Characterization of global gene expression during assurance of lifespan extension by caloric restriction in budding yeast

Background: Current therapeutic options in the course of metastatic castration-resistant prostate cancers (mCRPC) reinforce the need for reliable tools to characterize the tumor in a dynamic way. Circulating tumor cells (CTCs) have emerged as a viable solution to the problem, whereby patients with a variety of solid tumors, including PC, often do not have recent tumor tissue available for analysis. The biomarker characterization in CTCs could provide insights into the current state of the disease and an overall picture of the intra-tumor heterogeneity. Methods: in the present study, we applied a global gene expression characterization of the CTC population from mCRPC (n = 9), with the goal to better understand the biology of these cells and identify the relevant molecules favoring this tumor progression. Results: This analysis allowed the identification of 50 genes specifically expressed in CTCs from patients. Six of these markers (HOXB13, QKI, MAOA, MOSPD1, SDK1, and FGD4), were validated in a cohort of 28 mCRPC, showing clinical interest for the management of these patients. Of note, the activity of this CTC signature was related to the regulation of MYC, a gene strongly implicated in the biology of mCRPC. Conclusions: Overall, our results represent new evidence on the great value of CTCs as a non-invasive biopsy to characterize PC.

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Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast

Genetics ◽

10.1534/genetics.119.302978 ◽

2020 ◽

Vol 214 (3) ◽

pp. 651-667 ◽

Cited By ~ 2

Author(s):

Marco Di Stefano ◽

Francesca Di Giovanni ◽

Vasilisa Pozharskaia ◽

Mercè Gomar-Alba ◽

Davide Baù ◽

...

Keyword(s):

Gene Expression ◽

Budding Yeast ◽

Nuclear Organization ◽

Nuclear Periphery ◽

Three Dimensional ◽

Global Gene Expression ◽

3D Genome ◽

Expression Of Genes ◽

Genome Wide ◽

Chromosome Fusions

The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain 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 modeling and single-cell imaging to determine chromosome positions, 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 the expression of genes displaced away from the periphery. The increase in transcription is inversely proportional to the propensity of a given locus to be at the nuclear periphery; for example, a 10% decrease in the propensity of a gene to reside at the nuclear envelope is accompanied by a 10% increase in gene expression. Modeling suggests that this is due to both deletion of telomeres and to displacement of genes relative to the nuclear periphery. These data suggest that basal transcriptional activity is sensitive to radial changes in gene position, and provide insight into the functional relevance of budding yeast chromosome-level 3D organization in gene expression.

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Genome-Wide Analysis of the Relationship between Transcriptional Regulation by Rpd3p and the Histone H3 and H4 Amino Termini in Budding Yeast

Molecular and Cellular Biology ◽

10.1128/mcb.24.20.8823-8833.2004 ◽

2004 ◽

Vol 24 (20) ◽

pp. 8823-8833 ◽

Cited By ~ 35

Author(s):

Nevin Sabet ◽

Sam Volo ◽

Cailin Yu ◽

James P. Madigan ◽

Randall H. Morse

Keyword(s):

Gene Expression ◽

Budding Yeast ◽

Histone H3 ◽

Global Gene Expression ◽

Amino Terminus ◽

Histone H4 ◽

Histone Tails ◽

Genome Wide ◽

Lysine Residues ◽

The Relationship

ABSTRACT The histone amino termini have emerged as key targets for a variety of modifying enzymes that function as transcriptional coactivators and corepressors. However, an important question that has remained largely unexplored is the extent to which specific histone amino termini are required for the activating and repressive functions of these enzymes, Here we address this issue by focusing on the prototypical histone deacetylase, Rpd3p, in the budding yeast Saccharomyces cerevisiae. We show that targeting Rpd3p to a reporter gene in this yeast can partially repress transcription when either the histone H3 or the histone H4 amino terminus is deleted, indicating that the “tails” are individually dispensable for repression by Rpd3p. In contrast, we find that the effect of rpd3 gene disruption on global gene expression is considerably reduced in either a histone H3Δ1-28 (H3 lacking the amino-terminal 28 amino acids) or a histone H4(K5,8,12,16Q) (H4 with lysine residues 5, 8, 12, and 16 changed to glutamine residues) background compared to the wild-type background, indicating a requirement for one or both of these histone tails in Rpd3p-mediated regulation for many genes. These results suggest that acetylation of either the H3 or the H4 amino terminus could suffice to allow the activation of such genes. We also examine the relationship between H3 tails and H4 tails in global gene expression and find substantial overlap among the gene sets regulated by these histone tails. We also show that the effects on genome-wide expression of deleting the H3 or H4 amino terminus are similar but not identical to the effects of mutating the lysine residues in these same regions. These results indicate that the gene regulatory potential of the H3 and H4 amino termini is substantially but not entirely contained in these modifiable lysine residues.

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Intestinal DCs global gene expression dynamics affected by recombinant baker’s yeasts saccharomyces cerevisiae

10.21203/rs.2.9896/v1 ◽

2019 ◽

Author(s):

Baoquan Han ◽

Tingting Zhang ◽

Xinyi Li ◽

Rui Zhao ◽

Wei Ge ◽

...

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Inflammatory Response ◽

Budding Yeast ◽

Global Gene Expression ◽

Transcriptome Profile ◽

Delivery Vehicle ◽

Gene Delivery Vehicle ◽

Gene Expression Dynamics

Abstract Background The baker’s yeast, saccharomyces cerevisiae, has been widely used throughout our daily life in diverse aspects for thousands of years. The saccharomyces cerevisiae was found to specifically target the dendritic cells (DCs) in mammalian with a manner of antigen-receptor interaction as described previously. It is necessary to investigate the effect of the baker’s yeasts on global gene expression dynamics of intestinal DCs and explore the possibilities of using baker’s yeast as gene delivery vehicle to modulate animal’s immune functions Results with a murine oral delivery model in vivo, we confirmed the feasibility of using budding yeast as gene delivery vehicle to the intestinal DCs using the Western blots. We then examined the transcriptome profile of the mouse intestinal DCs upon yeast stimulus. The enrichment analysis of unique transcripts indicated the beneficial role of yeast in modulating the DC-mediated adaptive immunity. Compared with previous study, we also found that a large fraction of the regulated genes is coincident with the response induced by other fungus, suggesting that the budding yeast induces a similar tailored unique genetic re-programming of DCs. Another analysis of transcriptome profile indicated that expression of β-catenin gene significantly changes DCs gene expression related to inflammatory response and cell adhesion. Conclusions Here, we defined the role of budding yeast on global gene expression of intestinal DCs, and confirmed the important role of β-catenin gene on the DCs-related inflammatory response, which provides a framework for the development of mucosa yeast-based DNA vaccine.

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