Evidence map›Paper›PMID 41335281›Full record

ArticleCell regeneration (London, England)2025

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

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

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell regeneration (London, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Yuting Yuan *Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, 264003, China.
Dongmei He *Center for Cell Lineage Atlas, China-New Zealand Joint Laboratory On Biomedicine and Health, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory On Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
Mingqiang Deng *Center for Cell Lineage Atlas, China-New Zealand Joint Laboratory On Biomedicine and Health, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory On Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
Ying YeDepartment of Clinical Pathobiology and Immunological Testing, School of Medical Laboratory, Qilu Medical University, Zibo, 255300, China.
Peixin ChenCam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, 215123, China.
Hao WuCam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, 215123, China.
Jie ZhangDepartment of Clinical Pathobiology and Immunological Testing, School of Medical Laboratory, Qilu Medical University, Zibo, 255300, China.
Xichen BaoCenter for Cell Lineage Atlas, China-New Zealand Joint Laboratory On Biomedicine and Health, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory On Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. bao_xichen@gibh.ac.cn.
Xiwei WangDepartment of Basic Research, Guangzhou National Laboratory, Guangzhou, 510005, China. wang_xiwei@gzlab.ac.cn.
Wensheng ZhangPeninsula Cancer Research Center, Binzhou Medical University, Yantai, 264003, China. zhangwensheng@suda.edu.cn.ORCID http://orcid.org/0000-0002-6876-3173

Funding

5511 Science and Technology Innovation Talent Project of Jiangxi Province GPYC202411National Key Research and Development Program of China Stem Cell and Translational Research 2021YFA1100401National Key Research and Development Program of China Stem Cell and Translational Research 2024YFA1108201National Natural Science Foundation of China 32170745National Natural Science Foundation of China 32170797National Natural Science Foundation of China 32470842
6 · The paper itself

Abstract

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.

Indexed as

Auxin-inducible degron (AID) systemMouse embryonic stem cells (mESCs)Nascent RNA sequencingOct4Transcription targets

Identifiers

PMID41335281
PMCPMC12675901

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.