Inter-chromosomal insertions into wild-type chromosomes induced by SCRaMbLE

Abstract

Genomic rearrangements play a crucial role in shaping biological phenotypic diversity and driving species evolution. Synthetic chromosome rearrangement and modification by LoxP-mediated evolution (SCRaMbLE) has been applied to explore large-scale genomic rearrangements, yet it has been observed that these rearrangements occur exclusively in genomic regions containing loxPsym sites. Here, we found that SCRaMbLE of synthetic yeast harboring synthetic chromosome V and X can generate a variety of synthetic segment insertions into wild-type chromosomes, ranging from 1 to 300 kb. Furthermore, it was revealed that the novel insertions impacted the transcriptional level of neighboring regions and affected the production of exemplar pathway of zeaxanthin. Collectively, our results improve the understanding of the ability of SCRaMbLE to generate complex structural variations in nonsynthetic regions and provide a potential model to explore genomic transposable events.

Graphical abstract

Keywords

genomic rearrangements / synthetic yeast genome / SCRaMbLE / inter-chromosomal insertions / synthetic biology

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Competing interests

The authors declare that they have no competing interests.

Acknowledgements

The authors would like to thank Bin Jia from Tianjin University for discussions and advice. The authors would also like to thank Jianting Zhou from Tianjin University for helpful comments during manuscript preparation. This study was supported by the National Key Research and Development Program of China (Grant No. 2021YFC2100800), the National Natural Science Foundation of China (Grant No. 22208241), China Postdoctoral Science Foundation (Grant No. 2023M732591), and the Key R&D Program of Shandong Province, China (Grant No. 2022SFGC0102).

Electronic Supplementary Material

Supplementary material is available in the online version of this article at https://doi.org/10.1007/s11705-024-2458-5 and is accessible for authorized users.

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