Abstract
Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12ac ChIP-seq data for wild-type and mip6Δ strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress. Raw data, processed data and preprocessing scripts are made available.
Highlights
Background & SummaryEukaryotic gene expression is a complex process in which the information coded in genes is transformed into functions that support living cells
These newly synthetized RNA molecules are extensively modified prior to their export to the cytoplasm, where they can be degraded by the mRNA decay machinery, stored in specific foci or translated into proteins[6,7]
The encoded protein products participate in numerous processes, including cellular metabolism where organic compounds are transformed and/or stored
Summary
Background & SummaryEukaryotic gene expression is a complex process in which the information coded in genes is transformed into functions that support living cells. In this Data Descriptor, we present a yeast multi-omics dataset that features three basic layers of the transcriptional circuit, measured in the same set of samples. These include one epigenetic modification - H4K12ac, a mark for active promoters-, gene expression -RNA-seq- and targeted metabolomics.
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