Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex
The peripheral and central auditory subsystems together form a complex sensory network that allows an organism to hear. The genetic programs of the two subsystems must therefore be tightly coordinated during development. Yet, their interactions and common expression pathways have never been systemat...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2023-12-01
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| Series: | RNA Biology |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/15476286.2023.2247628 |
| _version_ | 1797403962608975872 |
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| author | Mor Bordeynik-Cohen Michal Sperber Lena Ebbers Naama Messika-Gold Constanze Krohs Tal Koffler-Brill Yael Noy Ran Elkon Hans Gerd Nothwang Karen B. Avraham |
| author_facet | Mor Bordeynik-Cohen Michal Sperber Lena Ebbers Naama Messika-Gold Constanze Krohs Tal Koffler-Brill Yael Noy Ran Elkon Hans Gerd Nothwang Karen B. Avraham |
| author_sort | Mor Bordeynik-Cohen |
| collection | DOAJ |
| description | The peripheral and central auditory subsystems together form a complex sensory network that allows an organism to hear. The genetic programs of the two subsystems must therefore be tightly coordinated during development. Yet, their interactions and common expression pathways have never been systematically explored. MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression and are essential for normal development of the auditory system. We performed mRNA and small-RNA sequencing of organs from both auditory subsystems at three critical developmental timepoints (E16, P0, P16) to obtain a comprehensive and unbiased insight of their expression profiles. Our analysis reveals common and organ-specific expression patterns for differentially regulated mRNAs and miRNAs, which could be clustered with a particular selection of functions such as inner ear development, Wnt signalling, K+ transport, and axon guidance, based on gene ontology. Bioinformatics detected enrichment of predicted targets of specific miRNAs in the clusters and predicted regulatory interactions by monitoring opposite trends of expression of miRNAs and their targets. This approach identified six miRNAs as strong regulatory candidates for both subsystems. Among them was miR-96, an established critical factor for proper development in both subsystems, demonstrating the strength of our approach. We suggest that other miRNAs identified by this analysis are also common effectors of proper hearing acquirement. This first combined comprehensive analysis of the developmental program of the peripheral and central auditory systems provides important data and bioinformatics insights into the shared genetic program of the two sensory subsystems and their regulation by miRNAs. |
| first_indexed | 2024-03-09T02:46:12Z |
| format | Article |
| id | doaj.art-52292a900357441c8821cdf77955ae5d |
| institution | Directory Open Access Journal |
| issn | 1547-6286 1555-8584 |
| language | English |
| last_indexed | 2024-03-09T02:46:12Z |
| publishDate | 2023-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | RNA Biology |
| spelling | doaj.art-52292a900357441c8821cdf77955ae5d2023-12-05T16:09:52ZengTaylor & Francis GroupRNA Biology1547-62861555-85842023-12-0120162964010.1080/15476286.2023.22476282247628Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complexMor Bordeynik-Cohen0Michal Sperber1Lena Ebbers2Naama Messika-Gold3Constanze Krohs4Tal Koffler-Brill5Yael Noy6Ran Elkon7Hans Gerd Nothwang8Karen B. Avraham9Tel Aviv UniversityTel Aviv UniversityCarl von Ossietzky University OldenburgTel Aviv UniversityCarl von Ossietzky University OldenburgTel Aviv UniversityTel Aviv UniversityTel Aviv UniversityCarl von Ossietzky University OldenburgTel Aviv UniversityThe peripheral and central auditory subsystems together form a complex sensory network that allows an organism to hear. The genetic programs of the two subsystems must therefore be tightly coordinated during development. Yet, their interactions and common expression pathways have never been systematically explored. MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression and are essential for normal development of the auditory system. We performed mRNA and small-RNA sequencing of organs from both auditory subsystems at three critical developmental timepoints (E16, P0, P16) to obtain a comprehensive and unbiased insight of their expression profiles. Our analysis reveals common and organ-specific expression patterns for differentially regulated mRNAs and miRNAs, which could be clustered with a particular selection of functions such as inner ear development, Wnt signalling, K+ transport, and axon guidance, based on gene ontology. Bioinformatics detected enrichment of predicted targets of specific miRNAs in the clusters and predicted regulatory interactions by monitoring opposite trends of expression of miRNAs and their targets. This approach identified six miRNAs as strong regulatory candidates for both subsystems. Among them was miR-96, an established critical factor for proper development in both subsystems, demonstrating the strength of our approach. We suggest that other miRNAs identified by this analysis are also common effectors of proper hearing acquirement. This first combined comprehensive analysis of the developmental program of the peripheral and central auditory systems provides important data and bioinformatics insights into the shared genetic program of the two sensory subsystems and their regulation by miRNAs.http://dx.doi.org/10.1080/15476286.2023.2247628micrornastranscriptomicsgene regulatory networksinner earbrainstem |
| spellingShingle | Mor Bordeynik-Cohen Michal Sperber Lena Ebbers Naama Messika-Gold Constanze Krohs Tal Koffler-Brill Yael Noy Ran Elkon Hans Gerd Nothwang Karen B. Avraham Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex RNA Biology micrornas transcriptomics gene regulatory networks inner ear brainstem |
| title | Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex |
| title_full | Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex |
| title_fullStr | Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex |
| title_full_unstemmed | Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex |
| title_short | Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex |
| title_sort | shared and organ specific gene expression programs during the development of the cochlea and the superior olivary complex |
| topic | micrornas transcriptomics gene regulatory networks inner ear brainstem |
| url | http://dx.doi.org/10.1080/15476286.2023.2247628 |
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