Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella

Christine Rempfer,Gertrud Wiedemann,Gabriele Schween,Jan M Lucht,Ralf Horres,Eva L Decker,Klaus L Kerres,Ralf Reski

doi:10.1007/s00299-021-02794-2

Abstract

Key messageIn Physcomitrella, whole-genome duplications affected the expression of about 3.7% of the protein-encoding genes, some of them relevant for DNA repair, resulting in a massively reduced gene-targeting frequency.Qualitative changes in gene expression after an autopolyploidization event, a pure duplication of the whole genome (WGD), might be relevant for a different regulation of molecular mechanisms between angiosperms growing in a life cycle with a dominant diploid sporophytic stage and the haploid-dominant mosses. Whereas angiosperms repair DNA double-strand breaks (DSB) preferentially via non-homologous end joining (NHEJ), in the moss Physcomitrella homologous recombination (HR) is the main DNA–DSB repair pathway. HR facilitates the precise integration of foreign DNA into the genome via gene targeting (GT). Here, we studied the influence of ploidy on gene expression patterns and GT efficiency in Physcomitrella using haploid plants and autodiploid plants, generated via an artificial WGD. Single cells (protoplasts) were transfected with a GT construct and material from different time-points after transfection was analysed by microarrays and SuperSAGE sequencing. In the SuperSAGE data, we detected 3.7% of the Physcomitrella genes as differentially expressed in response to the WGD event. Among the differentially expressed genes involved in DNA–DSB repair was an upregulated gene encoding the X-ray repair cross-complementing protein 4 (XRCC4), a key player in NHEJ. Analysing the GT efficiency, we observed that autodiploid plants were significantly GT suppressed (p < 0.001) attaining only one third of the expected GT rates. Hence, an alteration of global transcript patterns, including genes related to DNA repair, in autodiploid Physcomitrella plants correlated with a drastic suppression of HR.

Highlights

The duplication of entire genomes leads to polyploidy and occurs in many cell types and organisms
We assume that transformation of the genome (= integration of the heterologous DNA) is completed before the first cell division of the protoplast, that happens under our conditions within the first 72 h
At 24 h, 933 additional differentially expressed genes (DEGs) that were not identified at earlier time-points were detectable. 10 of the DEGs detected at 4 h and 6 h were not significantly differentially expressed at 24 h anymore

Summary

Introduction

The duplication of entire genomes leads to polyploidy and occurs in many cell types and organisms. Evidence is accumulating that polyploidization may be a driving force in evolution as it increases the adaptive potential in stressful conditions (van de Peer et al 2017), leading to evolutionary innovations and diversification (Walden et al 2020; Ostendorf et al 2021). Polyploid cells lose parts of their chromosome set, resulting in aneuploidy. It is well established that chromosomal instability causes aneuploidy which drives tumour formation, but there is growing evidence that aneuploidy itself might contribute to tumorigenesis (Ben-David and Amon, 2020). Regions with altered gene expression occur all over the genome, revealing that aneuploidy affects global transcript patterns (Letourneau et al 2014)

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Results

Conclusion