Systematic identification of Oct4 transcriptional targets in embryonic stem cells using the auxin-inducible degron system and nascent RNA sequencing
Oct4 is a key transcription factor essential for maintaining pluripotency and self-renewal in embryonic stem cells (ESCs), where it activates pluripotency-related genes and represses differentiation-associated genes. While previous studies have identified OCT4 target genes using methods such as chromatin immunoprecipitation sequencing (ChIP-seq) and RNA interference (RNAi), these approaches may not fully capture direct transcriptional regulation. The auxin-inducible degron (AID) system, which enables rapid and reversible protein degradation, combined with nascent RNA sequencing, provides a refined method for identifying direct transcriptional targets by detecting immediate transcriptional changes in both protein-coding genes and non-coding RNAs. In this study, we utilized mouse Oct4-mAID ESCs and nascent RNA sequencing with 5-ethynyl uridine (5-EU) labeling to systematically identify direct OCT4 targets. Our results uncovered novel potential OCT4 targets, providing a dataset for further research into the functions and regulatory networks of Oct4 and related transcription factors.
Authors
- Hao Wu (ORCID: https://orcid.org/0000-0002-2350-8865)
- Mingqiang Deng
- Yuting Yuan (ORCID: https://orcid.org/0000-0001-5431-1478)
- Xiwei Wang (ORCID: https://orcid.org/0000-0001-6953-9790)
- Xichen Bao (ORCID: https://orcid.org/0000-0003-0389-4233)
- Ying Ye (ORCID: https://orcid.org/0000-0002-2683-3321)
- Wensheng Zhang (ORCID: https://orcid.org/0000-0002-6876-3173)
- Jie Zhang (ORCID: https://orcid.org/0000-0002-5016-9192)
- Peixin Chen (ORCID: https://orcid.org/0000-0002-4192-8396)
- Dongmei He (ORCID: https://orcid.org/0009-0002-4099-441X)
Institutions
- Shandong University of Technology (CN)
- Binzhou Medical University (CN)
- Shandong University of Aeronautics (CN)
- Xinjiang Medical University (CN)
- Fifth Affiliated Hospital of Xinjiang Medical University (CN)
- Guangzhou Institutes of Biomedicine and Health (CN)
- Soochow University (CN)
- Guangzhou Experimental Station (CN)
- University of Chinese Academy of Sciences (CN)
- University of Hong Kong (HK)
- Guangzhou Medical University (CN)
Publication Details
- Journal
- Cell Regeneration
- Published
- 2025-12-03
- DOI
- https://doi.org/10.1186/s13619-025-00269-3
- Primary Topic
- Pluripotent Stem Cells Research
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Natural Science Foundation of China
- National Key Research and Development Program of China
- Science and Technology Planning Project of Guangdong Province