A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain

Abstract

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.

Figure 1

RBP expression in proliferative zones of the E13.5 mouse forebrain. In situ hybridization patterns for four RBPs on sections through the forebrain of E13.5 mice. Labels indicate Locuslink gene names. All images show the same magnification.

Figure 2

RBP expression in post-mitotic areas of the E13.5 mouse forebrain. In situ hybridization patterns for four RBPs on sections through the forebrain of E13.5 mice. Labels indicate Locuslink gene names. bg, basal ganglia; hy, hypothalamus; nc, neocortex. All images show the same magnification.

Figure 3

Diversity of RBP expression in major cellular subtypes of the P0 retina. In situ hybridization for four representative RBPs that exhibit laminar-specific expression in the P0 mouse retina. Labels indicate Locuslink gene names. A, B) A2bp1, C, D) Pcbp3, E, F) Safb, G, H) Rbm15. Panels A, C, E, and G show the same magnification. Panels B, D, F, and H show the same magnification. gcl, granule cell layer; inl, inner nuclear layer, onbl; outer neuroblastic layer.

Figure 4

Representative examples of RBP synexpression in E13.5 and P0 mouse tissues. snRNP E and Son are transcribed in the perventricular areas of the E13.5 brain (A, E), in the P0 subventricular area of the lateral ventricle (B, F), in the external granule layer of the P0 cerebellum (C, G), as well as in postnatal developing teeth (D, H).

Figure 5

In situ hybridization profiling uncovers the non-neural, restricted expression of novel RBPs. Data from ISH performed on (A, C) coronal E13.5 and on (B, D, E) E15 sagittal sections are presented for RRM-encoding RBPS. A, B) The Riken gene 2210008M09 is transcribed in epithelia covering the facial skeleton. C-E) BC013481 is detected in the choroid plexus, in the intestinal lining, and in the lining of the placenta. Panels C-E show the same magnification.