Identification of disease-associated non-coding variants and regions has led to innovative therapies, but technological limitations have hindered the study of non-coding elements. The proposed research, using FIND-seq, aims to overcome these limitations. FIND-seq enables the genome-wide screening of coding and non-coding elements without requiring large sgRNA libraries. It's not affected by sequence variants and can be used in various organisms. FIND-seq can identify unannotated functional elements, particularly in the case of enhancers. The research focuses on understanding drug resistance from a non-coding genome perspective, aiming to identify target genes and their regulating transcription factors through TF-binding motifs. The results may reveal new approaches to combat drug resistance, often linked to distinct epigenetic changes. The FIND-base concept represents a transformative approach in contrast to current CRISPR screens. Enrichment scores in traditional screens link sgRNAs to target genes and indicate a gene's importance in a phenotype, but they are also influenced by sgRNA cleavage efficiencies. FIND-base, however, delves directly into mutations linked to functional changes in cell behavior, particularly in non-coding DNA. This method can provide detailed information, such as discriminating between mutations that disrupt a critical binding motif within an enhancer and those that do not alter transcription factor recruitment capacity. Furthermore, incorporating base editors and advanced nucleases enhances the resolution of mutagenesis screens. FIND-base will be applied to study oncogenic non-coding mutations in B-cell derived acute lymphoblastic leukemia, focusing on non-coding regions linked to SNPs associated with the disease based on multiple GWAS studies.
