Extreme restructuring of < i > cis < /i > -regulatory regions controlling a deeply conserved plant stem cell regulator

by Danielle Ciren, Sophia Zebell, Zachary B. Lippman A striking paradox is that genes with conserved protein sequence, function and expression pattern over deep time often exhibit extremely divergentcis-regulatory sequences. It remains unclear how such drasticcis-regulatory evolution across species allows preservation of gene function, and to what extent these differences influence howcis-regulatory variation arising within species impacts phenotypic change. Here, we investigated these questions using a plant stem cell regulator conserved in expression pattern and function over ~125 million years. Usingin-vivo genome editing in two distantly related models,Arabidopsis thaliana (Arabidopsis) andSolanum lycopersicum (tomato), we generated over 70 deletion alleles in the upstream and downstream regions of the stem cell repressor geneCLAVATA3 (CLV3) and compared their individual and combined effects on a shared phenotype, the number of carpels that make fruits. We found that sequences upstream of tomatoCLV3 are highly sensitive to even small perturbations compared to its downstream region. In contrast, ArabidopsisCLV3 function is tolerant to severe disruptions both upstream and downstream of the coding sequence. Combining upstream and downstream deletions also revealed a different regulatory outcome. Whereas phenotypic enhancement from adding downstream mutations was predominantly weak and additive in tomato, mutating both regions of ArabidopsisCLV3 caused substantial and synerg...
Source: PLoS Genetics - Category: Genetics & Stem Cells Authors: Source Type: research