CRISPR–Cas based repair of a deleterious mutation in tomato plants

The action of SSP2 is partially redundant with that of its paralog SSP in regulating shoot and inflorescence architecture. However, such redundancy was impaired during tomato domestication. To determine whether the deleterious variant of SSP2 affects binding to genome-wide targets, DNA affinity purification sequencing (DAP-seq) was performed with SSP, ancestral SSP2 and domesticated SSP2.

The BICC staff performed a genome-wide analysis of the DAP-seq data, using the csaw workflow, which led to the identification of differentially bound regions between ancestral and domesticated transcription factors. Using the MEME suite family of tools, the team also performed de novo motif enrichment analysis that identified a G-box binding motif (CACGTG) with a subtle variation for the deleterious SSP2 outside the core motif. Furthermore, by analysing the distribution of the target genes, it was found that only a subset of the ancestral target genes were bound by the deleterious transcription factor, suggesting that the ability of the deleterious SSP2 to bind its targets genome-wide is compromised.

By leveraging the genome-wide binding data, the BICC's team helped reveal that SSP and the ancestral variant of SSP2 bind a broadly shared set of targets, whereas the domesticated SSP2 has a reduced ability to bind the targets of the ancestral protein.