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Tan K, Jones SH, Lake BB, Chousal JN, Shum EY, Zhang L, Chen S, Sohni A, Pandya S, Gallo RL, Zhang K, Cook-Andersen H, Wilkinson MF. The role of the NMD factor UPF3B in olfactory sensory neurons. eLife 2020; 9:e57525. [PMID: 32773035 PMCID: PMC7452722 DOI: 10.7554/elife.57525] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/09/2020] [Indexed: 12/13/2022] Open
Abstract
The UPF3B-dependent branch of the nonsense-mediated RNA decay (NMD) pathway is critical for human cognition. Here, we examined the role of UPF3B in the olfactory system. Single-cell RNA-sequencing (scRNA-seq) analysis demonstrated considerable heterogeneity of olfactory sensory neuron (OSN) cell populations in wild-type (WT) mice, and revealed that UPF3B loss influences specific subsets of these cell populations. UPF3B also regulates the expression of a large cadre of antimicrobial genes in OSNs, and promotes the selection of specific olfactory receptor (Olfr) genes for expression in mature OSNs (mOSNs). RNA-seq and Ribotag analyses identified classes of mRNAs expressed and translated at different levels in WT and Upf3b-null mOSNs. Integrating multiple computational approaches, UPF3B-dependent NMD target transcripts that are candidates to mediate the functions of NMD in mOSNs were identified in vivo. Together, our data provides a valuable resource for the olfactory field and insights into the roles of NMD in vivo.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Samantha H Jones
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Blue B Lake
- Department of Bioengineering, University of California, San DiegoSan DiegoUnited States
| | - Jennifer N Chousal
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Eleen Y Shum
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Lingjuan Zhang
- Department of Dermatology, University of California, San DiegoSan DiegoUnited States
| | - Song Chen
- Department of Bioengineering, University of California, San DiegoSan DiegoUnited States
| | - Abhishek Sohni
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Shivam Pandya
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Richard L Gallo
- Department of Dermatology, University of California, San DiegoSan DiegoUnited States
| | - Kun Zhang
- Department of Bioengineering, University of California, San DiegoSan DiegoUnited States
| | - Heidi Cook-Andersen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
- Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
- Institute of Genomic Medicine, University of California, San DiegoSan DiegoUnited States
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