A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Katrin Sameith - , University Medical Center (UMC) Utrecht (Author)
  • Saman Amini - , University Medical Center (UMC) Utrecht (Author)
  • Marian J A Groot Koerkamp - , University Medical Center (UMC) Utrecht (Author)
  • Dik van Leenen - , University Medical Center (UMC) Utrecht (Author)
  • Mariel Brok - , University Medical Center (UMC) Utrecht (Author)
  • Nathalie Brabers - , University Medical Center (UMC) Utrecht (Author)
  • Philip Lijnzaad - , University Medical Center (UMC) Utrecht (Author)
  • Sander R van Hooff - , University Medical Center (UMC) Utrecht (Author)
  • Joris J Benschop - , University Medical Center (UMC) Utrecht (Author)
  • Tineke L Lenstra - , University Medical Center (UMC) Utrecht (Author)
  • Eva Apweiler - , University Medical Center (UMC) Utrecht (Author)
  • Sake van Wageningen - , University Medical Center (UMC) Utrecht (Author)
  • Berend Snel - , Utrecht University (Author)
  • Frank C P Holstege - , University Medical Center (UMC) Utrecht (Author)
  • Patrick Kemmeren - , University Medical Center (UMC) Utrecht (Author)

Abstract

BACKGROUND: Genetic interactions, or non-additive effects between genes, play a crucial role in many cellular processes and disease. Which mechanisms underlie these genetic interactions has hardly been characterized. Understanding the molecular basis of genetic interactions is crucial in deciphering pathway organization and understanding the relationship between genotype, phenotype and disease.

RESULTS: To investigate the nature of genetic interactions between gene-specific transcription factors (GSTFs) in Saccharomyces cerevisiae, we systematically analyzed 72 GSTF pairs by gene expression profiling double and single deletion mutants. These pairs were selected through previously published growth-based genetic interactions as well as through similarity in DNA binding properties. The result is a high-resolution atlas of gene expression-based genetic interactions that provides systems-level insight into GSTF epistasis. The atlas confirms known genetic interactions and exposes new ones. Importantly, the data can be used to investigate mechanisms that underlie individual genetic interactions. Two molecular mechanisms are proposed, "buffering by induced dependency" and "alleviation by derepression".

CONCLUSIONS: These mechanisms indicate how negative genetic interactions can occur between seemingly unrelated parallel pathways and how positive genetic interactions can indirectly expose parallel rather than same-pathway relationships. The focus on GSTFs is important for understanding the transcription regulatory network of yeast as it uncovers details behind many redundancy relationships, some of which are completely new. In addition, the study provides general insight into the complex nature of epistasis and proposes mechanistic models for genetic interactions, the majority of which do not fall into easily recognizable within- or between-pathway relationships.

Details

Original languageEnglish
Article number112
JournalBMC biology
Volume13
Publication statusPublished - 23 Dec 2015
Peer-reviewedYes
Externally publishedYes

External IDs

PubMedCentral PMC4690272
Scopus 84951861771
ORCID /0000-0003-4306-930X/work/141545232

Keywords

Keywords

  • Epigenesis, Genetic, Gene Expression Profiling, Gene Library, Gene Ontology, Molecular Sequence Annotation, Mutation, Saccharomyces cerevisiae/genetics, Saccharomyces cerevisiae Proteins/genetics, Transcription Factors/genetics