Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation

Brion, Christian; Lutz, Sheila; Albert, Frank W.

doi:10.7554/elife.60645

Cited by 44 publications

(52 citation statements)

References 115 publications

(195 reference statements)

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“…Similarly, our approach represents a viable strategy for mapping genetic effects on the degradation of individual proteins. Considerable discrepancies exist between genetic influences on gene expression at the mRNA and protein levels 42,71,73 . Many protein-specific QTLs could result from genetic effects on protein degradation, either through loci that alter the activity of protein degradation pathways or the degradation of individual proteins.…”

Section: Discussionmentioning

confidence: 99%

“…between the strains can serve as markers in a genetic mapping experiment 43,44,71,73 .…”

Section: Yeast Strainsmentioning

confidence: 99%

“…We collected populations of segregant cells for QTL mapping using a previously-described approach for isolating phenotypically extreme cell populations by FACS 71,73 . Segregant populations were thawed approximately 16 hours prior to cell sorting and grown overnight in 5 mL of SGA medium containing G418 and canavanine.…”

Section: Fluorescence-activated Cell Sortingmentioning

confidence: 99%

“…We processed sequencing data to identify QTLs using a previously-described approach for genetic mapping by bulk segregant analysis 44,71,73 . We initially filtered reads to include only those reads with mapping quality scores greater than 30.…”

Section: Qtl Mappingmentioning

confidence: 99%

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Variation in Ubiquitin System Genes Creates Substrate-Specific Effects on Proteasomal Protein Degradation

Collins

Mekonnen

Albert

2021

Preprint

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The ubiquitin-proteasome system (UPS) is the cell's primary pathway for targeted protein degradation. Although the molecular mechanisms controlling UPS activity are well-characterized, we have almost no knowledge of how these mechanisms are shaped by heritable genetic variation. To address this limitation, we developed an approach that combines fluorescent UPS activity reporters with a statistically powerful genetic mapping framework to comprehensively characterize genetic influences on UPS activity in the yeast Saccharomyces cerevisiae. We applied this approach to substrates of the UPS N-end rule, which relates a protein's degradation rate to the identity of its N-terminal amino acid ("N-degron") through the Arg/N-end and Ac/N-end pathways. Genetic influences on UPS activity were numerous and complex, comprising 149 loci influencing UPS activity across the 20 N-degrons. Many loci specifically affected individual pathways or degrons and multiple loci exerted divergent effects on distinct UPS pathways. One Arg/N-end pathway-specific locus resulted from multiple causal variants in the promoter, open reading frame, and terminator of the UBR1 E3 ubiquitin ligase gene. These variants differentially affected substrates bound by the Type 1 and Type 2 recognition sites of Ubr1p. Collectively, our results provide the first systematic characterization of genetic influences on UPS activity and a generalizable approach for mapping genetic effects on protein degradation with high statistical power and quantitative precision.

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Section: Discussionmentioning

confidence: 99%

“…between the strains can serve as markers in a genetic mapping experiment 43,44,71,73 .…”

Section: Yeast Strainsmentioning

confidence: 99%

Section: Fluorescence-activated Cell Sortingmentioning

confidence: 99%

Section: Qtl Mappingmentioning

confidence: 99%

See 2 more Smart Citations

Variation in Ubiquitin System Genes Creates Substrate-Specific Effects on Proteasomal Protein Degradation

Collins

Mekonnen

Albert

2021

Preprint

Self Cite

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“…Similarly, recent work has shown that the number of trans -acting loci affecting gene expression throughout the genome may have been greatly underestimated due to linkage in experimental crosses with limited recombination ( Metzger and Wittkopp, 2019 ). These results paint an emerging picture of a highly polygenic architecture of gene expression variation, with dozens of trans -acting loci across the genome ( Albert et al, 2018 ; Albert et al, 2014b ; Brion et al, 2020 ; Metzger and Wittkopp, 2019 ), each of which may harbor multiple causal variants.…”

Section: Discussionmentioning

confidence: 99%

Systematic identification of cis-regulatory variants that cause gene expression differences in a yeast cross

Renganaath

Cheung

Day

et al. 2020

eLife

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Sequence variation in regulatory DNA alters gene expression and shapes genetically complex traits. However, the identification of individual, causal regulatory variants is challenging. Here, we used a massively parallel reporter assay to measure the cis-regulatory consequences of 5832 natural DNA variants in the promoters of 2503 genes in the yeast Saccharomyces cerevisiae. We identified 451 causal variants, which underlie genetic loci known to affect gene expression. Several promoters harbored multiple causal variants. In five promoters, pairs of variants showed non-additive, epistatic interactions. Causal variants were enriched at conserved nucleotides, tended to have low derived allele frequency, and were depleted from promoters of essential genes, which is consistent with the action of negative selection. Causal variants were also enriched for alterations in transcription factor binding sites. Models integrating these features provided modest, but statistically significant, ability to predict causal variants. This work revealed a complex molecular basis for cis-acting regulatory variation.

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Comparative analysis of diisononyl phthalate and di(isononyl)cyclohexane‐1,2 dicarboxylate plasticizers in regulation of lipid metabolism in 3T3‐L1 cells

Bereketoglu,

Häggblom,

Turanlı

et al. 2023

Environmental Toxicology

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Diisononyl phthalate (DINP) and di(isononyl)cyclohexane‐1,2‐dicarboxylate (DINCH) are plasticizers introduced to replace previously used phthalate plasticizers in polymeric products. Exposure to DINP and DINCH has been shown to impact lipid metabolism. However, there are limited studies that address the mechanisms of toxicity of these two plasticizers. Here, a comparative toxicity analysis has been performed to evaluate the impacts of DINP and DINCH on 3T3‐L1 cells. The preadipocyte 3T3‐L1 cells were exposed to 1, 10, and 100 μM of DINP or DINCH for 10 days and assessed for lipid accumulation, gene expression, and protein analysis. Lipid staining showed that higher concentrations of DINP and DINCH can induce adipogenesis. The gene expression analysis demonstrated that both DINP and DINCH could alter the expression of lipid‐related genes involved in adipogenesis. DINP and DINCH upregulated Pparγ, Pparα, C/EBPα Fabp4, and Fabp5, while both compounds significantly downregulated Fasn and Gata2. Protein analysis showed that both DINP and DINCH repressed the expression of FASN. Additionally, we analyzed an independent transcriptome dataset encompassing temporal data on lipid differentiation within 3T3‐L1 cells. Subsequently, we derived a gene set that accurately portrays significant pathways involved in lipid differentiation, which we subsequently subjected to experimental validation through quantitative polymerase chain reaction. In addition, we extended our analysis to encompass a thorough assessment of the expression profiles of this identical gene set across 40 discrete transcriptome datasets that have linked to diverse pathological conditions to foreseen any potential association with DINP and DINCH exposure. Comparative analysis indicated that DINP could be more effective in regulating lipid metabolism.

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Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation

Cited by 44 publications

References 115 publications

Variation in Ubiquitin System Genes Creates Substrate-Specific Effects on Proteasomal Protein Degradation

Variation in Ubiquitin System Genes Creates Substrate-Specific Effects on Proteasomal Protein Degradation

Systematic identification of cis-regulatory variants that cause gene expression differences in a yeast cross

Comparative analysis of diisononyl phthalate and di(isononyl)cyclohexane‐1,2 dicarboxylate plasticizers in regulation of lipid metabolism in 3T3‐L1 cells

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