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<p>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.</p>

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Systematic identification of Oct4 transcriptional targets in embryonic stem cells using the auxin-inducible degron system and nascent RNA sequencing

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月3日

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  • Yuting Yuan,
  • Dongmei He,
  • Mingqiang Deng,
  • Ying Ye,
  • Peixin Chen,
  • Hao Wu,
  • Jie Zhang,
  • Xichen Bao,
  • Xiwei Wang,
  • Wensheng Zhang

摘要

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.