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Fujii K, Zhulyn O, Byeon GW, Genuth NR, Kerr CH, Walsh EM, Barna M. Controlling tissue patterning by translational regulation of signaling transcripts through the core translation factor eIF3c. Dev Cell 2021; 56:2928-2937.e9. [PMID: 34752747 DOI: 10.1016/j.devcel.2021.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/06/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022]
Abstract
Although gene expression is tightly regulated during embryonic development, the impact of translational control has received less experimental attention. Here, we find that eukaryotic translation initiation factor-3 (eIF3) is required for Shh-mediated tissue patterning. Analysis of loss-of-function eIF3 subunit c (Eif3c) mice reveal a unique sensitivity to the Shh receptor patched 1 (Ptch1) dosage. Genome-wide in vivo enhanced cross-linking immunoprecipitation sequence (eCLIP-seq) shows unexpected specificity for eIF3 binding to a pyrimidine-rich motif present in subsets of 5'-UTRs and a corresponding change in the translation of these transcripts by ribosome profiling in Eif3c loss-of-function embryos. We further find a transcript specific effect in Eif3c loss-of-function embryos whereby translation of Ptch1 through this pyrimidine-rich motif is specifically sensitive to eIF3 amount. Altogether, this work uncovers hidden specificity of housekeeping translation initiation machinery for the translation of key developmental signaling transcripts.
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Affiliation(s)
- Kotaro Fujii
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Center for Neurogenetics, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA.
| | - Olena Zhulyn
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Gun Woo Byeon
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Electrical and Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Naomi R Genuth
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Craig H Kerr
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Erin M Walsh
- Center for Neurogenetics, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Maria Barna
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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