Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation
Background Human embryonic stem cells (hESC) have been an invaluable research tool to study motor neuron development and disorders. However, transcriptional regulation of multiple temporal stages from ESCs to spinal motor neurons (MNs) has not yet been fully elucidated. Thus, the goals of this study...
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PeerJ Inc.
2020-11-01
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| author | Xue-Jiao Sun Ming-Xing Li Chen-Zi Gong Jing Chen Mohammad Nasb Sayed Zulfiqar Ali Shah Muhammad Rehan Ya-Jie Li Hong Chen |
| author_facet | Xue-Jiao Sun Ming-Xing Li Chen-Zi Gong Jing Chen Mohammad Nasb Sayed Zulfiqar Ali Shah Muhammad Rehan Ya-Jie Li Hong Chen |
| author_sort | Xue-Jiao Sun |
| collection | DOAJ |
| description | Background Human embryonic stem cells (hESC) have been an invaluable research tool to study motor neuron development and disorders. However, transcriptional regulation of multiple temporal stages from ESCs to spinal motor neurons (MNs) has not yet been fully elucidated. Thus, the goals of this study were to profile the time-course expression patterns of lncRNAs during MN differentiation of ESCs and to clarify the potential mechanisms of the lncRNAs that are related to MN differentiation. Methods We utilized our previous protocol which can harvest motor neuron in more than 90% purity from hESCs. Then, differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) during MN differentiation were identified through RNA sequencing. Bioinformatic analyses were performed to assess potential biological functions of genes. We also performed qRT-PCR to validate the DElncRNAs and DEmRNAs. Results A total of 441 lncRNAs and 1,068 mRNAs at day 6, 443 and 1,175 at day 12, and 338 lncRNAs and 68 mRNAs at day 18 were differentially expressed compared with day 0. Bioinformatic analyses identified that several key regulatory genes including POU5F1, TDGF1, SOX17, LEFTY2 and ZSCAN10, which involved in the regulation of embryonic development. We also predicted 283 target genes of DElncRNAs, in which 6 mRNAs were differentially expressed. Significant fold changes in lncRNAs (NCAM1-AS) and mRNAs (HOXA3) were confirmed by qRT-PCR. Then, through predicted overlapped miRNA verification, we constructed a lncRNA NCAM1-AS-miRNA-HOXA3 network. |
| first_indexed | 2024-03-09T08:17:46Z |
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| language | English |
| last_indexed | 2024-03-09T08:17:46Z |
| publishDate | 2020-11-01 |
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| series | PeerJ |
| spelling | doaj.art-8b86ec23acbb48cabab5f023b4c3b88b2023-12-02T22:00:27ZengPeerJ Inc.PeerJ2167-83592020-11-018e1007510.7717/peerj.10075Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiationXue-Jiao Sun0Ming-Xing Li1Chen-Zi Gong2Jing Chen3Mohammad Nasb4Sayed Zulfiqar Ali Shah5Muhammad Rehan6Ya-Jie Li7Hong Chen8Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaDepartment of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaDepartment of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaDepartment of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaDepartment of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaDepartment of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaDepartment of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaDepartment of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaDepartment of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaBackground Human embryonic stem cells (hESC) have been an invaluable research tool to study motor neuron development and disorders. However, transcriptional regulation of multiple temporal stages from ESCs to spinal motor neurons (MNs) has not yet been fully elucidated. Thus, the goals of this study were to profile the time-course expression patterns of lncRNAs during MN differentiation of ESCs and to clarify the potential mechanisms of the lncRNAs that are related to MN differentiation. Methods We utilized our previous protocol which can harvest motor neuron in more than 90% purity from hESCs. Then, differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) during MN differentiation were identified through RNA sequencing. Bioinformatic analyses were performed to assess potential biological functions of genes. We also performed qRT-PCR to validate the DElncRNAs and DEmRNAs. Results A total of 441 lncRNAs and 1,068 mRNAs at day 6, 443 and 1,175 at day 12, and 338 lncRNAs and 68 mRNAs at day 18 were differentially expressed compared with day 0. Bioinformatic analyses identified that several key regulatory genes including POU5F1, TDGF1, SOX17, LEFTY2 and ZSCAN10, which involved in the regulation of embryonic development. We also predicted 283 target genes of DElncRNAs, in which 6 mRNAs were differentially expressed. Significant fold changes in lncRNAs (NCAM1-AS) and mRNAs (HOXA3) were confirmed by qRT-PCR. Then, through predicted overlapped miRNA verification, we constructed a lncRNA NCAM1-AS-miRNA-HOXA3 network.https://peerj.com/articles/10075.pdfEmbryonic stem cellsLong non-coding RNAMotor neuronDifferentiationRNA sequencing |
| spellingShingle | Xue-Jiao Sun Ming-Xing Li Chen-Zi Gong Jing Chen Mohammad Nasb Sayed Zulfiqar Ali Shah Muhammad Rehan Ya-Jie Li Hong Chen Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation PeerJ Embryonic stem cells Long non-coding RNA Motor neuron Differentiation RNA sequencing |
| title | Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation |
| title_full | Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation |
| title_fullStr | Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation |
| title_full_unstemmed | Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation |
| title_short | Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation |
| title_sort | temporal expression profiles of lncrna and mrna in human embryonic stem cell derived motor neurons during differentiation |
| topic | Embryonic stem cells Long non-coding RNA Motor neuron Differentiation RNA sequencing |
| url | https://peerj.com/articles/10075.pdf |
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