Conserved regulation of RNA processing in somatic cell reprogramming
Abstract Background Along with the reorganization of epigenetic and transcriptional networks, somatic cell reprogramming brings about numerous changes at the level of RNA processing. These include the expression of specific transcript isoforms and 3’ untranslated regions. A number of studies have un...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-01-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-019-5438-2 |
| _version_ | 1819153129865740288 |
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| author | Alexander Kanitz Afzal Pasha Syed Keisuke Kaji Mihaela Zavolan |
| author_facet | Alexander Kanitz Afzal Pasha Syed Keisuke Kaji Mihaela Zavolan |
| author_sort | Alexander Kanitz |
| collection | DOAJ |
| description | Abstract Background Along with the reorganization of epigenetic and transcriptional networks, somatic cell reprogramming brings about numerous changes at the level of RNA processing. These include the expression of specific transcript isoforms and 3’ untranslated regions. A number of studies have uncovered RNA processing factors that modulate the efficiency of the reprogramming process. However, a comprehensive evaluation of the involvement of RNA processing factors in the reprogramming of somatic mammalian cells is lacking. Results Here, we used data from a large number of studies carried out in three mammalian species, mouse, chimpanzee and human, to uncover consistent changes in gene expression upon reprogramming of somatic cells. We found that a core set of nine splicing factors have consistent changes across the majority of data sets in all three species. Most striking among these are ESRP1 and ESRP2, which accelerate and enhance the efficiency of somatic cell reprogramming by promoting isoform expression changes associated with mesenchymal-to-epithelial transition. We further identify genes and processes in which splicing changes are observed in both human and mouse. Conclusions Our results provide a general resource for gene expression and splicing changes that take place during somatic cell reprogramming. Furthermore, they support the concept that splicing factors with evolutionarily conserved, cell type-specific expression can modulate the efficiency of the process by reinforcing intermediate states resembling the cell types in which these factors are normally expressed. |
| first_indexed | 2024-12-22T15:00:17Z |
| format | Article |
| id | doaj.art-8234a9a2da3d4e89a2c16602d0eb0a4e |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-22T15:00:17Z |
| publishDate | 2019-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-8234a9a2da3d4e89a2c16602d0eb0a4e2022-12-21T18:22:08ZengBMCBMC Genomics1471-21642019-01-0120111910.1186/s12864-019-5438-2Conserved regulation of RNA processing in somatic cell reprogrammingAlexander Kanitz0Afzal Pasha Syed1Keisuke Kaji2Mihaela Zavolan3Biozentrum, University of BaselBiozentrum, University of BaselMRC Centre for Regenerative Medicine, University of EdinburghBiozentrum, University of BaselAbstract Background Along with the reorganization of epigenetic and transcriptional networks, somatic cell reprogramming brings about numerous changes at the level of RNA processing. These include the expression of specific transcript isoforms and 3’ untranslated regions. A number of studies have uncovered RNA processing factors that modulate the efficiency of the reprogramming process. However, a comprehensive evaluation of the involvement of RNA processing factors in the reprogramming of somatic mammalian cells is lacking. Results Here, we used data from a large number of studies carried out in three mammalian species, mouse, chimpanzee and human, to uncover consistent changes in gene expression upon reprogramming of somatic cells. We found that a core set of nine splicing factors have consistent changes across the majority of data sets in all three species. Most striking among these are ESRP1 and ESRP2, which accelerate and enhance the efficiency of somatic cell reprogramming by promoting isoform expression changes associated with mesenchymal-to-epithelial transition. We further identify genes and processes in which splicing changes are observed in both human and mouse. Conclusions Our results provide a general resource for gene expression and splicing changes that take place during somatic cell reprogramming. Furthermore, they support the concept that splicing factors with evolutionarily conserved, cell type-specific expression can modulate the efficiency of the process by reinforcing intermediate states resembling the cell types in which these factors are normally expressed.http://link.springer.com/article/10.1186/s12864-019-5438-2iPS cellsSomatic cell reprogrammingRNA processingAlternative splicing |
| spellingShingle | Alexander Kanitz Afzal Pasha Syed Keisuke Kaji Mihaela Zavolan Conserved regulation of RNA processing in somatic cell reprogramming BMC Genomics iPS cells Somatic cell reprogramming RNA processing Alternative splicing |
| title | Conserved regulation of RNA processing in somatic cell reprogramming |
| title_full | Conserved regulation of RNA processing in somatic cell reprogramming |
| title_fullStr | Conserved regulation of RNA processing in somatic cell reprogramming |
| title_full_unstemmed | Conserved regulation of RNA processing in somatic cell reprogramming |
| title_short | Conserved regulation of RNA processing in somatic cell reprogramming |
| title_sort | conserved regulation of rna processing in somatic cell reprogramming |
| topic | iPS cells Somatic cell reprogramming RNA processing Alternative splicing |
| url | http://link.springer.com/article/10.1186/s12864-019-5438-2 |
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