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Published on: February 11, 2019
Identification of transcription factor targets by phenotypic activation and microarray expression profiling in yeast
1Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4. gchua@ucalgary.ca
Methods in Molecular Biology (Clifton, N.J.)
|June 13, 2009
Summary
Identifying yeast transcription factors (TFs) and their targets is challenging. This study introduces phenotypic activation via overexpression to identify active TFs and their physiological roles, enabling large-scale TF characterization.
Area of Science:
- Molecular Biology
- Genetics
- Systems Biology
Background:
- Identifying physiological transcriptional targets is hindered by unknown induction conditions for most yeast transcription factors (TFs).
- Standard growth conditions render most TFs inactive, complicating functional studies.
- A significant portion of yeast TFs remain uncharacterized regarding their regulatory roles.
Purpose of the Study:
- To develop and validate a high-throughput method for identifying active transcription factors (TFs) in yeast.
- To characterize the transcriptional targets and physiological functions of TFs activated by overexpression.
- To discover novel DNA-binding sequences and regulatory networks.
Main Methods:
- Screening of yeast open reading frames (ORFs) for TFs causing reduced fitness upon overexpression (phenotypic activation).
- Microarray expression profiling of TF overexpression strains.
- Bioinformatic analysis including data analysis and motif searching to identify TF binding sites and regulated genes.
Main Results:
- Approximately one-third of yeast TFs exhibited phenotypic activation upon overexpression.
- Differentially regulated genes often corresponded to known physiological functions and targets of well-characterized TFs.
- Novel DNA-binding sequences and putative targets were identified for less-characterized TFs.
Conclusions:
- Phenotypic activation is an effective strategy for large-scale characterization of transcription factors (TFs) and their targets.
- This approach facilitates the identification of active TFs and their roles under specific conditions.
- The methodology is potentially applicable to TF characterization in other organisms.
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