Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification
Abstract Background The molecular mechanism controlling regional specific skin appendage phenotypes is a fundamental question that remains unresolved. We recently identified feather and scale primordium associated genes and with functional studies, proposed five major modules are involved in scale-t...
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| Format: | Article |
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BMC
2018-10-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5184-x |
| _version_ | 1828397714532990976 |
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| author | Yung-Chih Lai Ya-Chen Liang Ting-Xin Jiang Randall B. Widelitz Ping Wu Cheng-Ming Chuong |
| author_facet | Yung-Chih Lai Ya-Chen Liang Ting-Xin Jiang Randall B. Widelitz Ping Wu Cheng-Ming Chuong |
| author_sort | Yung-Chih Lai |
| collection | DOAJ |
| description | Abstract Background The molecular mechanism controlling regional specific skin appendage phenotypes is a fundamental question that remains unresolved. We recently identified feather and scale primordium associated genes and with functional studies, proposed five major modules are involved in scale-to-feather conversion and their integration is essential to form today’s feathers. Yet, how the molecular networks are wired and integrated at the genomic level is still unknown. Results Here, we combine classical recombination experiments and systems biology technology to explore the molecular mechanism controlling cell fate specification. In the chimeric explant, dermal fate is more stable, while epidermal fate is reprogrammed to be similar to the original appendage type of the mesenchyme. We analyze transcriptome changes in both scale-to-feather and feather-to-scale transition in the epidermis. We found a highly interconnected regulatory gene network controlling skin appendage types. These gene networks are organized around two molecular hubs, β-catenin and retinoic acid (RA), which can bind to regulatory elements controlling downstream gene expression, leading to scale or feather fates. ATAC sequencing analyses revealed about 1000 altered widely distributed chromatin open sites. We find that perturbation of a key gene alters the expression of many other co-expressed genes in the same module. Conclusions Our findings suggest that these feather / scale fate specification genes form an interconnected network and rewiring of the gene network can lead to changes of appendage phenotypes, acting similarly to endogenous reprogramming at the tissue level. This work shows that key hub molecules, β-catenin and retinoic acid, regulate scale / feather fate specification gene networks, opening up new possibilities to understand the switches controlling organ phenotypes in a two component (epithelial and mesenchyme) system. |
| first_indexed | 2024-12-10T08:51:08Z |
| format | Article |
| id | doaj.art-e53c5343e983494ea249db0ad56668ea |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-10T08:51:08Z |
| publishDate | 2018-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-e53c5343e983494ea249db0ad56668ea2022-12-22T01:55:34ZengBMCBMC Genomics1471-21642018-10-0119111210.1186/s12864-018-5184-xTranscriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specificationYung-Chih Lai0Ya-Chen Liang1Ting-Xin Jiang2Randall B. Widelitz3Ping Wu4Cheng-Ming Chuong5Integrative Stem Cell Center, China Medical University Hospital, China Medical UniversityIntegrative Stem Cell Center, China Medical University Hospital, China Medical UniversityDepartment of Pathology, Keck School of Medicine, University of Southern CaliforniaDepartment of Pathology, Keck School of Medicine, University of Southern CaliforniaDepartment of Pathology, Keck School of Medicine, University of Southern CaliforniaIntegrative Stem Cell Center, China Medical University Hospital, China Medical UniversityAbstract Background The molecular mechanism controlling regional specific skin appendage phenotypes is a fundamental question that remains unresolved. We recently identified feather and scale primordium associated genes and with functional studies, proposed five major modules are involved in scale-to-feather conversion and their integration is essential to form today’s feathers. Yet, how the molecular networks are wired and integrated at the genomic level is still unknown. Results Here, we combine classical recombination experiments and systems biology technology to explore the molecular mechanism controlling cell fate specification. In the chimeric explant, dermal fate is more stable, while epidermal fate is reprogrammed to be similar to the original appendage type of the mesenchyme. We analyze transcriptome changes in both scale-to-feather and feather-to-scale transition in the epidermis. We found a highly interconnected regulatory gene network controlling skin appendage types. These gene networks are organized around two molecular hubs, β-catenin and retinoic acid (RA), which can bind to regulatory elements controlling downstream gene expression, leading to scale or feather fates. ATAC sequencing analyses revealed about 1000 altered widely distributed chromatin open sites. We find that perturbation of a key gene alters the expression of many other co-expressed genes in the same module. Conclusions Our findings suggest that these feather / scale fate specification genes form an interconnected network and rewiring of the gene network can lead to changes of appendage phenotypes, acting similarly to endogenous reprogramming at the tissue level. This work shows that key hub molecules, β-catenin and retinoic acid, regulate scale / feather fate specification gene networks, opening up new possibilities to understand the switches controlling organ phenotypes in a two component (epithelial and mesenchyme) system.http://link.springer.com/article/10.1186/s12864-018-5184-xFeatherScalePtilopodyEvo-devoRegionalizationRecombination |
| spellingShingle | Yung-Chih Lai Ya-Chen Liang Ting-Xin Jiang Randall B. Widelitz Ping Wu Cheng-Ming Chuong Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification BMC Genomics Feather Scale Ptilopody Evo-devo Regionalization Recombination |
| title | Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification |
| title_full | Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification |
| title_fullStr | Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification |
| title_full_unstemmed | Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification |
| title_short | Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification |
| title_sort | transcriptome analyses of reprogrammed feather scale chimeric explants revealed co expressed epithelial gene networks during organ specification |
| topic | Feather Scale Ptilopody Evo-devo Regionalization Recombination |
| url | http://link.springer.com/article/10.1186/s12864-018-5184-x |
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