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Massively Parallel Reporter Assays in Cultured Mammalian Cells

Massively Parallel Reporter Assays in Cultured Mammalian Cells

Published on: August 17, 2014

Promoter sequence determines the relationship between expression level and noise.

Lucas B Carey¹, David van Dijk, Peter M A Sloot

¹Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.

|April 9, 2013

Summary

This summary is machine-generated.

Cellular gene expression noise changes with transcription factor (TF) activity. Different regulatory mechanisms controlling TF targets impact noise levels, revealing distinct cellular transcriptional states.

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Area of Science:

Molecular Biology
Systems Biology
Genetics

Background:

Cellular gene expression is inherently noisy due to stochastic transcriptional regulation.
Understanding how transcription factor (TF) activity influences this noise and affects target genes is crucial but largely unknown.

Purpose of the Study:

To investigate how cell-to-cell variability in gene expression (noise) changes with transcription factor Zap1 activity.
To determine if different regulatory mechanisms of Zap1 targets impact expression noise similarly.

Main Methods:

Measured gene expression and noise for 16 native Zap1 targets across varying TF activities.
Employed kinetic modeling to understand the mechanisms influencing transcriptional bursts.

Main Results:

For most Zap1 targets, gene expression noise decreased as expression levels increased.
Zap1-mediated repression via promoter DNA reduced transcriptional burst size, leading to low expression and low noise.
Co-activation and repression by a single TF further reduced noise.

Conclusions:

Gene expression noise dynamics are specific to the regulatory mechanism of each gene.
TF concentration influences whether burst frequency or size dominates expression variability.