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Genome-wide analysis reveals the importance of histone acetyltransferase Esa1 in transcriptional regulation during nitrogen starvation.

ABSTRACT: Macroautophagy/autophagy is a cellular process that degrades cell components and is strongly triggered by nitrogen starvation (-N). Some ATG (autophagy related) genes are activated at the transcriptional level; however, a full understanding of how transcription is induced and the role of chromatin during this process under conditions of nitrogen starvation remains unclear. To address these questions, we measured the occupancy of RNA polymerase II (Pol II), histone H3, and levels of acetylated H4 (H4Ac) under nutrient-rich and nitrogen-starved conditions using ChIP-seq. The Pol II data showed that most genes are rapidly downregulated within 15-30 minutes, including ribosomal protein (RP) and biogenesis (RiBi) genes. Meanwhile, genes involved in amino acid (AA) biosynthesis are upregulated, along with a subset of ATG genes. Interestingly, RP and RiBi genes are reactivated within 1-3 hours, suggesting that the reduction in ribosomal biosynthetic gene activity during -N is only temporary. Furthermore, many upregulated genes continue to be transcribed even in cells that are exposed to long-term starvation. Histones are typically removed from promoters during transcription activation. Consistent with this, we found that most of the induced genes exhibited histone eviction and increased H4 acetylation at their promoters, indicating a possible role for histone acetylation in their activation. Along these lines, depleting Esa1, an essential H4 histone acetyltransferase, nearly abolished the induction of ribosomal biosynthetic genes and many AA biosynthetic genes. Transcription of many genes continues during prolonged starvation, highlighting the vital role of this process in supporting autophagy and cell survival. This is the first comprehensive study to detail changes in chromatin, histone acetylation, and transcription during nitrogen starvation, emphasizing the roles of Esa1 and H4Ac in this process.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE330872 | GEO | 2026/08/26

REPOSITORIES: GEO

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Project description:ESA1 (essential SAS-family acetyltransferase) is the only known yeast histone acetyltransferase (HAT) required for cell viability. It is a member of the MYST (MOZ, YBF2/SAS3, SAS2, Tip60) family of HAT proteins and contains a conserved acetyltransferase domain in addition to a chromodomain. While ESA1’s HAT activity is important in processes such as deoxyribonucleic acid (DNA) repair, acetylation is likely not its essential function. Our lab has shown that mutants with a single point mutation in the active site cysteine are still viable even though their acetyltransferase abilities are abolished. Furthermore, chromatin immunoprecipitation assays have shown ESA1 distributed evenly along the length of chromatin, not localized to specific promoters as would be expected from a HAT protein involved in transcriptional regulation. As is the case for other HAT proteins, ESA1’s acetyltransferase activity is significant, but in processes such as DNA replication, DNA repair and cell cycle progression. The aim of this project is to determine the essential function of ESA1 - the catalytic subunit of the yeast HAT complex, NuA4 (nucleosome acetyltransferase of H4) – using a bypass suppression screen to identify suppressors of ESA1. It is proposed that suppressing mutations will alter a gene involved in the process that is the essential function of ESA1. Thus, identifying a suppressor that can bypass the need for ESA1 may provide insight into its essential function. Since ESA1 is an essential gene, a haploid esa1∆ strain in which wild-type ESA1 is provided on a centromeric plasmid was utilized. The bypass suppression screen resulted in suppressors of ESA1 that allowed esa1∆ cells to be viable even in the absence of the essential gene. These second site suppressors (sup-) of ESA1 each show the Mendelian segregation pattern of the suppressing gene and ESA1 in 2:2 ratios, implying they are single genes unlinked to ESA1. Microarray and nuclear morphology studies show abnormal gene expression and morphology of the esa1- sup- cells, further implicating the suppressing mutation in DNA repair and replication processes. Investigating ESA1’s essential role and a probable conservation of function across species can provide a deeper understanding of the capabilities of HAT complexes. Keywords: Comparison of strains lacking essential ESA1 gene to those containing an ESA1 bypass suppressor.

Project description:ESA1 (essential SAS-family acetyltransferase) is the only known yeast histone acetyltransferase (HAT) required for cell viability. It is a member of the MYST (MOZ, YBF2/SAS3, SAS2, Tip60) family of HAT proteins and contains a conserved acetyltransferase domain in addition to a chromodomain. While ESA1âs HAT activity is important in processes such as deoxyribonucleic acid (DNA) repair, acetylation is likely not its essential function. Our lab has shown that mutants with a single point mutation in the active site cysteine are still viable even though their acetyltransferase abilities are abolished. Furthermore, chromatin immunoprecipitation assays have shown ESA1 distributed evenly along the length of chromatin, not localized to specific promoters as would be expected from a HAT protein involved in transcriptional regulation. As is the case for other HAT proteins, ESA1âs acetyltransferase activity is significant, but in processes such as DNA replication, DNA repair and cell cycle progression. The aim of this project is to determine the essential function of ESA1 - the catalytic subunit of the yeast HAT complex, NuA4 (nucleosome acetyltransferase of H4) â using a bypass suppression screen to identify suppressors of ESA1. It is proposed that suppressing mutations will alter a gene involved in the process that is the essential function of ESA1. Thus, identifying a suppressor that can bypass the need for ESA1 may provide insight into its essential function. Since ESA1 is an essential gene, a haploid esa1â strain in which wild-type ESA1 is provided on a centromeric plasmid was utilized. The bypass suppression screen resulted in suppressors of ESA1 that allowed esa1â cells to be viable even in the absence of the essential gene. These second site suppressors (sup-) of ESA1 each show the Mendelian segregation pattern of the suppressing gene and ESA1 in 2:2 ratios, implying they are single genes unlinked to ESA1. Microarray and nuclear morphology studies show abnormal gene expression and morphology of the esa1ï sup- cells, further implicating the suppressing mutation in DNA repair and replication processes. Investigating ESA1âs essential role and a probable conservation of function across species can provide a deeper understanding of the capabilities of HAT complexes. Experiment Overall Design: Eight samples were analyzed. The only variables are the ESA1 and SUP2 genes. WT (ESA1 SUP2), 2 replicates. Single mutant (ESA1 sup2-), 3 replicates. Double mutant (esa1 sup2-), 3 replicates.

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Genome-wide analysis reveals the importance of histone acetyltransferase Esa1 in transcriptional regulation during nitrogen starvation.

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