Aaron Brooks from EMBL Germany presented at London Calling 2019 on “Measuring SCRaMbLEd transcription with direct RNA sequencing.” Direct RNA sequencing has interested me since we tried it last summer for bacterial transcriptomics. Brooks asked: “What if you could build a genome from scratch?” and “Where would you place the transcriptional units?” It is now possible to synthesize genomes. Brooks shared that the galactose genes have conserved organization in yeast. Brooks said in highly compact genomes like the yeast genome, where genes are located can have a major effect on transcription. The yeast chromosomes have been synthesized to create Sc2.0 as part of an initiative by Jeff Boeke. The SCRaMbLE system is Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution. You can induce genome scrambling with LoxP sites. Full-length RNA sequencing can help learn about transcript isoform expression after scrambling. Brooks and team used several cDNA and other library prep approaches. With SQK-RNA002, they obtained sequence data from dozens of strains. Even within SCRaMbLEd genomes, transcriptional alterations were detected with transcript sequencing. Brooks concluded by asking: is genome organization an engineerable design feature? They shared evidence of RNA isoforms altered in rearranged genomes and were able to quantify changes in gene expression. This is certainly a fascinating use case! I wonder how this project has evolved since 2019…
