A genome-wide in situhybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain
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Background: In eukaryotic cells, RNA-binding proteins (RBPs) contribute to gene expression by regulating the form, abundance, and stability of both coding and non-coding RNA. In the vertebrate brain, RBPs account for many distinctive features of RNA processing such as activity-dependent transcript localization and localized protein synthesis. Several RBPs with activities that are important for the proper function of adult brain have been identified, but how many RBPs exist and where these genes are expressed in the developing brain is uncharacterized. Results: Here we describe a comprehensive catalogue of the unique RBPs encoded in the mouse genome and provide an online database of RBP expression in developing brain. We identified 380 putative RBPs in the mouse genome. Using in situ hybridization, we visualized the expression of 323 of these RBP genes in the brains of developing mice at embryonic day 13.5, when critical fate choice decisions are made and at P0, when major structural components of the adult brain are apparent. We demonstrate i) that 16 of the 323 RBPs examined show neural-specific expression at the stages we examined, and ii) that a far larger subset (221) shows regionally restricted expression in the brain. Of the regionally restricted RBPs, we describe one group that is preferentially expressed in the E13.5 ventricular areas and a second group that shows spatially restricted expression in post-mitotic regions of the embryonic brain. Additionally, we find a subset of RBPs that share the same complex pattern of expression, in proliferating regions of the embryonic and postnatal NS and peripheral tissues. Conclusion: Our data show that, in contrast to their proposed ubiquitous involvement in gene regulation, most RBPs are not uniformly expressed. Here we demonstrate the region-specific expression of RBPs in proliferating vs. post-mitotic brain regions as well as cell-type-specific RBP expression. We identify uncharacterized RBPs that exhibit neural-specific expression as well as novel RBPs that show expression in non-neural tissues. The data presented here and in an online database provide a visual filter for the functional analysis of individual RBPs.
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All three Rbfox genes are broadly expressed in the brain, with individual neuronal cell types expressing different combinations at different developmental times.
“All three Rbfox genes are broadly expressed in the brain, with individual neuronal cell types expressing different combinations at different developmental times51–55.”
From The neurogenetics of alternative splicing (2016) · cites this paper as [51]
ELAVL1 is widely expressed in non-neuronal tissues.
“ELAVL1 (also known as HuR or HuA) is widely expressed in non-neuronal tissues”
From The neurogenetics of alternative splicing (2016) · cites this paper as [51]
ELAVL2, ELAVL3 and ELAVL4 show neuronal-specific expression.
“whereas ELAVL2 (also known as HuB), ELAVL3 (also known as HuC) and ELAVL4 (also known as HuD) show neuronal-specific expression”
From The neurogenetics of alternative splicing (2016) · cites this paper as [51]
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- Authors
- McKee, A. E., Minet, E., Stern, C., Riahi, S., Stiles, C. D., & Silver, P. A.
- Affiliations
- Harvard University (US)
- University of Namur (BE)
- Dana-Farber Cancer Institute (US)
- Corresponding author
- Silver, Pamela A
- Venue
- BMC Developmental Biology
- Published
- 2005-07-20
- Volume
- 5
- Issue
- 1
- Pages
- 14-14
- ISSN
- 1471-213X (ISSN-L)
- PMC
- PMC1199591
- OpenAlex
- W2140526178
- Cited by
- 166
- References
- 50
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 8 · 2023: 4 · 2022: 3 · 2021: 7 · 2020: 4 · 2019: 9 · 2018: 8 · 2017: 7 · 2016: 7 · 2015: 9 · 2014: 12 · 2013: 12 · 2012: 14
- FWCI
- 2.90
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- BMC Developmental Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DIAL (Catholic University of Leuven) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Repository of the University of Namur (submittedVersion)
- Funders
- American Cancer Society
- Dana Foundation
- Belgian American Educational Foundation
- Fonds National de la Recherche Luxembourg
- Fonds De La Recherche Scientifique - FNRS
- National Cancer Institute (T32-CA 09361, T32CA009361)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
- Keywords
- RNA-binding proteins, mouse brain development, embryonic brain, postnatal brain, regional gene expression, neural stem cells, cell type-specific gene expression, transcript localization
- MeSH terms
- Animals, Brain, Embryo, Mammalian, Mice, Inbred C57BL, Tissue Distribution, RNA-Binding Proteins, Genome, In Situ Hybridization, Gene Expression Regulation, Developmental, Databases, Nucleic Acid, Cell Proliferation, Mice
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