Inositol polyphosphate multikinase physically binds to the SWI/SNF complex and modulates BRG1 occupancy in mouse embryonic stem cells

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.

A new CUT&RUN low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/β-catenin tissue-specific genomic targets

“…Finally, non-DNA binders would constitute the most difficult type of target, as exemplified by our C&R attempts and the previous need for ChIP-seq protocols to adopt a dual cross-linking approach ( Cantù et al, 2018 ; Salazar et al, 2019 ; Schuijers et al, 2014 ). Consistently, to our knowledge only a few C&R attempts targeting co-Fs have been reported ( Beon et al, 2022 ). Therefore, we tested whether C&R-LoV-U could adequately detect other non-DNA-binding transcriptional co-Fs, in addition to β-catenin.…”

Arg1 from Cryptococcus neoformans lacks PI3 kinase activity and conveys virulence roles via its IP 3-4 kinase activity

“…Next, we used the dkArg1 strains to investigate whether the phenotypes we previously observed in Cnarg1 Δ depend specifically on the IP 3-4 K activity or whether Cn Arg1 possesses potential chaperone or scaffold functions, as has been reported for Sc Arg82 and Hs IPMK ( 36 – 45 , 47 , 48 ). The phenotypes we focused on were those we found to be compromised in Cnarg1 Δ , such as growth at human body temperature (37°C), cell wall integrity, and utilization of non-glucose carbon sources, which we assessed using a spot dilution assay ( 8 ).…”

“…Sc Arg82-Mcm1-Arg80 then functions as a transcriptional regulatory complex that binds to arginine boxes in the promoters of arginine anabolic and catabolic genes, including ARG1 , ARG3 , ARG5,6 , ARG8 , and CAR1 , CAR2 , respectively ( 37 , 38 , 40 , 46 ). Like Sc Arg82 , human Hs IPMK also functions via catalytically independent mechanisms, as an adapter or chaperone involved in transcription and signaling ( 32 , 41 , 42 , 47 – 49 ) (also reviewed in references 44 , 50 ). For example, Hs IPMK stabilizes mTOR (mammalian target of rapamycin) signaling complexes, which are important for regulating cell growth, survival and proliferation, protein synthesis, and transcription ( 41 ), and promotes toll-like receptor-induced inflammation by stabilizing tumor necrosis factor receptor–associated factor 6, thereby preventing its degradation by the proteasome ( 42 ).…”

Conservation of heat stress acclimation by the inositol polyphosphate multikinase, IPMK responsible for 4/6-InsP7production in land plants

“…6A and 6B). Considering that the atipk2β -/- atipk2α kd lines suffered with the compromised expression of genes that are regulated by different heat shock transcription factors (HSF-TFs) and that IPMK/AtIPK2 is already implicated in transcriptional regulation in various eukaryotes (Beon et al, 2022; Malabanan and Blind, 2016; Odom et al, 2000; Sang et al, 2017), we asked whether IPMK controls HSF activity. To this aim, we monitored the HSF activity by measuring luciferase activity under control of HSP18.2 promoter element(Luo et al, 2022).…”