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The Swi-Snf chromatin remodeling complex mediates gene activation through metabolic control [RNA-seq I]

ABSTRACT: In eukaryotes, ATP-dependent chromatin remodelers regulate gene expression in response to nutritional and metabolic stimuli. The Swi-Snf complex is one such remodeler that has been implicated in disease, where loss of Swi-Snf function leads to dysregulated gene transcription. However, altered transcription of metabolic genes may have consequences for entire pathways that remain poorly understood. In this study, we use genetic and molecular approaches to uncover a role for Swi-Snf as a critical regulator of metabolism. We find that Δsnf mutants are cysteine-deficient, despite growth in nutrient-rich media. This cysteine deficiency causes widespread perturbations in sulfur metabolic gene transcription. This includes global alteration and redistribution of the transcription factor Met4 which senses cysteine deficiency and also has roles in heavy metal stress response and cell cycle progression. Additionally, we show that in its role as a metabolic regulator, Swi-Snf is a critical determinant of survival following oxidative stress. Our findings show how a chromatin remodeler can have a significant impact on a whole metabolic pathway by directly regulating an important gene subset and demonstrate an emerging role for chromatin remodeling complexes as key determinants of metabolic control.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE197918 | GEO | 2023/08/22

REPOSITORIES: GEO

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The Swi-Snf chromatin remodeling complex mediates gene activation through metabolic control [ChIP-seq]

Project description:In eukaryotes, ATP-dependent chromatin remodelers regulate gene expression in response to nutritional and metabolic stimuli. The Swi-Snf complex is one such remodeler that has been implicated in disease, where loss of Swi-Snf function leads to dysregulated gene transcription. However, altered transcription of metabolic genes may have consequences for entire pathways that remain poorly understood. In this study, we use genetic and molecular approaches to uncover a role for Swi-Snf as a critical regulator of metabolism. We find that Δsnf mutants are cysteine-deficient, despite growth in nutrient-rich media. This cysteine deficiency causes widespread perturbations in sulfur metabolic gene transcription. This includes global alteration and redistribution of the transcription factor Met4 which senses cysteine deficiency and also has roles in heavy metal stress response and cell cycle progression. Additionally, we show that in its role as a metabolic regulator, Swi-Snf is a critical determinant of survival following oxidative stress. Our findings show how a chromatin remodeler can have a significant impact on a whole metabolic pathway by directly regulating an important gene subset and demonstrate an emerging role for chromatin remodeling complexes as key determinants of metabolic control.

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Project description:A systems understanding of nuclear organization and events is critical for determining how cells divide, differentiate and respond to stimuli and for identifying the causes of diseases. Chromatin remodeling complexes such as SWI/SNF have been implicated in a wide variety of cellular processes including gene expression, nuclear organization, centromere function and chromosomal stability, and mutations in SWI/SNF components have been linked to several types of cancer. To better understand the biological processes in which chromatin remodeling proteins participate we globally mapped binding regions for several components of the SWI/SNF complex throughout the human genome using ChIP-Seq. SWI/SNF components were found to lie near regulatory elements integral to transcription (e.g. 5M-bM-^@M-^Y ends, RNA Polymerases II and III and enhancers) as well as regions critical for chromosome organization (e.g. CTCF, lamins and DNA replication origins). To further elucidate the association of SWI/SNF subunits with each other as well as with other nuclear proteins we also analyzed SWI/SNF immunoprecipitated complexes by mass spectrometry. Individual SWI/SNF factors are associated with their own family members as well as with cellular constituents such as nuclear matrix proteins, key transcription factors and centromere components implying a ubiquitous role in gene regulation and nuclear function. We find an overrepresentation of both SWI/SNF-associated regions and proteins in cell cycle and chromosome organization. Taken together the results from our ChIP and immunoprecipitation experiments suggest that SWI/SNF facilitates gene regulation and genome function more broadly and through a greater diversity of interactions than previously appreciated. ChIP-Seq analysis of the SWI/SNF subunits Ini1, Brg1, BAF155 and BAF170 in HeLa S3 cells

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