Linking yeast Gcn5p catalytic function and gene regulation using a quantitative, graded dominant mutant approach.

PloS One
Amanda M LanzaHal S Alper

Abstract

Establishing causative links between protein functional domains and global gene regulation is critical for advancements in genetics, biotechnology, disease treatment, and systems biology. This task is challenging for multifunctional proteins when relying on traditional approaches such as gene deletions since they remove all domains simultaneously. Here, we describe a novel approach to extract quantitative, causative links by modulating the expression of a dominant mutant allele to create a function-specific competitive inhibition. Using the yeast histone acetyltransferase Gcn5p as a case study, we demonstrate the utility of this approach and (1) find evidence that Gcn5p is more involved in cell-wide gene repression, instead of the accepted gene activation associated with HATs, (2) identify previously unknown gene targets and interactions for Gcn5p-based acetylation, (3) quantify the strength of some Gcn5p-DNA associations, (4) demonstrate that this approach can be used to correctly identify canonical chromatin modifications, (5) establish the role of acetyltransferase activity on synthetic lethal interactions, and (6) identify new functional classes of genes regulated by Gcn5p acetyltransferase activity--all six of these major ...Continue Reading

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Datasets Mentioned

BETA
GSE26923

Methods Mentioned

BETA
gene knockout
acetylation
histone acetylation
gene knockouts
ChIP
PCR
Bioscreen
Fluorescence
FACS
Genome Sequencing

Software Mentioned

Affy
Chromatin DB
Expression Console Software
OrOperator
Metamorph
Affymetrix
Linear Models for Microarray Data ( LIMMA )
Bioconductor

Related Concepts

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