Research article
A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain
- † Equal contributors
1 Department of Systems Biology, Harvard Medical School, Boston, MA 02115 USA
2 Department of Cancer Biology, The Dana-Farber Cancer Institute, Boston, MA 02115 USA
3 URBC-FUNDP, 61 rue de Bruxelles, 5000 Namur, Belgium
4 Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115 USA
BMC Developmental Biology 2005, 5:14 doi:10.1186/1471-213X-5-14
Published: 20 July 2005Additional files
Additional File 1:
RNA-binding proteins identified in silico and profiled by in situ hybridization. List of annotated RNA-binding domains and the number of family members that were identified in silico and analyzed by in situ hybridization.
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Additional File 2:
List of 380 genes identified as putative RBPs in the mouse genome and analyzed in this study. Columns indicate LocusID, gene name, type of RBD, primer sequences used to isolate the target cDNA, the size of the cDNA fragment, the presence call by PCR from E13.5 and P0 brain cDNA, cloning status ('c' indicates cloned, 'u' indicates uncloned, 'small' indicates that the target gene had less than 400 bp of unique sequence, 'na' indicates that cloning was not attempted), the RNA polymerase used to generate the anti-sense riboprobe, the tissue from which the cDNA was isolated (if not from E13.5 or P0 mouse brain), and whether the gene was analyzed by in situ hybridization ('x' indicates yes).
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Additional File 3:
Complete list of gene expression patterns for all in situ hybridizations performed. Of the 323 RBPs examined, 221 showed restricted expression patterns in the brain. The remaining genes either show restricted expression in non-neural tissues, ubiquitous expression that is difficult to distinguish from background, or no expression. Caution is needed in interpreting the results. First, non-expression could be due to the sensitivity limit of non-radioactive in situ hybridization. Second, the background level of individual probes may differ. Third, some probes with high background hybridization may mask the real expression of the transcript. Fourth, we cannot rule out the possibility that some probes may show variable levels of background hybridization in different brain areas, resulting in a false positive signal. Columns A-D describe the LocusID, gene name, type of RBD, and number (internal Mahoney reference number). Columns E and, L (E13.5, P0 "Informativity"): "1" for restricted expression in the nervous system and "0" for either ubiquitous expression that is difficult to distinguish from background or no expression. As noted in Gray et al [25], some of the genes in the "0" category show uneven signals in different brain regions and are also annotated in the subsequent columns. Columns F and M (E13.5, P0 "Specificity"): "1" for restricted expression in neural tissues only, "2" for restricted expression in neural tissue with distinguishable expression in non-neural tissue, "3" for ubiquitous or no expression, and "4" for expression in non-neural tissues only. Columns G-K and N-U (E13.5, P0 "Expression"): "2" for expression, "1" for ubiquitous expression or background, "0" for no expression.
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Additional File 4:
RNA-binding proteins belonging to a synexpression group. Complete list of RBPs that demonstrate a similar complex pattern of expression. Columns A-D describe the LocusID, gene name, type of RBD, and number (internal Mahoney reference number).
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Additional File 5:
Examples of RBP synexpression in E13.5 and P0 mouse tissues. Additional examples of RBPs that share a similar pattern of expression. Shown are in situ hybridization results of expression in the periventricular areas of the E13.5 brain (A, E, I, M, Q), in the subventricular area of the P0 lateral ventricle (B, F, J, N, R), in the external granule layer of the P0 cerebellum (C, G, K, O, S), as well as in postnatal developing teeth (D, H, L P, T). A-D) Refbp1, E-H) hnRNP A1, I-L) PTBP1, M-P) Sfpq, Q-R) Hnrpl. Panels A, B, E, F, I, J, M, N, Q, R show the same magnification. Panels C, D, G, H, K, L, O, P, S, T show the same magnification.
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