Widespread Impact of Chromosomal Inversions on Gene Expression Uncovers Robustness via Phenotypic Buffering

Abstract

The nonrandom gene organization in eukaryotes plays a significant role in genome evolution and function. Chromosomal structural changes impact meiotic fitness and, in several organisms, are associated with speciation and rapid adaptation to different environments. Small sized chromosomal inversions, encompassing few genes, are pervasive in Saccharomyces “sensu stricto” species, while larger inversions are less common in yeasts compared with higher eukaryotes. To explore the effect of gene order on phenotype, reproductive isolation, and gene expression, we engineered 16 Saccharomyces cerevisiae strains carrying all possible paracentric and pericentric inversions between Ty1 elements, a natural substrate for rearrangements. We found that 4 inversions were lethal, while the other 12 did not show any fitness advantage or disadvantage in rich and minimal media. At meiosis, only a weak negative correlation with fitness was seen with the size of the inverted region. However, significantly lower fertility was seen in heterozygote invertant strains carrying recombination hotspots within the breakpoints. Altered transcription was observed throughout the genome rather than being overrepresented within the inversions. In spite of the large difference in gene expression in the inverted strains, mitotic fitness was not impaired in the majority of the 94 conditions tested, indicating that the robustness of the expression network buffers the deleterious effects of structural changes in several environments. Overall, our results support the notion that transcriptional changes may compensate for Ty-mediated rearrangements resulting in the maintenance of a constant phenotype, and suggest that large inversions in yeast are unlikely to be a selectable trait during vegetative growth.

Young inversion with multiple linked QTLs under selection in a hybrid zone

“…Although inversions can be engineered for proof of function in some organisms 30 , this is infeasible in Boechera . However, the KB model predicts that relatives of the ancestral haplotype that gave rise to the inversion might still exist as non-inverted genotypes nearby.…”

Nanopore sequencing enables near-completede novoassembly ofSaccharomyces cerevisiaereference strain CEN.PK113-7D

“…Identification of this translocation required reads to span at least 12 Kbp due to the large repetitive elements surrounding the translocation breakpoints, explaining why it was previously undetected. While the translocation did not disrupt any coding sequence and is unlikely to cause phenotypical changes (Naseeb et al 2016), there may be decreased spore viability upon mating with other CEN.PK strains. Our ability to detect structural heterogeneity within a culture shows that nanopore sequencing could also be valuable in detecting structural variation within a genome between different chromosome copies, which occurs frequently in aneuploid yeast genomes (Gorter de Vries, Pronk and Daran 2017).…”

History of genome editing in yeast

“…It has been shown that S. cerevisiae strains carrying single gene inversions can cause fitness defects in nutrient‐limited media (Naseeb & Delneri, ). However, large chromosomal inversions in S. cerevisiae can be either lethal or neutral depending upon the environmental conditions (Naseeb et al, ). Similar findings were observed by Avelar et al () in S. pombe , showing that inversions and translocations can have beneficial or deleterious growth affects for both meiotic and mitotic fitness.…”

“…Therefore, by the action of the Cre recombinase, the selectable marker can be rescued, leaving only one loxP 'scar' in the genome. The key benefit of this system is that the Cre recombinase can catalyse either multiple gene deletions (Akada et al, 2006), inversions (Naseeb et al, 2016;Naseeb & Delneri, 2012) or translocations of a chromosomal fragment (Delneri et al, 2003) depending on the orientation and location of loxP sequences flanking that fragment. When multiple deletions is the objective of the study, the availability of multiple different loxP sequences (Carter & Delneri, 2010) Overview of the yeast genome editing methods described here.…”

“…Alternatively, the Cas9 gene is integrated into the yeast genome and the gRNA is delivered on a plasmid. After expression, the gRNA locates the target sequence and the endonuclease cleaves the foreign DNA that subsequently leads to either NHEJ or HR events [Colour figure can be viewed at wileyonlinelibrary.com] large chromosomal inversions in S. cerevisiae can be either lethal or neutral depending upon the environmental conditions (Naseeb et al, 2016). Similar findings were observed by Avelar et al (2013) in S. pombe, showing that inversions and translocations can have beneficial or deleterious growth affects for both meiotic and mitotic fitness.…”