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Cited by 15Chromatin Remodeling and CancerGenomics and Chromatin DynamicsEpigenetics and DNA Methylation

Inositol Polyphosphate Multikinase Physically Binds to the SWI/SNF Complex and Modulates BRG1 Occupancy in Mouse Embryonic Stem Cells

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Beon, Jiyoon, Han, Sungwook, Yang, Hyeokjun, Park, Seung Eun, Hyun, Kwangbeom, Lee, Song-Yi, Rhee, Hyun-Woo, Seo, Jeong Kon +3 more·2022·eLife
DOI 10.7554/elife.73523PMC PMC9098221

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Abstract

Inositol polyphosphate multikinase (IPMK), a key enzyme in inositol polyphosphate (IP) metabolism, is a pleiotropic signaling factor involved in major biological events, including transcriptional control. In the yeast, IPMK and its IP products promote the activity of the chromatin remodeling complex SWI/SNF, which plays a critical role in gene expression by regulating chromatin accessibility. However, the direct link between IPMK and chromatin remodelers remains unclear, raising the question of how IPMK contributes to transcriptional regulation in mammals. By employing unbiased screening approaches and in vivo/in vitro immunoprecipitation, here we demonstrate that mammalian IPMK physically interacts with the SWI/SNF complex by directly binding to SMARCB1, BRG1, and SMARCC1. Furthermore, we identified the specific domains required for IPMK-SMARCB1 binding. Notably, using CUT&RUN and ATAC-seq assays, we discovered that IPMK co-localizes with BRG1 and regulates BRG1 localization as well as BRG1-mediated chromatin accessibility in a genome-wide manner in mouse embryonic stem cells. Together, these findings show that IPMK regulates the promoter targeting of the SWI/SNF complex, thereby contributing to SWI/SNF-meditated chromatin accessibility, transcription, and differentiation in mouse embryonic stem cells.

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  • IPMK has roles in nutrient sensing, growth factor signaling, mRNA transport, and transcription regulation.

    “Initially identified in yeast and later recognized as essential for mammalian embryonic development, IPMK has transitioned from a niche interest to a focal point in studies of nutrient sensing, growth factor signaling, mRNA transport, and transcription regulation.”

    From From Obscurity to Prominence: IPMK’s Expanding Role in Cellular Signaling, Physiology, and Disease (2025) · cites this paper as [20]

    The Introduction (no page available) identifies IPMK as originally cloned from yeast and describes its roles in metabolic and signaling pathways and transcriptional control; the Results (no page available) also show effects on gene expression in mouse embryonic stem cells. Our copy does not establish a role in mRNA transport. Its embryoid-body experiments do not establish that IPMK is essential for mammalian embryonic development. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • This interaction facilitates chromatin remodeling and transcriptional regulation in mammalian cells.

    “This interaction subsequently facilitates chromatin remodeling and transcriptional regulation in mammalian cells.”

    From From Obscurity to Prominence: IPMK’s Expanding Role in Cellular Signaling, Physiology, and Disease (2025) · cites this paper as [20]

    The Abstract and Introduction report that IPMK binds the SWI/SNF complex and contributes to chromatin accessibility and transcription in mouse embryonic stem cells. The claim’s broader wording, “in mammalian cells,” extends that finding beyond the cell type studied. No page numbers are available in our copy. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • Unlike in yeast, the effect of IPMK on chromatin remodeling in mammalian cells is kinase-independent.

    “Importantly, Beon et al. [20] found that, unlike in yeast, where inositol phosphate is required for chromatin remodeling, the effect of IPMK on chromatin remodeling in mammalian cells is kinase-independent.”

    From From Obscurity to Prominence: IPMK’s Expanding Role in Cellular Signaling, Physiology, and Disease (2025) · cites this paper as [20]

    The Results section on BRG1 occupancy reports that catalytically dead IPMK increased BRG1 occupancy in IPMK-depleted mouse embryonic stem cells, supporting kinase independence for that effect. The paper does not establish kinase independence for chromatin remodeling generally across mammalian cells; its yeast discussion describes IP products promoting remodeling and impaired remodeling after mutation, rather than showing that inositol phosphate is universally required. Page numbers were not available in our copy. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

  • IPMK functions in mRNA export, chromatin remodeling, transcription, nutrient sensing, and growth factor signaling.

    “Its diverse functions span a wide range of cellular processes, including mRNA export [17,18], chromatin remodeling [19,20], transcription [21,22], nutrient sensing [23], and growth factor signaling [15].”

    From From Obscurity to Prominence: IPMK’s Expanding Role in Cellular Signaling, Physiology, and Disease (2025) · cites this paper as [20]

  • IPMK physically interacts with the mammalian SWI/SNF complex by directly binding to SMARCB1, BRG1, and SMARCC1.

    “Recent research by Beon et al. [20] expanded on these findings, showing that IPMK physically interacts with the mammalian SWI/SNF complex by directly binding to SWI/SNF complex components SMARCB1, BRG1, and SMARCC1.”

    From From Obscurity to Prominence: IPMK’s Expanding Role in Cellular Signaling, Physiology, and Disease (2025) · cites this paper as [20]

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Cited by

Sorted by citations

Authors
Beon, J., Han, S., Yang, H., Park, S. E., Hyun, K., Lee, S.-Y., Rhee, H.-W., Seo, J. K., Kim, J., Kim, S., & Lee, D.
Affiliations
  • Korea Advanced Institute of Science and Technology (KR)
  • Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST)
  • Seoul National University (KR)
  • Ulsan National Institute of Science and Technology (KR)
Corresponding author
  • Kim, Seyun
  • Lee, Daeyoup
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2022-05-12
Volume
11
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.73523
PMC
PMC9098221
OpenAlex
W4280511624
Cited by
15
References
2
Citations by year
2026: 3 · 2025: 4 · 2024: 4 · 2023: 2 · 2022: 2
FWCI
0.98
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Seoul National University Open Repository (Seoul National University) (submittedVersion)
  • Scholarworks@UNIST (Ulsan National Institute of Science and Technology) (submittedVersion)
Funders
National Research Foundation of Korea (NRF-2020R1A2C3005765, NRF-2018R1A5A1024261)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
inositol polyphosphate multikinase, SWI/SNF complex, SMARCA4, SMARCB1, SMARCC1, chromatin accessibility, transcriptional regulation, protein-protein interaction, promoter targeting, mouse embryonic stem cells, chromatin remodeling, inositol polyphosphate metabolism
MeSH terms
Mouse Embryonic Stem Cells, Animals, Chromatin, Chromosomal Proteins, Non-Histone, DNA Helicases, Mammals, Nuclear Proteins, Phosphotransferases (Alcohol Group Acceptor), Mice

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