A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress

Viéitez, Cristina; Martínez-Cebrián, Gerard; Solé, Carme; Böttcher, René; Potel, Clement M; Savitski, Mikhail M.; Onnebo, Sara M.N.; Fabregat, Marc; Shilatifard, Ali; Posas, Francesc; Nadal, Eulàlia de

doi:10.1093/nar/gkaa081

Cited by 15 publications

(23 citation statements)

References 89 publications

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“…To validate IgemRNA we used Sacharomyces cerevisiae consensus genome scale metabolic model (47) version 8.4.0 (48) and appropriate transcriptome validation dataset was taken from (32), where were performed high-throughput genetic screenings that provide a novel global map of the histone residues required for transcriptional reprogramming in response to heat and osmotic stress in steady state growth conditions. All validation details are found in supplementary material 2.…”

Section: Resultsmentioning

confidence: 99%

“…Publicly available and previously published (32) gene expression dataset from Saccharomyces cerevisiae BY4741 strain and mutant strain H4-S47D were used for analysis. Reads were aligned using STAR aligner (33) and assigned to genomic features using featureCounts (34).…”

Section: Methodsmentioning

confidence: 99%

“…To validate IgemRNA we used Sacharomyces cerevisiae consensus genome scale metabolic model (47) version 8.4.0 (48) and appropriate transcriptome validation dataset was taken from (32),…”

Section: Igemrna Demonstrationmentioning

confidence: 99%

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Integrative Gene Expression and Metabolic Analysis tool IgemRNA

Grausa

Pleiko

Mozga

et al. 2021

Preprint

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Genome scale metabolic modelling is widely used technique to research metabolism impacts on organism properties. Additional omics data integration enables a more precise genotype-phenotype analysis for biotechnology, medicine and life sciences. Transcriptome data amounts rapidly increase each year. Many transcriptome analysis tools with integrated genome scale metabolic modelling are proposed. But these tools have own restrictions, compatibility issues and the necessity of previous experience and advanced user skills. We have analysed and classified published tools, summarized possible transcriptome pre-processing, and analysis methods and implemented them in the new transcriptome analysis tool IgemRNA. Tool novelty is the possibility of transcriptomics data pre-processing approach, analysis of transcriptome with or without genome scale metabolic models and different thresholding and gene mapping approach availability. In comparison with usual Gene set enrichment analysis methods, IgemRNA options provide additional transcriptome data validation, where minimal metabolic network connectivity and flux requirements are met. IgemRNA allows to process transcriptome datasets, compare data between different phenotypes, execute multiple analysis and data filtering functions. All this is done via graphical user interface. IgemRNA is compatible with Cobra Toolbox 3.0 and uses some of its functions for genome scale metabolic model optimization tasks. IgemRNA is open access software available at https://github.com/BigDataInSilicoBiologyGroup/IgemRNA.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Integrative Gene Expression and Metabolic Analysis tool IgemRNA

Grausa

Pleiko

Mozga

et al. 2021

Preprint

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“…in yeast, plants and animals (Delaney et al, 2018;Kim et al, 2015;Viéitez et al 2020). Likewise, upregulation of transcripts involved in the protein folding machinery, antioxidative defence and proteasome activity has been documented from bacteria to mammals (Evgen'ev et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Molecular adaptations to heat stress in the thermophilic ant genus Cataglyphis

2021

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Over the last decade, increasing attention has been paid to the molecular adaptations used by organisms to cope with thermal stress. However, to date, few studies have focused on thermophilic species living in hot, arid climates. In this study, we explored molecular adaptations to heat stress in the thermophilic ant genus Cataglyphis, one of the world's most thermotolerant animal taxa. We compared heat tolerance and gene expression patterns across six Cataglyphis species from distinct phylogenetic groups that live in different habitats and experience different thermal regimes. We found that all six species had high heat tolerance levels with critical thermal maxima (CT max ) ranging from 43℃ to 45℃ and a median lethal temperature (LT50) ranging from 44.5℃ to 46.8℃. Transcriptome analyses revealed that, although the number of differentially expressed genes varied widely for the six species (from 54 to 1118), many were also shared. Functional annotation of the differentially expressed and co-expressed genes showed that the biological pathways involved in heat-shock responses were similar among species and were associated with four major processes: the regulation of transcriptional machinery and DNA metabolism; the preservation of proteome stability; the elimination of toxic residues; and the maintenance of cellular integrity. Overall, our results suggest that molecular responses to heat stress have been evolutionarily conserved in the ant genus Cataglyphis and that their diversity may help workers withstand temperatures close to their physiological limits.

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“…The reactions were quenched by transferring the reaction mixture onto dry ice at the corresponding times. Ypk1 kinase activity assays ( Figure S4 C) were performed using the incorporation of γ-32P ATP as a readout, as described before ( Viéitez et al., 2020 ).…”

Section: Methodsmentioning

confidence: 99%

A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress

Cited by 15 publications

References 89 publications

Integrative Gene Expression and Metabolic Analysis tool IgemRNA

Integrative Gene Expression and Metabolic Analysis tool IgemRNA

Molecular adaptations to heat stress in the thermophilic ant genus Cataglyphis

Sequence and Structure-Based Analysis of Specificity Determinants in Eukaryotic Protein Kinases

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