P. H. (2000) · Nature · doi:10.1038/35017558 · Cited by 967 · see citing works
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
Ramsköld, D., Wang, E. T., Burge, C. B., & Sandberg, R. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000598 · Cited by 820 · see citing works
RNA processing and its regulation: global insights into biological networks
Licatalosi, D. D., & Darnell, R. B. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2673 · Cited by 760 · see citing works
Widespread A-to-I RNA Editing of Alu-Containing mRNAs in the Human Transcriptome
Athanasiadis, A., Rich, A. S., & Maas, S. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020391 · Cited by 743 · see citing works
't Hoen, P. A. C., Ariyurek, Y., Thygesen, H. H., Vreugdenhil, E., Vossen, R. H. A. M., de Menezes, R. X., Boer, J. M., van Ommen, G.-J. B., & den Dunnen, J. T. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn705 · Cited by 742 · see citing works
Functional consequences of developmentally regulated alternative splicing
Kalsotra, A., & Cooper, T. A. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3052 · Cited by 729 · see citing works
Temporal dynamics and genetic control of transcription in the human prefrontal cortex
Colantuoni, C., Lipska, B. K., Ye, T., Hyde, T. M., Tao, R., Leek, J. T., Colantuoni, E. A., Elkahloun, A. G., Herman, M. M., Weinberger, D. R., et al. (2011) · Nature · doi:10.1038/nature10524 · Cited by 685 · see citing works
Regulation of alternative splicing by RNA editing
Rueter, S. M., Dawson, T. R., & Emeson, R. B. (1999) · Nature · doi:10.1038/19992 · Cited by 637 · see citing works
Exuberance in the development of cortical networks
Innocenti, G. M., & Price, D. J. (2005) · Nature Reviews Neuroscience · doi:10.1038/nrn1790 · Cited by 512 · see citing works
Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome
Peng, Z., Cheng, Y., Tan, B. C., Kang, L., Tian, Z., Zhu, Y., Zhang, W., Liang, Y., Hu, X., Tan, X., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2122 · Cited by 497 · see citing works
The Fate of dsRNA in the Nucleus
Zhang, Z., & Carmichael, G. (2001) · Cell · doi:10.1016/s0092-8674(01)00466-4 · Cited by 468 · see citing works
Widespread RNA and DNA Sequence Differences in the Human Transcriptome
Li, M., Wang, I. X., Li, Y., Bruzel, A., Richards, A. L., Toung, J. M., & Cheung, V. G. (2011) · Science · doi:10.1126/science.1207018 · Cited by 463 · see citing works
Ullrich, B., Ushkaryov, Y. A., & Südhof, T. C. (1995) · Neuron · doi:10.1016/0896-6273(95)90306-2 · Cited by 460 · see citing works
Neuronal regulation of alternative pre-mRNA splicing
Li, Q., Lee, J.-A., & Black, D. L. (2007) · Nature Reviews Neuroscience · doi:10.1038/nrn2237 · Cited by 376 · see citing works
Wojtowicz, W. M., Flanagan, J. J., Millard, S. S., Zipursky, S. L., & Clemens, J. C. (2004) · Cell · doi:10.1016/j.cell.2004.08.021 · Cited by 332 · see citing works
Large-scale mRNA sequencing determines global regulation of RNA editing during brain developmentPreprint
Wahlstedt, H., Daniel, C., Ensterö, M., & Öhman, M. (2009) · Genome Research · doi:10.1101/gr.089409.108 · Cited by 287 · see citing works
The development of cortical connections
Price, D. J., Kennedy, H., Dehay, C., Zhou, L., Mercier, M., Jossin, Y., Goffinet, A. M., Tissir, F., Blakey, D., & Molnár, Z. (2006) · European Journal of Neuroscience · doi:10.1111/j.1460-9568.2006.04620.x · Cited by 215 · see citing works
Genome-wide gene expression profiles of the developing mouse hippocampus
Mody, M., Cao, Y., Cui, Z., Tay, K.-Y., Shyong, A., Shimizu, E., Pham, K., Schultz, P., Welsh, D., & Tsien, J. Z. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.141244998 · Cited by 205 · see citing works
Tau isoform regulation is region‐ and cell‐specific in mouse brain
McMillan, P., Korvatska, E., Poorkaj, P., Evstafjeva, Z., Robinson, L., Greenup, L., Leverenz, J., Schellenberg, G. D., & D'Souza, I. (2008) · Journal of Comparative Neurology · doi:10.1002/cne.21867 · Cited by 179 · see citing works
Comment on “Widespread RNA and DNA Sequence Differences in the Human Transcriptome”
Pickrell, J. K., Gilad, Y., & Pritchard, J. K. (2012) · Science · doi:10.1126/science.1210484 · Cited by 167 · see citing works
A-to-I RNA Editing: Effects on Proteins Key to Neural Excitability
Rosenthal, J. J. C., & SEEBURG, P. H. (2012) · Neuron · doi:10.1016/j.neuron.2012.04.010 · Cited by 166 · see citing works
RNA editing level in the mouse is determined by the genomic repeat repertoire
Neeman, Y., Levanon, E. Y., Jantsch, M. F., & Eisenberg, E. (2006) · RNA · doi:10.1261/rna.165106 · Cited by 154 · see citing works
