Evidence map›Paper›PMID 38701759›Full record

ArticleCell stem cell2024

Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of stem cell maintenance and neuronal differentiation.

Mohammad Nazim, Chia-Ho Lin, An-Chieh Feng, Wen Xiao, Kyu-Hyeon Yeom, Mulin Li, Allison E Daly, Xianglong Tan, Ha Vu, Jason Ernst and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell stem cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.

0numbers the graph read from it
0cells of the map it votes in
23citing 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

23 citing papers in PubMed.

  1. RNA splicing in health and disease.Molecular biomedicine · 2026
    Review
  2. Review
  3. Article
  4. Article
  5. Article
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  8. Article
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  12. The Role of mRNA Alternative Processing in Mammalian Neurodevelopment.International journal of molecular sciences · 2025
    Review
  13. Article
  14. Article
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  17. Review
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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.

Mohammad NazimDepartment of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
Chia-Ho LinDepartment of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
An-Chieh FengDepartment of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
Wen XiaoDepartment of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
Kyu-Hyeon YeomDepartment of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
Mulin LiDepartment of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
Allison E DalyDepartment of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
Xianglong TanDepartment of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
Ha VuDepartment of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
Jason ErnstDepartment of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
Michael F CareyDepartment of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
Stephen T SmaleDepartment of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
Douglas L BlackDepartment of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA. Electronic address: dougb@microbio.ucla.edu.

Funding

Leveraging genetic variation to dissect gene regulatory networks of reprogramming to pluripotencyU01HG012079 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Chongyuan Luo, Kathrin Plath · 2021 to 2026
$6.9M
Interplay Between Chromatin and Co-Activator ComplexesR01GM074701 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CAREY, MICHAEL F · 2005 to 2025
$6.7M
Mechanisms of Post-transcriptional Gene Regulation by RNA Binding ProteinsR35GM136426 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Douglas L Black · 2020 to 2026
$5.4M
NHGRI NIH HHS U01 HG012079NIGMS NIH HHS R01 GM074701NIGMS NIH HHS R35 GM136426
6 · The paper itself

Abstract

Development of embryonic stem cells (ESCs) into neurons requires intricate regulation of transcription, splicing, and translation, but how these processes interconnect is not understood. We found that polypyrimidine tract binding protein 1 (PTBP1) controls splicing of DPF2, a subunit of BRG1/BRM-associated factor (BAF) chromatin remodeling complexes. Dpf2 exon 7 splicing is inhibited by PTBP1 to produce the DPF2-S isoform early in development. During neuronal differentiation, loss of PTBP1 allows exon 7 inclusion and DPF2-L expression. Different cellular phenotypes and gene expression programs were induced by these alternative DPF2 isoforms. We identified chromatin binding sites enriched for each DPF2 isoform, as well as sites bound by both. In ESC, DPF2-S preferential sites were bound by pluripotency factors. In neuronal progenitors, DPF2-S sites were bound by nuclear factor I (NFI), while DPF2-L sites were bound by CCCTC-binding factor (CTCF). DPF2-S sites exhibited enhancer modifications, while DPF2-L sites showed promoter modifications. Thus, alternative splicing redirects BAF complex targeting to impact chromatin organization during neuronal development.

Indexed as

Alternative SplicingCell DifferentiationChromatinHeterogeneous-Nuclear RibonucleoproteinsNeuronsPolypyrimidine Tract-Binding ProteinTranscription FactorsAnimalsCell Self RenewalDNA-Binding ProteinsEmbryonic Stem CellsExonsHumansMiceTranscription, GeneticChromatinDNA-Binding ProteinsHeterogeneous-Nuclear RibonucleoproteinsPolypyrimidine Tract-Binding ProteinPtbp1 protein, mouseTranscription Factorsalternative splicingBAF complexchromatin remodelingDPF2embryonic stem cellhistone modificationmammalian SWI/SNF complexneuronal differentiationPTBP1transcription

Identifiers

PMID38701759
PMCPMC11126784

What Socratic holds

Textmetadata
LicenceTDM
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.