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Yeasts are single-celled organisms, but unlike bacteria, they are eukaryotes (cells with a nucleus). Cell signaling in yeast is similar to signaling in other eukaryotic cells. A ligand, such as a protein or a small molecule released from a yeast cell, attaches to a receptor on the cell surface. The binding stimulates second-messenger kinases to activate or inactivate transcription factors that further regulate gene expression. Many of the yeast intracellular signaling cascades have similar...
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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Mapping yeast transcriptional networks.

Timothy R Hughes1, Carl G de Boer

  • 1Banting and Best Department of Medical Research and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.

Genetics
|September 11, 2013
PubMed
Summary
This summary is machine-generated.

Mapping yeast transcriptional networks reveals key regulators but faces challenges. Renewed systematic efforts are needed for a complete understanding of gene regulation mechanisms in Saccharomyces cerevisiae.

Keywords:
chromatingene expressionregulatory networkstranscription factorsyeast

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Area of Science:

  • Molecular Biology
  • Systems Biology
  • Genetics

Background:

  • Transcriptional networks govern coordinated gene expression through transcription factors (TFs) and their interactions with gene promoters.
  • Extensive research in Saccharomyces cerevisiae has focused on mapping these networks over the past two decades.
  • Key data types include TF sequence preferences, in vivo promoter occupancy, and gene expression changes in TF deletion mutants.

Purpose of the Study:

  • To review the methodologies, achievements, and challenges in mapping yeast transcriptional networks.
  • To highlight the progress made in identifying gene regulators and understanding yeast gene regulation.
  • To propose future directions for comprehensive mapping of transcriptional regulatory mechanisms.

Main Methods:

  • Review of existing literature on yeast transcriptional network studies.
  • Analysis of data on transcription factor sequence preferences.
  • Examination of in vivo promoter occupancy data and gene expression profiles from mutant studies.

Main Results:

  • Systematic studies have identified numerous regulators of cellular functions and illuminated yeast gene regulation organization.
  • Data exist for most yeast TFs regarding sequence preferences, promoter binding, and expression profiles.
  • Many TFs are inactive under standard lab conditions, and some data were generated using outdated techniques.

Conclusions:

  • Despite significant progress, comprehensive and accurate mapping of TF binding and its effect on gene expression remains challenging.
  • Existing datasets provide a foundation but require updated methodologies for complete accuracy.
  • A renewed, systematic approach is essential to fully elucidate yeast transcriptional regulatory mechanisms.