Histone modification in Saccharomyces cerevisiae: A review of the current status

Chou, Kwon Young; Lee, Jun-Yeong; Kim, Kee-Beom; Kim, Eunjeong; Lee, Hyun‐Shik; Ryu, Hong‐Yeoul

doi:10.1016/j.csbj.2023.02.037

Cited by 5 publications

(2 citation statements)

References 142 publications

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“…2015 ; Al-Hadid, White, and Clarke 2016 ; Jethmalani and Green 2020 ; Ismail et al . 2022 ; Chou et al . 2023 ).…”

Section: Introductionunclassified

Profiling the compendium of changes in Saccharomyces cerevisiae due to mutations that alter availability of the main methyl donor S-Adenosylmethionine

Remines,

Schoonover,

Knox

et al. 2024

G3: Genes, Genomes, Genetics

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The SAM1 and SAM2 genes encode for S-AdenosylMethionine (AdoMet) synthetase enzymes, with AdoMet serving as the main cellular methyl donor. We have previously shown that independent deletion of these genes alters chromosome stability and AdoMet concentrations in opposite ways in Saccharomyces cerevisiae. To characterize other changes occurring in these mutants, we grew wildtype, sam1Δ/sam1Δ, and sam2Δ/sam2Δ strains in 15 different Phenotypic Microarray plates with different components and measured growth variations. RNA-Sequencing was also carried out on these strains and differential gene expression determined for each mutant. We explored how the phenotypic growth differences are linked to the altered gene expression, and hypothesize mechanisms by which loss of the SAM genes and subsequent AdoMet level changes, impact pathways and processes. We present six stories, discussing changes in sensitivity or resistance to azoles, cisplatin, oxidative stress, arginine biosynthesis perturbations, DNA synthesis inhibitors, and tamoxifen, to demonstrate the power of this novel methodology to broadly profile changes due to gene mutations. The large number of conditions that result in altered growth, as well as the large number of differentially expressed genes with wide-ranging functionality, speaks to the broad array of impacts that altering methyl donor abundance can impart. Our findings demonstrate that some cellular changes are directly related to AdoMet-dependent methyltransferases and AdoMet availability, some are directly linked to the methyl cycle and its role in production of several important cellular components, and others reveal impacts of SAM gene mutations on previously unconnected pathways.

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“…2015 ; Al-Hadid, White, and Clarke 2016 ; Jethmalani and Green 2020 ; Ismail et al . 2022 ; Chou et al . 2023 ).…”

Section: Introductionunclassified

Profiling the compendium of changes in Saccharomyces cerevisiae due to mutations that alter availability of the main methyl donor S-Adenosylmethionine

Remines,

Schoonover,

Knox

et al. 2024

G3: Genes, Genomes, Genetics

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“…However, nucleosomal organization of eukaryotic chromatin may negatively in uence access of factors such as TFIID to DNA (Hu et al 2014), requiring e cient mechanisms to allow a transition from "closed" to "open" chromatin at regulated genes. This may be achieved by covalent modi cation of histones (Chou et al 2023) and/or by ATP-dependent chromatin remodelling complexes (SWI/SNF, RSC, INO80 and others) which are able to mobilize nucleosomes by sliding but can also eject nucleosomes from their position or change their composition by histone dissociation (Clapier et al 2017;Eustermann et al 2024). As a result of their enzymatic function, nucleosome-depleted regions are generated at basal promoters which are now more easily accessible for general factors nally initiating gene expression.…”

Section: Introductionmentioning

confidence: 99%

Transcriptional activation domains interact with ATPase subunits of yeast chromatin remodelling complexes SWI/SNF, RSC and INO80

Wendegatz,

Engelhardt,

Schüller

2024

Preprint

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Chromatin remodelling complexes (CRC) are ATP-dependent molecular machines important for the dynamic organization of nucleosomes along eukaryotic DNA. CRCs SWI/SNF, RSC and INO80 can move positioned nucleosomes in promoter DNA, leading to nucleosome-depleted regions which facilitate access of general transcription factors. This function is strongly supported by transcriptional activators being able to interact with subunits of various CRCs. In this work we show that SWI/SNF subunits Swi1, Swi2, Snf5 and Snf6 can bind to activation domains of Ino2 required for expression of phospholipid biosynthetic genes in yeast. We identify an activator binding domain (ABD) of ATPase Swi2 and show that this ABD is functionally dispensable, presumably because ABDs of other SWI/SNF subunits can compensate for the loss. In contrast, mutational characterization of the ABD of the Swi2-related ATPase Sth1 revealed that some conserved basic and hydrophobic amino acids within this domain are essential for the function of Sth1. While ABDs of Swi2 and Sth1 define separate functional protein domains, mapping of an ABD within ATPase Ino80 showed co-localization with its HSA domain also required for binding actin-related proteins. Comparative interaction studies finally demonstrated that several unrelated activators each exhibit a specific binding pattern with ABDs of Swi2, Sth1 and Ino80.

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Role of the NLRP3 inflammasome in gynecological disease

Zheng,

Zhao,

Jin

et al. 2023

Biomedicine & Pharmacotherapy

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Histone modification in Saccharomyces cerevisiae: A review of the current status

Cited by 5 publications

References 142 publications

Profiling the compendium of changes in Saccharomyces cerevisiae due to mutations that alter availability of the main methyl donor S-Adenosylmethionine

Profiling the compendium of changes in Saccharomyces cerevisiae due to mutations that alter availability of the main methyl donor S-Adenosylmethionine

Transcriptional activation domains interact with ATPase subunits of yeast chromatin remodelling complexes SWI/SNF, RSC and INO80

Role of the NLRP3 inflammasome in gynecological disease

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