RNA_sequencing_of_LINE1_edited_clones

The induction of hundreds of simulatenous structural variants would allow the investigation of genome design and limitations at scale. To enable this, we used CRISPR prime editing to target repetitive sequences in the genome and insert recombinase sites. We have inserted hundreds of symmetrical loxP sites into LINE1 mobile elements and derived several stable cell clones. By performing bulk transcriptome sequencing on these clones we try to address three questions. (1) Understand if the insertion of short sequences into LINE1 elements would change the gene expression of the derived cell clones. (2) Explore if a specific gene program is activated following the induction of editing at repetitive elements. (3) Characterize the cell lines we plan to take forward for future experiments.