Intersecting transcription networks constrain gene regulatory evolution.

Bibliographic Collection: 
Publication Type: Journal Article
Authors: Sorrells, Trevor R; Booth, Lauren N; Tuch, Brian B; Johnson, Alexander D
Year of Publication: 2015
Journal: Nature
Volume: 523
Issue: 7560
Pagination: 361-5
Date Published: 2015 Jul 16
Publication Language: eng
ISSN: 1476-4687
Keywords: Base Sequence, Binding Sites, DNA, Fungal, DNA-Binding Proteins, Enhancer Elements, Genetic, Epistasis, Genetic, Evolution, Molecular, Gene Expression Regulation, Fungal, Gene Regulatory Networks, Genes, Fungal, Kluyveromyces, Peptides, Pheromones, Promoter Regions, Genetic, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors

Epistasis-the non-additive interactions between different genetic loci-constrains evolutionary pathways, blocking some and permitting others. For biological networks such as transcription circuits, the nature of these constraints and their consequences are largely unknown. Here we describe the evolutionary pathways of a transcription network that controls the response to mating pheromone in yeast. A component of this network, the transcription regulator Ste12, has evolved two different modes of binding to a set of its target genes. In one group of species, Ste12 binds to specific DNA binding sites, while in another lineage it occupies DNA indirectly, relying on a second transcription regulator to recognize DNA. We show, through the construction of various possible evolutionary intermediates, that evolution of the direct mode of DNA binding was not directly accessible to the ancestor. Instead, it was contingent on a lineage-specific change to an overlapping transcription network with a different function, the specification of cell type. These results show that analysing and predicting the evolution of cis-regulatory regions requires an understanding of their positions in overlapping networks, as this placement constrains the available evolutionary pathways.

DOI: 10.1038/nature14613
Alternate Journal: Nature