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Chip-seq of S. cerevisiae to investigate post-transcriptional buffering of low nascent RNA transcription by Puf5

ABSTRACT: Chip-seq of S. cerevisiae to investigate post-transcriptional buffering of low nascent RNA transcription by Puf5

PROVIDER: PRJEB43114 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5296840.fastq.gz	Fastqsanger.gz
	ERR5296841.fastq.gz	Fastqsanger.gz
	ERR5296832.fastq.gz	Fastqsanger.gz
	ERR5296842.fastq.gz	Fastqsanger.gz
	ERR5296833.fastq.gz	Fastqsanger.gz

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Post-transcriptional buffering of low nascent RNA transcription by Puf5

Project description:Post-transcriptional buffering of low nascent RNA transcription by Puf5

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Post-transcriptional buffering of low nascent RNA transcription by Puf5

Project description:Gene expression is a dynamic process regulated on several layers starting with transcription, mRNA export, translation and finally, mRNA degradation. While subsequent layers heavily influence each other, it is not clear if the most extreme layers, chromatin architecture and mRNA decay are linked. Here, we show that changes in nascent transcription mediated by mutating H3K56 to alanine are buffered at a post-transcriptional level by the Pumilio protein Puf5, which stabilizes transcripts in a context-dependent manner. Depleting Puf5 in an H3K56A background leads to downregulation of its direct targets, largely consisting of ribosomal protein genes. This is followed by a decrease in translation efficiency and finally, cell cycle arrest. Importantly, we show that this phenomenon of post-transcriptional buffering is not only linked to H3K56A, but might be a more widespread phenomenon to ensure physiological mRNA levels and to maintain cellular homeostasis.

2021-07-19 | E-MTAB-10107 | biostudies-arrayexpress

Chip-seq of S. cerevisiae to investigate post-transcriptional buffering of low nascent RNA transcription by Puf5

2021-07-19 | E-MTAB-10105 | biostudies-arrayexpress

Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast

Project description:Gene expression is known to vary among individuals, and this variability can impact the phenotypic diversity observed in natural populations. While the transcriptome and proteome have been extensively studied, little is known about the translation process itself. Here, we therefore performed ribosome and transcriptomic profiling on a genetically and ecologically diverse subset of natural isolates of the Saccharomyces cerevisiae yeast. Interestingly, we found that the Euclidean distances between each profile and the expression fold changes in each pairwise isolate comparison were approximately 10% higher at the transcriptomic level. This observation clearly indicates that the transcriptional variation observed in the different isolates is buffered through a phenomenon known as post-transcriptional buffering at the translation level. Furthermore, this phenomenon seemed to have a specific signature by preferentially affecting essential genes as well as genes involved in complex-forming proteins, and low transcribed genes. We also explored the translation of the S. cerevisiae pangenome and found that the accessory genes related to introgression events displayed similar transcription and translation levels as the core genome. By contrast, genes acquired through horizontal gene transfer events tended to be less efficiently translated. Together, our results highlight both the extant and signature of the post- transcriptional buffering.

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Post-translational buffering leads to convergent protein expression levels between primates

Project description:Differences in gene regulation between human and closely related species influence phenotypes that are distinctly human. While gene regulation is a multi-step process, the majority of research concerning divergence in gene regulation among primates has focused on transcription. To gain a comprehensive view of gene regulation, we surveyed genome-wide ribosome occupancy, which reflects levels of protein translation, in lymphoblastoid cell lines derived from human, chimpanzee and rhesus macaque. We further integrated mRNA and protein level measurements collected from matching cell lines. We find that, in addition to transcriptional regulation, the major factor determining protein level divergence between human and closely related species is post-translational buffering. Inter-species divergence in transcription is generally propagated to the level of protein translation. In contrast, gene expression divergence is often attenuated post-translationally, potentially mediated through post-translational modifications. Results from our analysis indicate that post-translational buffering is a conserved mechanism that led to relaxation of selective constraint on transcript levels in humans.

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Post-translational buffering leads to convergent protein expression levels between primates

Project description:Post-translational buffering leads to convergent protein expression levels between primates

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Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast

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Genome-wide Analysis of Nascent Transcription in Saccharomyces cerevisiae

Project description:We combined the nuclear run-on (NRO) assay which labels and captures nascent transcripts with high throughput DNA sequencing to examine transcriptional activity in Saccharomyces cerevisiae. Examination of nascent transcripts and steady-state transcripts in exponentially growing and heat-shock treated yeast.

2011-11-01 | E-GEOD-33136 | biostudies-arrayexpress

RNA buffering upon transcriptional distorsion

Project description:RNA buffering upon transcriptional distorsion

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Translational buffering tunes gene expression in mouse and human

Project description:Translational buffering refers to the regulation of ribosome occupancy to offset the effects of transcriptional variation. While previous work reported translational buffering in a limited set of conditions, it remains unknown whether this is an intrinsic property of specific genes across a large number of different cell types. To identify genes exhibiting this phenomenon on a global scale and across different experimental conditions, we uniformly analyzed 1515 matched ribosome profiling and RNA-seq datasets from human and mouse tissues or cell lines. This resource enabled us to determine the set of genes exhibiting translational buffering by comparative analysis of variation at ribosome occupancy and the RNA levels across cell types and the relationship between mRNA abundance and translation efficiency. We demonstrate that translational buffering is a conserved property of genes using homologous gene pairs from humans and mice. Genes exhibiting translational buffering have lower variation in protein abundance in cancer cell lines, primary human tissues and mouse samples. Moreover, we observed that translationally buffered genes are more likely to be haploinsufficient and triplosensitive suggesting a demand for stringent dosage limits in these genes. We hypothesized two models of translational buffering, namely “differential accessibility model” and “change in translation initiation rate model”. Our experiment suggests that some transcripts conform to the former and others align with the alternate model. Overall, our work broadens the catalog of genes subjected to translational buffering, underscores the characteristics of genes that demonstrate this phenomenon and additionally provides an insight into the rationale driving this effect.

2025-06-24 | GSE297442 | GEO

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