Inositol polyphosphate multikinase physically binds to the SWI/SNF complex and modulates BRG1 occupancy in mouse embryonic stem cells
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Evaluation Summary:
This study describes a physical interaction between the Inositol polyphosphate multikinase enzyme (IPMK) and the SWI/SNF chromatin-remodeling complex. IMPK modulates SWI/SNF chromatin binding in particular at the transcription start sites of promoters with bivalent chromatin modifications in embryonic stem cells to regulate gene expression. This study will be of general interest to the epigenetics and gene expression communities.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)
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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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Evaluation Summary:
This study describes a physical interaction between the Inositol polyphosphate multikinase enzyme (IPMK) and the SWI/SNF chromatin-remodeling complex. IMPK modulates SWI/SNF chromatin binding in particular at the transcription start sites of promoters with bivalent chromatin modifications in embryonic stem cells to regulate gene expression. This study will be of general interest to the epigenetics and gene expression communities.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)
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Reviewer #1 (Public Review):
In this study, Beon et al., show that the Inositol polyphosphate multikinase enzyme (IPMK) interacts with several subunits of the SWI/SNF chromatin remodeling complex. They describe a direct interaction between the SMARCB1 (BAF47) subunit and IPMK and determine the regions of each protein required for interaction. Using ChIP-seq in presence or absence of IPMK siRNA silencing they show that IPMK modulates BRG1 occupancy primarily at the -1 and/or +1 nucleosome at the transcription start site. BRG1 occupancy is preferentially affected at promoters with bivalent chromatin modifications and its diminished occupancy regulates gene expression. The authors show convincing data that IPMK interacts with SWI/SNF and modulates is genomic occupancy in embryonic stem (ES) cells to regulate gene expression. However, the …
Reviewer #1 (Public Review):
In this study, Beon et al., show that the Inositol polyphosphate multikinase enzyme (IPMK) interacts with several subunits of the SWI/SNF chromatin remodeling complex. They describe a direct interaction between the SMARCB1 (BAF47) subunit and IPMK and determine the regions of each protein required for interaction. Using ChIP-seq in presence or absence of IPMK siRNA silencing they show that IPMK modulates BRG1 occupancy primarily at the -1 and/or +1 nucleosome at the transcription start site. BRG1 occupancy is preferentially affected at promoters with bivalent chromatin modifications and its diminished occupancy regulates gene expression. The authors show convincing data that IPMK interacts with SWI/SNF and modulates is genomic occupancy in embryonic stem (ES) cells to regulate gene expression. However, the study does not address if these effects regulate ES cell differentiation nor whether they involve IPMK enzymatic activity.
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Reviewer #2 (Public Review):
SWI/SNF subunits were identified as IPMK interacting proteins in two unbiased screening assays (yeast two hybrid with IPMK as bait and a human cDNA library as prey as well as in vivo proximity-labeling). The interactions were further characterized in mammalian cells using over-expressed tagged proteins and endogenous proteins by immunoprecipitations. Direct interactions were elucidated using baculovirus-purified proteins and interaction domains identified by deletion studies. Overall the protein-protein interaction studies are very convincing with the exception of one endogenous co-immunoprecipitation. The cut and run as well as the ATAC-seq data also look strong. However, important experimental and analysis details are missing regarding. While the emphasis of the chromatin occupancy and accessibility …
Reviewer #2 (Public Review):
SWI/SNF subunits were identified as IPMK interacting proteins in two unbiased screening assays (yeast two hybrid with IPMK as bait and a human cDNA library as prey as well as in vivo proximity-labeling). The interactions were further characterized in mammalian cells using over-expressed tagged proteins and endogenous proteins by immunoprecipitations. Direct interactions were elucidated using baculovirus-purified proteins and interaction domains identified by deletion studies. Overall the protein-protein interaction studies are very convincing with the exception of one endogenous co-immunoprecipitation. The cut and run as well as the ATAC-seq data also look strong. However, important experimental and analysis details are missing regarding. While the emphasis of the chromatin occupancy and accessibility studies is on the regulation of BRG1 by IPMK, the manuscript loses focus by performing gene expression profiling in Smarcb1 and not BRG1 depleted cells. Suggestions for increasing the focus and broader appeal of the work include providing a more extensive integration of chromatin occupancy and chromatin accessibility data with the effects of either BRG1 or Smarcb1 knockdown on gene expression.
In its current state, the findings may not be of broad interest. Experiments to link the molecular studies of IPMK depletion with biological effects of IPMK depletion on aspects of embryonic stem cell biology would increase the impact of the work and broaden the interest level to other fields.
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Reviewer #3 (Public Review):
The authors explored in mammalian cells the linkage between inositol polyphosphates, chromatin remodeling, and transcription regulation.
They first used a combination of experimental approaches including yeast two-hybrid screening, in vivo proximity labeling, in vitro binding assays and co-immunoprecipitation experiments to show that IMPK interacts with several subunits of the mammalian SWI/SNF complex. Altogether, these experiments provide strong evidence that IMPK and SWI/SNF complex(es) interact in vivo.
They next used CUT&RUN and ATAC-seq to probe the importance of the interaction between SWI/SNF and IMPK for chromatin remodeling at transcription cis-regulatory elements.
A major concern of the BRG1 CUT&RUN experiments realized in mouse ES cells is that the authors did not identify enhancers as regions of …
Reviewer #3 (Public Review):
The authors explored in mammalian cells the linkage between inositol polyphosphates, chromatin remodeling, and transcription regulation.
They first used a combination of experimental approaches including yeast two-hybrid screening, in vivo proximity labeling, in vitro binding assays and co-immunoprecipitation experiments to show that IMPK interacts with several subunits of the mammalian SWI/SNF complex. Altogether, these experiments provide strong evidence that IMPK and SWI/SNF complex(es) interact in vivo.
They next used CUT&RUN and ATAC-seq to probe the importance of the interaction between SWI/SNF and IMPK for chromatin remodeling at transcription cis-regulatory elements.
A major concern of the BRG1 CUT&RUN experiments realized in mouse ES cells is that the authors did not identify enhancers as regions of enrichment for BRG1 : enhancers are expected to be present in the intergenic fraction of the genome, which in the manuscript was identified as lacking BRG1 enrichment (Figure 4D,E). Previous publications and their associated ChIP-seq datasets for BRG1 in mouse ES cells and other cell types all revealed a strong BRG1 enrichment at enhancer elements (PMID: 28945250, PMID: 25803486, PMID: 26814966). This discrepancy suggests that something might have gone wrong with the BRG1 CUT&RUN experiments, and thus it is very important that the authors clarify this point.
Another concern is that the impact of IPMK knockdown on BRG1 enrichment appears to be very mild in Fig. 4B,C,F,G. Interpretation of low amplitude changes in ChIP-seq or CUT&RUN signal is always a difficult task because non-specific variations in signal might make strong contributions to heat-map and average profile analyses. Further analysis of the data should be done to validate these low amplitude changes.
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