Model of haplotype and phenotype in the evolution of a duplicated autoregulatory activator

TL;DR

This paper models how regulatory interactions in diploid and haploid genomes influence the evolution and spread of duplicated autoregulatory activator genes, revealing mechanisms for phenotypic diversity and gene backup.

Contribution

It introduces a novel model of haplotype and phenotype evolution in duplicated autoregulatory genes, highlighting the role of allelic interactions and regulatory divergence in gene retention.

Findings

Mutually exclusive expression states emerge from cis-regulatory divergence.

Heterozygous diploid genotypes enable stable and transient phenotypic oscillations.

Haplotype inheritance models show how phenotypic states facilitate gene duplication spread.

Abstract

Gene duplication is believed to play a major role in the evolution of genomic complexity. The presence of a duplicate removes the constraint of natural selection upon the gene, leading to its likely loss of function or, occasionally, the gain of a novel one. Alternately, a pleiotropic gene might partition its functions among its duplicates, thus preserving both copies. Duplicate genes is not a novelty for diploid genotypes, but only for haplotypes. In this paper, we study the consequences of regulatory interactions in diploid genotypes and explore how the context of allelic interactions gives rise to dynamical phenotypes that enable duplicate genes to spread in a population. The regulatory network we study is that of a single autoregulatory activator gene, and the two copies of the gene diverge either as alleles in a diploid species or as duplicates in haploids. These differences are in their transcriptional ability -- either via alterations to its activating domain, or to its cis-regulatory binding repertoire. When cis-regulatory changes are introduced that partition multiple regulatory triggers among the duplicates, it is shown that mutually exclusive expression states of the duplicates that emerge are accompanied by a back-up facility: when a highly expressed gene is deleted, the previously unexpressed duplicate copy compensates for it. The diploid version of the regulatory network model can account for allele-specific expression variants, and a model of inheritance of the haplotype network enables us to trace the evolutionary consequence of heterozygous phenotypes. This is modelled for the variations in the activating domain of one copy, whereby stable as well as transiently bursting oscillations ensue in single cells. The evolutionary model shows that these phenotypic states accessible to a diploid, heterozygous genotype enable the spread of a duplicated haplotype.