Chromosomal rearrangements, such as chromosome segment inversions, may affect the epigenetic landscape as well as gene expression. Different kinds of chromosome segment inversions have been found in many prominent crops like rice, maize, and barley.
Until now, it has only been possible to study historical chromosome rearrangements that have occurred naturally. Researchers in Germany recently used CRISPR/Cas-based chromosome engineering to induce pre-defined chromosome rearrangements. As a result, genetic and epigenetic consequences can be analyzed immediately after the chromosome rearrangements occur.
The team, which published its study “Epigenetic state and gene expression remain stable after CRISPR/Cas-mediated chromosomal inversions” in New Phytologist, relied on CRISPR/Cas-based chromosome engineering to generate chromosomal inversions of different sizes in the model plant Arabidopsis thaliana. The epigenetic state of these lines was compared to wild-type plants. Finally, the effect of the chromosomal rearrangements on the activity of genes was analyzed.
Two chromosomal inversions
“The epigenetic state of chromatin, gene activity and chromosomal positions are interrelated in plants. In Arabidopsis thaliana, chromosome arms are DNA-hypomethylated and enriched with the euchromatin-specific histone mark H3K4me3, while pericentromeric regions are DNA-hypermethylated and enriched with the heterochromatin-specific mark H3K9me2. We aimed to investigate how the chromosomal location affects epigenetic stability and gene expression by chromosome engineering,” wrote the investigators.
“Two chromosomal inversions of different sizes were induced using CRISPR/Cas9 to move heterochromatic, pericentric sequences into euchromatic regions. The epigenetic status of these lines was investigated using whole-genome bisulfite sequencing and chromatin immunoprecipitation. Gene expression changes following the induction of the chromosomal inversions were studied via transcriptome analysis.
“Both inversions had a minimal impact on the global distribution of histone marks and DNA methylation patterns, although minor epigenetic changes were observed across the genome. Notably, the inverted chromosomal regions and their borders retained their original epigenetic profiles. Gene expression analysis showed that only 0.5–1% of genes were differentially expressed genome-wide following the induction of the inversions.
“CRISPR/Cas-induced chromosomal inversions minimally affect epigenetic landscape and gene expression, preserving their profiles in subsequent generations.”
According to Holger Puchta, PhD, professor at the Karlsruhe Institute of Technology and an author of the paper, “This is of great importance for future applications of chromosome engineering in the breeding of crops.”
“Our results indicated that none of the studied inverted chromosome segments and their neighboring regions changed in epigenetic marks and gene expression besides minor genome-wide effects,” explained Solmaz Khosravi, PhD, a postdoc at the IPK Leibniz Institute of Plant Genetics and Crop Plant Research and first author of the study.
Gene expression analysis showed that genome-wide, only 0.5–1% of genes were differentially expressed following the induction of the inversions.
“The findings demonstrate the robustness of the epigenome and the transcriptome following CRISPR/Cas-induced chromosomal restructuring, at least in the following generations,” added Andreas Houben, PhD, head of IPK’s research group “Chromosome Structure and Function.” “Our study is the first in the plant scientific community which shows the effect of structural variations on the epigenetic state of chromatin in the following generations after the occurrence of an inversion.”
