Profiling the role of m6A effectors in the regulation of pluripotent reprogramming
Abstract The N6-methyladenosine (m6A) RNA modification plays essential roles in multiple biological processes, including stem cell fate determination. To explore the role of the m6A modification in pluripotent reprogramming, we used RNA-seq to map m6A effectors in human iPSCs, fibroblasts, and H9 ES...
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| Format: | Article |
| Language: | English |
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BMC
2024-04-01
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| Series: | Human Genomics |
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| Online Access: | https://doi.org/10.1186/s40246-024-00597-6 |
| _version_ | 1797219640391237632 |
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| author | Wenjun Wang Lei Zhou Hui Li Tingge Sun Xue Wen Wei Li Miguel A. Esteban Andrew R. Hoffman Ji-Fan Hu Jiuwei Cui |
| author_facet | Wenjun Wang Lei Zhou Hui Li Tingge Sun Xue Wen Wei Li Miguel A. Esteban Andrew R. Hoffman Ji-Fan Hu Jiuwei Cui |
| author_sort | Wenjun Wang |
| collection | DOAJ |
| description | Abstract The N6-methyladenosine (m6A) RNA modification plays essential roles in multiple biological processes, including stem cell fate determination. To explore the role of the m6A modification in pluripotent reprogramming, we used RNA-seq to map m6A effectors in human iPSCs, fibroblasts, and H9 ESCs, as well as in mouse ESCs and fibroblasts. By integrating the human and mouse RNA-seq data, we found that 19 m6A effectors were significantly upregulated in reprogramming. Notably, IGF2BPs, particularly IGF2BP1, were among the most upregulated genes in pluripotent cells, while YTHDF3 had high levels of expression in fibroblasts. Using quantitative PCR and Western blot, we validated the pluripotency-associated elevation of IGF2BPs. Knockdown of IGF2BP1 induced the downregulation of stemness genes and exit from pluripotency. Proteome analysis of cells collected at both the beginning and terminal states of the reprogramming process revealed that the IGF2BP1 protein was positively correlated with stemness markers SOX2 and OCT4. The eCLIP-seq target analysis showed that IGF2BP1 interacted with the coding sequence (CDS) and 3’UTR regions of the SOX2 transcripts, in agreement with the location of m6A modifications. This study identifies IGF2BP1 as a vital pluripotency-associated m6A effector, providing new insight into the interplay between m6A epigenetic modifications and pluripotent reprogramming. |
| first_indexed | 2024-04-24T12:36:51Z |
| format | Article |
| id | doaj.art-0538708e10884724abb35f2ecfeb727e |
| institution | Directory Open Access Journal |
| issn | 1479-7364 |
| language | English |
| last_indexed | 2024-04-24T12:36:51Z |
| publishDate | 2024-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Human Genomics |
| spelling | doaj.art-0538708e10884724abb35f2ecfeb727e2024-04-07T11:24:47ZengBMCHuman Genomics1479-73642024-04-0118111410.1186/s40246-024-00597-6Profiling the role of m6A effectors in the regulation of pluripotent reprogrammingWenjun Wang0Lei Zhou1Hui Li2Tingge Sun3Xue Wen4Wei Li5Miguel A. Esteban6Andrew R. Hoffman7Ji-Fan Hu8Jiuwei Cui9Cancer Center, The First Hospital of Jilin UniversityCancer Center, The First Hospital of Jilin UniversityCancer Center, The First Hospital of Jilin UniversityCancer Center, The First Hospital of Jilin UniversityCancer Center, The First Hospital of Jilin UniversityCancer Center, The First Hospital of Jilin UniversityGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesVA Palo Alto Health Care System, Stanford University School of MedicineCancer Center, The First Hospital of Jilin UniversityCancer Center, The First Hospital of Jilin UniversityAbstract The N6-methyladenosine (m6A) RNA modification plays essential roles in multiple biological processes, including stem cell fate determination. To explore the role of the m6A modification in pluripotent reprogramming, we used RNA-seq to map m6A effectors in human iPSCs, fibroblasts, and H9 ESCs, as well as in mouse ESCs and fibroblasts. By integrating the human and mouse RNA-seq data, we found that 19 m6A effectors were significantly upregulated in reprogramming. Notably, IGF2BPs, particularly IGF2BP1, were among the most upregulated genes in pluripotent cells, while YTHDF3 had high levels of expression in fibroblasts. Using quantitative PCR and Western blot, we validated the pluripotency-associated elevation of IGF2BPs. Knockdown of IGF2BP1 induced the downregulation of stemness genes and exit from pluripotency. Proteome analysis of cells collected at both the beginning and terminal states of the reprogramming process revealed that the IGF2BP1 protein was positively correlated with stemness markers SOX2 and OCT4. The eCLIP-seq target analysis showed that IGF2BP1 interacted with the coding sequence (CDS) and 3’UTR regions of the SOX2 transcripts, in agreement with the location of m6A modifications. This study identifies IGF2BP1 as a vital pluripotency-associated m6A effector, providing new insight into the interplay between m6A epigenetic modifications and pluripotent reprogramming.https://doi.org/10.1186/s40246-024-00597-6m6AEpigeneticsIGF2BPsiPSCStem cellsReprogramming |
| spellingShingle | Wenjun Wang Lei Zhou Hui Li Tingge Sun Xue Wen Wei Li Miguel A. Esteban Andrew R. Hoffman Ji-Fan Hu Jiuwei Cui Profiling the role of m6A effectors in the regulation of pluripotent reprogramming Human Genomics m6A Epigenetics IGF2BPs iPSC Stem cells Reprogramming |
| title | Profiling the role of m6A effectors in the regulation of pluripotent reprogramming |
| title_full | Profiling the role of m6A effectors in the regulation of pluripotent reprogramming |
| title_fullStr | Profiling the role of m6A effectors in the regulation of pluripotent reprogramming |
| title_full_unstemmed | Profiling the role of m6A effectors in the regulation of pluripotent reprogramming |
| title_short | Profiling the role of m6A effectors in the regulation of pluripotent reprogramming |
| title_sort | profiling the role of m6a effectors in the regulation of pluripotent reprogramming |
| topic | m6A Epigenetics IGF2BPs iPSC Stem cells Reprogramming |
| url | https://doi.org/10.1186/s40246-024-00597-6 |
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