Global regulation of alternative splicing during myogenic differentiation
Bland, C. S., Wang, E. T., Vu, A. Q., David, M. P., Castle, J. C., Johnson, J. M., Burge, C. B., & Cooper, T. A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq614 · Cited by 153 · see citing works
Blanc, V., & Davidson, N. O. (2010) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.82 · Cited by 138 · see citing works
RNA Editing by Mammalian ADARs
Hogg, M. C., Paro, S., Keegan, L. P., & O’Connell, M. A. (2011) · Advances in genetics · doi:10.1016/b978-0-12-380860-8.00003-3 · Cited by 109 · see citing works
Gu, T., Buaas, F. W., Simons, A. K., Ackert‐Bicknell, C. L., Braun, R. E., & Hibbs, M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033720 · Cited by 79 · see citing works
Pronouced instability of tandem IU base pairs in RNA
Serra, M. J. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh501 · Cited by 59 · see citing works
Tian, N., Wu, X., Zhang, Y., & Jin, Y. (2007) · RNA · doi:10.1261/rna.797108 · Cited by 47 · see citing works
Microarray analysis of the developing cortex
Semeralul, M. O., Boutros, P. C., Likhodi, O., Okey, A. B., Tol, H. H. M. V., & Wong, A. H. C. (2006) · Journal of Neurobiology · doi:10.1002/neu.20302 · Cited by 45 · see citing works
Exon expression profiling reveals stimulus-mediated exon use in neural cells
McKee, A. E., Neretti, N., Carvalho, L. E., Meyer, C. A., Fox, E. A., Brodsky, A. S., & Silver, P. A. (2007) · Genome biology · doi:10.1186/gb-2007-8-8-r159 · Cited by 40 · see citing works
Investigation of differentially expressed genes during the development of mouse cerebellum
Kagami, Y., & Furuichi, T. (2001) · Gene Expression Patterns · doi:10.1016/s1567-133x(01)00007-2 · Cited by 36 · see citing works
A novel RNA pentaloop fold involved in targeting ADAR2
Štefl, R., & Allain, F. H. ‐. (2005) · RNA · doi:10.1261/rna.7276805 · Cited by 32 · see citing works
Matsuki, T., Hori, G., & Furuichi, T. (2005) · Molecular Brain Research · doi:10.1016/j.molbrainres.2005.02.008 · Cited by 28 · see citing works
SINEs point to abundant editing in the human genome.
DeCerbo, J. N., & Carmichael, G. (2005) · Genome biology · doi:10.1186/gb-2005-6-4-216 · Cited by 28 · see citing works
Itoh, K. (2002) · Brain Research Protocols · doi:10.1016/s1385-299x(02)00177-0 · Cited by 22 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Weyn-Vanhentenryck, S. M., Mele, A., Yan, Q., Sun, S., Farny, N., Zhang, Z., Xue, C., Herre, M., Silver, P. A., Zhang, M. Q., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.02.005 · Cited by 333 · see citing works
The hallmarks of fibroblast ageing
Tigges, J., Krutmann, J., Fritsche, E., Haendeler, J., Schaal, H., Fischer, J. W., Kalfalah, F., Reinke, H., Reifenberger, G., Stühler, K., et al. (2014) · Mechanisms of Ageing and Development · doi:10.1016/j.mad.2014.03.004 · Cited by 250 · see citing works
Jaffe, A. E., Shin, J., Collado-Torres, L., Leek, J. T., Tao, R., Li, C., Gao, Y., Jia, Y., Maher, B. J., Hyde, T. M., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.3898 · Cited by 156 · see citing works
- Authors
- Dillman, A. A., Hauser, D. N., Gibbs, J. R., Nalls, M. A., McCoy, M. K., Rudenko, I. N., Galter, D., & Cookson, M. R.
- Affiliations
- National Institutes of Health (US)
- Karolinska Institutet (SE)
- Corresponding author
- Cookson, Mark R
- Venue
- Nature Neuroscience
- Published
- 2013-02-17
- Volume
- 16
- Issue
- 4
- Pages
- 499-506
- ISSN
- 1097-6256 (ISSN-L)
- 1546-1726
- PMC
- PMC3609882
- OpenAlex
- W2002669455
- Cited by
- 148
- References
- 41
- Citations by year
- 2026: 4 · 2025: 10 · 2024: 7 · 2023: 8 · 2022: 4 · 2021: 10 · 2020: 13 · 2019: 13 · 2018: 14 · 2017: 16 · 2016: 14 · 2015: 14 · 2014: 16 · 2013: 5
- FWCI
- 7.32
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Neuroscience (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Vetenskapsrådet
- Swedish Brain Power
- National Institutes of Health
- National Institute on Aging (K01AG000947, AG000947, ZIAAG000947)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- cerebral cortex, embryonic development, adult brain, gene expression, alternative splicing, RNA editing, splice variants, exon-intron boundaries, transcriptome, mice, brain development
- MeSH terms
- Age Factors, Animals, Cerebral Cortex, Female, Mice, Inbred C57BL, Pregnancy, RNA Splicing, RNA, Messenger, RNA Editing, Sequence Analysis, RNA, Gene Expression Regulation, Developmental, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review