Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model
Abstract Background MicroRNAs (miRNAs) are important post-transcriptional gene regulators controlling cellular lineage specification and differentiation during embryonic development, including the gastrointestinal system. However, miRNA-mediated regulatory mechanisms involved in early embryonic deve...
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| Format: | Article |
| Language: | English |
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BMC
2023-10-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09743-1 |
| _version_ | 1797647376398155776 |
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| author | Yu-Han Hung Meghan Capeling Jonathan W. Villanueva Matt Kanke Michael T. Shanahan Sha Huang Rebecca Cubitt Vera D. Rinaldi John C. Schimenti Jason R. Spence Praveen Sethupathy |
| author_facet | Yu-Han Hung Meghan Capeling Jonathan W. Villanueva Matt Kanke Michael T. Shanahan Sha Huang Rebecca Cubitt Vera D. Rinaldi John C. Schimenti Jason R. Spence Praveen Sethupathy |
| author_sort | Yu-Han Hung |
| collection | DOAJ |
| description | Abstract Background MicroRNAs (miRNAs) are important post-transcriptional gene regulators controlling cellular lineage specification and differentiation during embryonic development, including the gastrointestinal system. However, miRNA-mediated regulatory mechanisms involved in early embryonic development of human small intestine (SI) remains underexplored. To explore candidate roles for miRNAs in prenatal SI lineage specification in humans, we used a multi-omic analysis strategy in a directed differentiation model that programs human pluripotent stem cells toward the SI lineage. Results We leveraged small RNA-seq to define the changing miRNA landscape, and integrated chromatin run-on sequencing (ChRO-seq) and RNA-seq to define genes subject to significant post-transcriptional regulation across the different stages of differentiation. Small RNA-seq profiling revealed temporal dynamics of miRNA signatures across different developmental events of the model, including definitive endoderm formation, SI lineage specification and SI regional patterning. Our multi-omic, integrative analyses showed further that the elevation of miR-182 and reduction of miR-375 are key events during SI lineage specification. We demonstrated that loss of miR-182 leads to an increase in the foregut master marker SOX2. We also used single-cell analyses in murine adult intestinal crypts to support a life-long role for miR-375 in the regulation of Zfp36l2. Finally, we uncovered opposing roles of SMAD4 and WNT signaling in regulating miR-375 expression during SI lineage specification. Beyond the mechanisms highlighted in this study, we also present a web-based application for exploration of post-transcriptional regulation and miRNA-mediated control in the context of early human SI development. Conclusion The present study uncovers a novel facet of miRNAs in regulating prenatal SI development. We leveraged multi-omic, systems biology approaches to discover candidate miRNA regulators associated with early SI developmental events in a human organoid model. In this study, we highlighted miRNA-mediated post-transcriptional regulation relevant to the event of SI lineage specification. The candidate miRNA regulators that we identified for the other stages of SI development also warrant detailed characterization in the future. |
| first_indexed | 2024-03-11T15:15:25Z |
| format | Article |
| id | doaj.art-02087dfb606b46d7bd6a6a50830c592e |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-11T15:15:25Z |
| publishDate | 2023-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-02087dfb606b46d7bd6a6a50830c592e2023-10-29T12:15:37ZengBMCBMC Genomics1471-21642023-10-0124111910.1186/s12864-023-09743-1Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid modelYu-Han Hung0Meghan Capeling1Jonathan W. Villanueva2Matt Kanke3Michael T. Shanahan4Sha Huang5Rebecca Cubitt6Vera D. Rinaldi7John C. Schimenti8Jason R. Spence9Praveen Sethupathy10Department of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityDepartment of Cell and Developmental Biology, University of MichiganDepartment of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityDepartment of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityDepartment of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityDepartment of Cell and Developmental Biology, University of MichiganDepartment of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityDepartment of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityDepartment of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityDepartment of Cell and Developmental Biology, University of MichiganDepartment of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityAbstract Background MicroRNAs (miRNAs) are important post-transcriptional gene regulators controlling cellular lineage specification and differentiation during embryonic development, including the gastrointestinal system. However, miRNA-mediated regulatory mechanisms involved in early embryonic development of human small intestine (SI) remains underexplored. To explore candidate roles for miRNAs in prenatal SI lineage specification in humans, we used a multi-omic analysis strategy in a directed differentiation model that programs human pluripotent stem cells toward the SI lineage. Results We leveraged small RNA-seq to define the changing miRNA landscape, and integrated chromatin run-on sequencing (ChRO-seq) and RNA-seq to define genes subject to significant post-transcriptional regulation across the different stages of differentiation. Small RNA-seq profiling revealed temporal dynamics of miRNA signatures across different developmental events of the model, including definitive endoderm formation, SI lineage specification and SI regional patterning. Our multi-omic, integrative analyses showed further that the elevation of miR-182 and reduction of miR-375 are key events during SI lineage specification. We demonstrated that loss of miR-182 leads to an increase in the foregut master marker SOX2. We also used single-cell analyses in murine adult intestinal crypts to support a life-long role for miR-375 in the regulation of Zfp36l2. Finally, we uncovered opposing roles of SMAD4 and WNT signaling in regulating miR-375 expression during SI lineage specification. Beyond the mechanisms highlighted in this study, we also present a web-based application for exploration of post-transcriptional regulation and miRNA-mediated control in the context of early human SI development. Conclusion The present study uncovers a novel facet of miRNAs in regulating prenatal SI development. We leveraged multi-omic, systems biology approaches to discover candidate miRNA regulators associated with early SI developmental events in a human organoid model. In this study, we highlighted miRNA-mediated post-transcriptional regulation relevant to the event of SI lineage specification. The candidate miRNA regulators that we identified for the other stages of SI development also warrant detailed characterization in the future.https://doi.org/10.1186/s12864-023-09743-1Micro-RNAPost-transcriptional regulationIntestineDevelopmentFunctional genomics |
| spellingShingle | Yu-Han Hung Meghan Capeling Jonathan W. Villanueva Matt Kanke Michael T. Shanahan Sha Huang Rebecca Cubitt Vera D. Rinaldi John C. Schimenti Jason R. Spence Praveen Sethupathy Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model BMC Genomics Micro-RNA Post-transcriptional regulation Intestine Development Functional genomics |
| title | Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model |
| title_full | Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model |
| title_fullStr | Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model |
| title_full_unstemmed | Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model |
| title_short | Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model |
| title_sort | integrative genome scale analyses reveal post transcriptional signatures of early human small intestinal development in a directed differentiation organoid model |
| topic | Micro-RNA Post-transcriptional regulation Intestine Development Functional genomics |
| url | https://doi.org/10.1186/s12864-023-09743-1 |
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