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Effect of ribosomal protein intron deletion on gene expression

ABSTRACT: Ribosomal proteins are essential to life. While the functions of ribosomal protein-encoding genes (RPGs) are highly conserved, the evolution of their regulatory mechanisms is remarkably dynamic. In Saccharomyces cerevisiae, RPGs are unusual in that they are commonly present as two highly similar gene copies and that they are over-represented among intron-containing genes. To investigate the role of introns in the regulation of RPG expression, we constructed 16 S. cerevisiae strains with precise deletions of RPG introns. We found that several yeast introns function to repress rather than to increase steady-state mRNA levels. Among these, the RPS9A and RPS9B introns were required for cross-regulation of the two paralogous gene copies, which is consistent with the duplication of an autoregulatory circuit.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE35541 | GEO | 2012/03/01

SECONDARY ACCESSION(S): PRJNA152269

REPOSITORIES: GEO

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Effect of ribosomal protein intron deletion on gene expression

Project description:Ribosomal proteins are essential to life. While the functions of ribosomal protein-encoding genes (RPGs) are highly conserved, the evolution of their regulatory mechanisms is remarkably dynamic. In Saccharomyces cerevisiae, RPGs are unusual in that they are commonly present as two highly similar gene copies and that they are over-represented among intron-containing genes. To investigate the role of introns in the regulation of RPG expression, we constructed 16 S. cerevisiae strains with precise deletions of RPG introns. We found that several yeast introns function to repress rather than to increase steady-state mRNA levels. Among these, the RPS9A and RPS9B introns were required for cross-regulation of the two paralogous gene copies, which is consistent with the duplication of an autoregulatory circuit. Splicing specific microarrays were used to assess the genome-wide defects in gene expression and pre-mRNA splicing that result from a deletion of a single ribosomal protein gene intron.

2012-03-01 | E-GEOD-35541 | biostudies-arrayexpress

Transcriptome analysis of budding yeast strains manipulated in RPL22A and RPL22B genes

Project description:Most Saccharomyces cerevisiae ribosomal protein genes (RPGs) are present as two paralogous copies that emerged during a whole genome duplication. The preservation of two copies of the same gene during the past ~100 million years enabled diversification of the regulation of their expression, and also partially of their functional properties. One example of such paralogous genes are RPL22A and RPL22B that are asymmetrically expressed and their protein sequences represent one of the most divergent pairs among budding yeast RPG paralogs. It was shown that introns in the RPL22A and RPL22B genes are important for regulation of their expression levels. To investigate functional differences between RPL22A and RPL22B we performed RNA-seq analysis of strains with complete deletions of either RPL22A or RPL22B, and also of strains with intron deletions in the RPL22 genes, in comparison with a wild-type strain. Cells were grown to mid-exponential phase in the rich YPAD medium. Total RNA was isolated by combining phenol-chlorophorm extraction with MasterPure Yeast RNA Purification Kit (Epicentre). Ribodepletion, library preparation and sequencing were performed by BGI Genomics.

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The regulation of ribosomal protein genes expression by the protein kinase DYRK1A contributes to the maintenance of ribosome mass and protein translation

Project description:Ribosomal protein genes (RPGs) coding sequences are highly conserved along evolution; however, promoter features and the machinery involved in their transcriptional regulation are not. In eukaryotes, the main genomic elements and players involved in RPG transcriptional regulation have been mostly characterized in Saccharomyces cerevisiae. However, given the lack of evolutionary conservation of the yeast factors, studies in higher eukaryotes have focused on searching for differential enrichment of transcription factor-binding motifs within the RPG promoters. Among them, the palindromic motif TCTCGCGAGA, which is currently acknowledged as a ZBTB33/KAISO motif, also matches the genomic sequence bound by the protein kinase DYRK1A. DYRK1A, a member of the human family of DYRK kinases, fulfills many diverse functions by phosphorylating a broad set of proteins involved in different cellular processes. One of such functions is to be a chromatin-associated kinase capable of regulating gene expression. Here, we analyze in-depth the presence of DYRK1A at the promoters of human and mouse RPGs and explore its functional consequences. Our results indicate that DYRK1A is a positive regulator of RPGs’ expression at the transcriptional level, and that this effect could, at least in part, contribute to the global reduction in ribosome amounts and protein synthesis observed when DYRK1A is silenced. Therefore, our results further expand the functional spectrum of the kinase as a contributor to the regulation of cell growth in mammalian cells.

