Evidence map›Paper›PMID 38580401›Full record

ArticleGenome research2024

Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches.

Muyoung Lee, Qingqing Guo, Mijeong Kim, Joonhyuk Choi, Alia Segura, Alper Genceroglu, Lucy LeBlanc, Nereida Ramirez, Yu Jin Jang, Yeejin Jang and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

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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

13 authors.

Muyoung Lee *Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.ORCID 0000-0002-4913-6289
Qingqing Guo *Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
Mijeong Kim *Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
Joonhyuk ChoiDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
Alia SeguraDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
Alper GencerogluDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
Lucy LeBlancDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
Nereida RamirezDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
Yu Jin JangDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
Yeejin JangDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
Bum-Kyu LeeDepartment of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, New York 12144, USA.ORCID 0000-0001-7835-419X
Edward M MarcotteDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
Jonghwan KimDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA; jonghwankim@mail.utexas.edu.ORCID 0000-0002-9919-9843

Funding

Proteomics and model organism humanization to decode human geneticsR35GM122480 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI EDWARD M MARCOTTE · 2017 to 2026
$5.4M
Investigating regulators controlling differentiation potential of ES cellsR01GM112722 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI KIM, JONGHWAN · 2015 to 2023
$2.8M
Deciphering gene regulatory networks modulating human trophoblast stem cell self-renewal and differentiationR01HD101512 · NICHD · UNIVERSITY OF TEXAS AT AUSTIN · PI KIM, JONGHWAN · 2021 to 2025
$2.3M
NICHD NIH HHS R01 HD101512NIGMS NIH HHS R01 GM112722NIGMS NIH HHS R35 GM122480Wellcome Trust 1017294
6 · The paper itself

Abstract

Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem cells identified multiple TFs that trigger rapid transcriptome changes indicative of differentiation within a day of induction. Moreover, cells expressing these potent TFs often show a slower cell cycle and increased cell death. Further analysis using bioChIP-seq revealed that GCM1 and OTX2 act as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.

Indexed as

Cell DifferentiationTranscription FactorsAnimalsCell LineageGene Expression ProfilingMiceMouse Embryonic Stem CellsMultiomicsRNA-SeqRNA, Small CytoplasmicSequence Analysis, RNASingle-Cell Gene Expression AnalysisTranscriptomeRNA, Small CytoplasmicTranscription Factors

Identifiers

PMID38580401
PMCPMC11067882

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Registered trials

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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 OpenQuestion graph.