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IPMK physically binds to the SWI/SNF complex and modulates BRG1 occupancy

View ORCID ProfileJiyoon Beon, Sungwook Han, Seung Eun Park, Kwangbeom Hyun, Song-Yi Lee, View ORCID ProfileHyun-Woo Rhee, Jeong Kon Seo, Jaehoon Kim, View ORCID ProfileSeyun Kim, View ORCID ProfileDaeyoup Lee
doi: https://doi.org/10.1101/2021.09.15.460446
Jiyoon Beon
1Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
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Sungwook Han
1Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
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Seung Eun Park
1Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
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Kwangbeom Hyun
1Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
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Song-Yi Lee
2Department of Chemistry, Seoul National University, Seoul, 08826, Korea.
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Hyun-Woo Rhee
2Department of Chemistry, Seoul National University, Seoul, 08826, Korea.
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Jeong Kon Seo
3UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea.
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Jaehoon Kim
1Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
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Seyun Kim
1Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
4KAIST Institute for the BioCentury, KAIST, Daejeon 34141, Korea.
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  • For correspondence: seyunkim@kaist.ac.kr daeyoup@kaist.ac.kr
Daeyoup Lee
1Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
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  • ORCID record for Daeyoup Lee
  • For correspondence: seyunkim@kaist.ac.kr daeyoup@kaist.ac.kr
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ABSTRACT

Inositol polyphosphate multikinase (IPMK), a key enzyme in the inositol polyphosphate (IP) metabolism, is a pleiotropic signaling factor involved in major biological events including transcriptional control. In yeasts, IPMK and its IP products were known to promote the activity of SWI/SNF chromatin remodeling complex, which plays a critical role in gene expression by regulating chromatin accessibility. However, the direct linkage between IPMK and chromatin remodelers remains unclear, raising a question on how IPMK contributes to the transcriptional regulation in mammals. By employing unbiased screenings and in vivo/in vitro immunoprecipitations, here we demonstrated that IPMK physically associates with native mammalian SWI/SNF complexes by directly binding to SMARCB1, BRG1, and SMARCC1. Furthermore, we identified the specific domains required for the 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 (including promoter-TSS) in mouse embryonic stem cells. Finally, our mRNA-seq analyses revealed that IPMK and SMARCB1 regulate common gene sets, validating a functional link between IPMK and SWI/SNF complex. Together, these findings establish an importance of IPMK in promoter targeting of the SWI/SNF complex, thereby contributing to SWI/SNF-meditated chromatin accessibility and transcription.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 15, 2021.
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IPMK physically binds to the SWI/SNF complex and modulates BRG1 occupancy
Jiyoon Beon, Sungwook Han, Seung Eun Park, Kwangbeom Hyun, Song-Yi Lee, Hyun-Woo Rhee, Jeong Kon Seo, Jaehoon Kim, Seyun Kim, Daeyoup Lee
bioRxiv 2021.09.15.460446; doi: https://doi.org/10.1101/2021.09.15.460446
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IPMK physically binds to the SWI/SNF complex and modulates BRG1 occupancy
Jiyoon Beon, Sungwook Han, Seung Eun Park, Kwangbeom Hyun, Song-Yi Lee, Hyun-Woo Rhee, Jeong Kon Seo, Jaehoon Kim, Seyun Kim, Daeyoup Lee
bioRxiv 2021.09.15.460446; doi: https://doi.org/10.1101/2021.09.15.460446

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