Dataset Information

Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae.

ABSTRACT:

Background

Generation of induced pluripotent stem cells (iPSCs) and converting one cell type to another (transdifferentiation) by manipulating the expression of a small number of genes highlight the progress of cellular reprogramming, which holds great promise for regenerative medicine. A key challenge is to find the recipes of perturbing genes to achieve successful reprogramming such that the reprogrammed cells function in the same way as the natural cells.

Results

We present here a systems biology approach that allows systematic search for effective reprogramming recipes and monitoring the reprogramming progress to uncover the underlying mechanisms. Using budding yeast as a model system, we have curated a genetic network regulating cell cycle and sporulation. Phenotypic consequences of perturbations can be predicted from the network without any prior knowledge, which makes it possible to computationally reprogram cell fate. As the heterogeneity of natural cells is important in many biological processes, we find that the extent of this heterogeneity restored by the reprogrammed cells varies significantly upon reprogramming recipes. The heterogeneity difference between the reprogrammed and natural cells may have functional consequences.

Conclusions

Our study reveals that cellular reprogramming can be achieved by many different perturbations and the reprogrammability of a cell depends on the heterogeneity of the original cell state. We provide a general framework that can help discover new recipes for cellular reprogramming in human.

SUBMITTER: Ding S

PROVIDER: S-EPMC3094211 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature

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Publications

Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae.

Ding Shengchao S Wang Wei W

BMC systems biology 20110412

<h4>Background</h4>Generation of induced pluripotent stem cells (iPSCs) and converting one cell type to another (transdifferentiation) by manipulating the expression of a small number of genes highlight the progress of cellular reprogramming, which holds great promise for regenerative medicine. A key challenge is to find the recipes of perturbing genes to achieve successful reprogramming such that the reprogrammed cells function in the same way as the natural cells.<h4>Results</h4>We present her ...[more]

PMID: 21486480

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Project description:In the budding yeast Saccharomyces cerevisiae, transcription factors (TFs) regulate the periodic expression of many genes during the cell cycle, including gene products required for progression through cell-cycle events. Experimental evidence coupled with quantitative models suggests that a network of interconnected TFs is capable of regulating periodic genes over the cell cycle. Importantly, these dynamical models were built on transcriptomics data and assumed that TF protein levels and activity are directly correlated with mRNA abundance. To ask whether TF transcripts match protein expression levels as cells progress through the cell cycle, we applied a multiplexed targeted mass spectrometry approach (parallel reaction monitoring) to synchronized populations of cells. We found that protein expression of many TFs and cell-cycle regulators closely followed their respective mRNA transcript dynamics in cycling wild-type cells. Discordant mRNA/protein expression dynamics was also observed for a subset of cell-cycle TFs and for proteins targeted for degradation by E3 ubiquitin ligase complexes such as SCF (Skp1/Cul1/F-box) and APC/C (anaphase-promoting complex/cyclosome). We further profiled mutant cells lacking B-type cyclin/CDK activity ( clb1-6) where oscillations in ubiquitin ligase activity, cyclin/CDKs, and cell-cycle progression are halted. We found that a number of proteins were no longer periodically degraded in clb1-6 mutants compared with wild type, highlighting the importance of posttranscriptional regulation. Finally, the TF complexes responsible for activating G1/S transcription (SBF and MBF) were more constitutively expressed at the protein level than at periodic mRNA expression levels in both wild-type and mutant cells. This comprehensive investigation of cell-cycle regulators reveals that multiple layers of regulation (transcription, protein stability, and proteasome targeting) affect protein expression dynamics during the cell cycle.

Project description:It is essential that cells orchestrate gene expression for the specific niche that they occupy, and this often requires coordination of the expression of large sets of genes. There are multiple regulatory systems that exist for modulation of gene expression, including the adjacent-gene coregulation of the rRNA and ribosome biogenesis and ribosomal protein families. Both gene families exhibit a nonrandom genomic distribution, often clustered directly adjacent to another member of the same family, which results in a tighter transcriptional coordination among adjacent paired genes than that of the unpaired genes within each regulon and can result in a shared promoter that coordinates expression of the pairs. This nonrandom genomic distribution has been seen in a few functionally related gene families, and many of these functional pairings are conserved across divergent fungal lineages. To date, the significance of these observations has not been extended in a systematic way to characterize how prevalent the role of adjacent-gene coregulation is in transcriptional regulation. In the present study, we systematically analyzed the transcriptional coherence of the functional pairs compared to the singletons within all gene families defined by the Gene Ontology Slim designation, using Saccharomyces cerevisiae as a model system, finding that clusters exhibit a tighter transcriptional correlation under specific contexts. We found that the longer a functional pairing is conserved the tighter its response to broad stress and nutritional responses, that roughly 25% of gene families exhibit a nonrandom genomic distribution, and that many of these clusters are conserved. This suggests that adjacent-gene coregulation is a widespread, yet underappreciated, transcriptional mechanism.IMPORTANCE The spatial positioning of genes throughout the genome arrangement can alter their expression in many eukaryotic organisms. Often this results in a genomic context-specific effect on transcription. One example of this is through the clustering of functionally related genes, which results in adjacent-gene coregulation in the budding yeast Saccharomyces cerevisiae In the present study, we set out to systematically characterize the prevalence of this phenomenon, finding the genomic organization of functionally related genes into clusters is a characteristic of myriad gene families. These arrangements are found in many evolutionarily divergent fungi and thus represent a widespread, yet underappreciated, layer of transcriptional regulation.

Dataset Information

Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae.

Background

Results

Conclusions

Publications

Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae.

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