Biology subjects

Carey, L. B.

Publications and source records attributed to Carey, L. B..

7 recordsLinked to original sources

bioRxiv2018

Empirical noise-mean fitness landscapes and the evolution of gene expression

The effects of cell-to-cell variation (noise) in gene expression have proven difficult to quantify, in part due to the mechanistic coupling of noise to mean expression. To independently evaluate the effects of changes in expression mean and noise we determined the fitness landscapes in mean-noise expression space for 33 genes in yeast. The landscapes can be decomposed into two principal topologies: the fitness effects of protein shortage and surplus. For most genes, the fitness impact of sustained (mean) and short-lived (noise) deviations away from the expression optimum are linked and of similar magnitude. Sensitivity to both protein shortage and surplus creates a fitness landscape in which an epistatic ratchet uncouples the evolution of noise from mean expression, promoting noise minimization. These results demonstrate that noise is detrimental for many genes and reveal non-trivial consequences of mean-noise-fitness topologies for the evolution of gene expression systems.\n\nHighlights- Expression fitness landscapes in mean-noise space allow quantitative independent assessment of the effects of noise and mean expression on fitness for 33 genes\n- Landscapes are described by a combination of just two principal topologies: fitness defects due protein shortage, or due to protein surplus\n- Direct evidence that high expression noise is detrimental to fitness for 50% of genes\n- Mean expression and noise have equivalent impact on organismal fitness\n- Landscapes created by sensitivities to protein shortage and surplus facilitate independent evolution of gene expression noise via an epistatic ratchet

systems biology↗

bioRxiv2018

Budding yeast complete DNA replication after chromosome segregation begins

To faithfully transmit genetic information, cells must replicate their entire genome before division. This is thought to be ensured by the temporal separation of replication and chromosome segregation. Here we show that in a substantial fraction of unperturbed yeast cells, DNA replication finishes during anaphase, late in mitosis. High cyclin-Cdk activity inhibits replication in metaphase, and the decrease in cyclin-Cdk activity during mitotic exit allows DNA replication to finish at difficult-to-replicate regions. Replication during late mitosis correlates with elevated mutation rates, including copy number variation. Thus, yeast cells temporally overlap replication and chromosome segregation during normal growth, possibly allowing cells to maximize population-level growth rate while simultaneously exploring greater genetic space.\n\nOne Sentence SummaryCompletion of DNA replication is coupled to downregulation of Cyclin-Dependent Kinase during mitotic exit.

cell biology↗

bioRxiv2018

Overdosage of balanced protein complexes reduces proliferation rate in aneuploid cells

Cells with complex aneuploidies, such as tumor cells, display a wide range of phenotypic abnormalities. However, molecular basis for this has been mainly studied in trisomic (2n+1) and disomic (n+1) cells. To determine how karyotype affects proliferation rate in cells with complex aneuploidies we generated forty 2n+x yeast strains in which each diploid cell has an extra 5 to 12 chromosomes and found that these strains exhibited abnormal cell-cycle progression. Proliferation rate was negatively correlated with the number of protein complexes in which all subunits were at the 3-copy level, but not with the number of imbalanced complexes made up of a mixture of 2-copy and 3-copy genes. Proteomics revealed that most 3-copy members of imbalanced complexes were expressed at only 2n protein levels whereas members of complexes in which all subunits are stoichiometrically balanced at 3 copies per cell had 3n protein levels. We identified individual protein complexes for which overdosage reduces proliferation rate, and found that deleting one copy of each member partially restored proliferation rate in cells with complex aneuploidies. Lastly, we validated this finding using orthogonal datasets from both yeast and from human cancers. Taken together, our study provides a novel explanation how aneuploidy affects phenotype.

systems biology↗

bioRxiv2018

Single cell functional genomics reveals the importance of mitochondria in cell-to-cell variation in proliferation, drug resistance and mutation outcome

Mutations frequently have outcomes that differ across individuals, even when these individuals are genetically identical and share a common environment. Moreover, individual microbial and mammalian cells can vary substantially in their proliferation rates, stress tolerance, and drug resistance, with important implications for the treatment of infections and cancer. To investigate the causes of cell-to-cell variation in proliferation, we developed a high-throughput automated microscopy assay and used it to quantify the impact of deleting >1,500 genes in yeast. Mutations affecting mitochondria were particularly variable in their outcome. In both mutant and wild-type cells mitochondria state - but not content - varied substantially across individual cells and predicted cell-to-cell variation in proliferation, mutation outcome, stress tolerance, and resistance to a clinically used anti-fungal drug. These results suggest an important role for cell-to-cell variation in the state of an organelle in single cell phenotypic variation.

genomics↗

bioRxiv2018

DNA local structure decreases mutation rates

BackgroundMutation rates vary across the genome. Whereas many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7 bp scale, cis elements remain poorly characterized. The lack of understanding why different sequences have different mutation rates hampers our ability to identify positive selection in evolution and to identify driver mutations in tumorigenesis.\n\nResultsHere we show, using a combination of synthetic genes and sequencing of thousands of isolated yeast colonies, that intrinsic DNA curvature is the major cis determinant of mutation rate. Mutation rate negatively correlates with DNA curvature within genes, and a 10% decrease in curvature results in a 70% increase in mutation rate. Consistently, both yeast cells and human tumors accumulate mutations in regions with small curvature. We further show that this effect is due to differences in the intrinsic mutation rate, likely due to differences in mutagen sensitivity, and not due to differences in the local activity of DNA repair.\n\nConclusionsOur study establishes a framework in understanding the cis properties of DNA sequence in modulating the local mutation rate and identifies a novel causal source of non-uniform mutation rates across the genome.

genetics↗

bioRxiv2017

The spatial position of budding yeast chromosomes affects gene expression

The three-dimensional organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remains debated. To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing chromosome fusions. We used computational modelling and single cell imaging to determine chromosome position and integrated these data with genome-wide transcriptional profiles from RNA sequencing. We find that chromosome fusions dramatically alter 3D nuclear organization without leading to strong genome-wide changes in transcription. However, we observe a mild but significant and reproducible increase in expression of genes near fusion sites. Modeling suggests that this is due to both disruption of telomere-associated silencing and the displacement of genes relative to the nuclear periphery. A 10% decrease in the predicted time a gene spends near the nuclear periphery is associated with a 10% increase in expression. These data suggest that basal transcriptional activity is sensitive to radial changes on gene position, and provide insight into the functional relevance of budding yeast chromosome-level three-dimensional organization in gene expression.

cell biology↗

bioRxiv2017

Promoter architecture determines co-translational regulation of mRNA

Information that regulates gene expression is encoded throughout each gene but if different regulatory regions can be understood in isolation, or if they interact, is unknown. Here we measure mRNA levels for 10,000 open reading frames (ORFs) transcribed from either an inducible or constitutive promoter. We find that the strength of co-translational regulation on mRNA levels is determined by promoter architecture. Using a novel computational-genetic screen of 6402 RNA-seq experiments we identify the RNA helicase Dbp2 as the mechanism by which co-translational regulation is reduced specifically for inducible promoters. Finally, we find that for constitutive genes, but not inducible genes, most of the information encoding regulation of mRNA levels in response to changes in growth rate is encoded in the ORF and not in the promoter. Thus the ORF sequence is a major regulator of gene expression, and a non-linear interaction between promoters and ORFs determines mRNA levels.

systems biology↗