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Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
Published on: June 15, 2016
Regulating the regulators: modulators of transcription factor activity.
Logan Everett1, Matthew Hansen, Sridhar Hannenhalli
1Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA. loganje@mail.med.upenn.edu
Methods in Molecular Biology (Clifton, N.J.)
|September 10, 2010
Summary
This study introduces PTM-Switchboard, a database cataloging gene regulatory triplets. It details how post-translational modifications (PTMs) by enzymes control transcription factor (TF) activity, mapping cellular signals to gene expression.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Gene transcription is primarily controlled by DNA-binding transcription factors (TFs).
- TF activity is dynamically regulated by post-translational modifications (PTMs) in response to cellular signals.
- TF-PTMs act as crucial molecular switches linking upstream signaling to downstream gene regulation.
Purpose of the Study:
- To establish a systematic catalog of known regulatory triplets involving TFs, target genes, and modifying enzymes.
- To facilitate the development of computational tools for genome-wide mapping of regulatory triplets.
- To provide a resource for understanding TF regulation by PTMs.
Main Methods:
- Description of the PTM-Switchboard database, which stores gene triplets where TF regulation is PTM-dependent.
- Review of current computational approaches for inferring regulatory triplets from genome-wide data.
- Discussion of future research directions in the field.
Main Results:
- Introduction of PTM-Switchboard, a database resource for gene regulatory triplets.
- Identification of PTMs as key modulators of TF activity and gene regulation.
- Overview of computational strategies for identifying regulatory relationships.
Conclusions:
- PTM-Switchboard serves as a foundational resource for studying TF-PTM regulatory networks.
- Systematic cataloging is essential for developing advanced computational methods to map regulatory triplets.
- Further research is needed to fully elucidate the complex interplay between TFs, PTMs, and gene expression.
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