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The DYRK1A protein kinase is recruited to a subset of ribosomal protein gene promoters in human and mouse cells [HeLa RNA-seq]

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The DYRK1A protein kinase is recruited to a subset of ribosomal protein gene promoters in human and mouse cells [RNA-seq]

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2023-08-01 | GSE155808 | GEO

The DYRK1A protein kinase is recruited to a subset of ribosomal protein gene promoters in human and mouse cells [ChIP-seq]

Project description:Ribosomal protein genes (RPGs) coding sequences are highly conserved along evolution; however, promoter features and the machinery involved in their transcriptional regulation are not. In eukaryotes, the main genomic elements and players involved in RPG transcriptional regulation have been mostly characterized in Saccharomyces cerevisiae. However, given the lack of evolutionary conservation of the yeast factors, studies in higher eukaryotes have focused on searching for differential enrichment of transcription factor-binding motifs within the RPG promoters. Among them, the palindromic motif TCTCGCGAGA, which is currently acknowledged as a ZBTB33/KAISO motif, also matches the genomic sequence bound by the protein kinase DYRK1A. DYRK1A, a member of the human family of DYRK kinases, fulfills many diverse functions by phosphorylating a broad set of proteins involved in different cellular processes. One of such functions is to be a chromatin-associated kinase capable of regulating gene expression. Here, we analyze in-depth the presence of DYRK1A at the promoters of human and mouse RPGs and explore its functional consequences. Our results indicate that DYRK1A is a positive regulator of RPGs’ expression at the transcriptional level, and further expand the functional spectrum of the kinase as a contributor to the regulation of cell growth in mammalian cells.

2023-08-01 | GSE155807 | GEO

Deletion of ribosomal protein genes is a common vulnerability in human cancer, particularly in concert with TP53 mutation

Project description:Heterozygous inactivating mutations in ribosomal protein genes (RPGs) are associated with hematopoietic and developmental abnormalities, activation of p53, and altered risk of cancer in humans and model organisms. As a part of a large-scale study aimed at identifying associations between RPG deletions, p53 activation, and perturbations of rRNA maturation patterns, we analyzed a series of blood and bone marrow samples from children with acute lymphoblastic leukemia (ALL), as a baseline genomic characterization.

2017-02-28 | E-MTAB-5450 | biostudies-arrayexpress

Rapid, transcript-specific changes in splicing in response to environmental stress

Project description:While the core splicing machinery is highly conserved between budding yeast and mammals, the absence of alternative splicing in Saccharomyces cerevisiae raises the fundamental question of why introns have been retained in ~5% of the 6,000 genes. Because Ribosomal Protein-encoding Genes (RPGs) are highly over-represented in the set of intron-containing genes, we tested the hypothesis that splicing of these transcripts would be regulated under conditions where translation is impaired. Using a microarraybased strategy, we find that within minutes after the induction of amino acid starvation the splicing of the majority of RPGs is specifically inhibited. In response to an unrelated stress, exposure to toxic levels of ethanol, splicing of a different group of transcripts is inhibited, while the splicing of a third set is actually improved. We propose that regulation of splicing, like transcription, can afford rapid and specific changes in gene expression in response to the environment. Keywords: stress, environmental stress, time course, splicing, splicing-specific microarray

2007-09-17 | GSE8817 | GEO

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

Project description:In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we identify two prevalent RPG promoter types, both characterized by upstream binding of the general transcription factor (TF) Rap1 followed by the RPG-specific Fhl1/Ifh1 pair, with one type also binding the HMG-B protein Hmo1. We show that the regulatory properties of the two promoter types are remarkably similar, suggesting that they are determined to a large extent by Rap1 and the Fhl1/Ifh1 pair. Rapid depletion experiments allowed us to define a hierarchy of TF binding in which Rap1 acts as a pioneer factor required for binding of all other TFs. We also uncovered unexpected features underlying recruitment of Fhl1, whose forkhead DNA-binding domain is not required for binding at most promoters, and Hmo1, whose binding is supported by repeated motifs. Finally, we describe unusually micrococcal nuclease (MNase)-sensitive nucleosomes at all RPG promoters, located between the canonical +1 and M-bM-^@M-^S1 nucleosomes, which coincide with sites of Fhl1/Ifh1 and Hmo1 binding. We speculate that these M-bM-^@M-^XM-bM-^@M-^XfragileM-bM-^@M-^YM-bM-^@M-^Y nucleosomes play an important role in regulating RPG transcriptional output. Genome-wide examination of binding sites for transcription factors controlling ribosomal protein genes expression and nucleosome positions in budding yeast cells

2014-10-01 | E-GEOD-61596 | biostudies-arrayexpress

Coordinate regulation of ribosomal protein gene transcription mediates embryonic secretory cell growth

Project description:Cell growth is well defined for the late (post-embryonic) stages of development, but evidence for early (embryonic) cell growth during post-mitotic morphogenesis is quite limited. Here, we identify early cell growth as a key characteristic of Drosophila embryonic salivary gland (SG) tubulogenesis. A BTB/POZ domain nuclear factor, Ribbon (Rib), mediates early cell growth without affecting endoreplication. Rib binds the transcription start site of nearly every SG-expressed ribosomal protein gene (RPG), and is required for full expression of all RPGs tested. Rib binding to RPG enhancers is, however, weak and not sequence-specific, suggesting that specificity is achieved through co-factor interactions. We demonstrate Rib’s ability to physically interact with each of the three known activators of RPG transcription. Surprisingly, Rib-dependent early cell growth in another tubular organ—the embryonic trachea—is not mediated by direct RPG transcription. Our results support a model for tissue-specific transcriptional regulation in early cell growth programs.

2022-02-15 | GSE181361 | GEO

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