Abstract

CRISPR interference (CRISPRi), leveraging catalytically inactive Cas9 (dCas9), has transformed transcriptional silencing. However, its application in Drosophila melanogaster has been constrained by inconsistent efficiency and limited repression amplitude. Here, we present embedded CRISPR interference (emCRISPRi), an advanced gene-silencing platform that integrates transcriptional repression domains (Mxi and TRD) into a structurally flexible region of dCas9. This design significantly enhances silencing efficiency, enabling robust repression of coding genes and cis-regulatory elements, particularly at transcription start site (TSS)-proximal regions. emCRISPRi demonstrates improved gene-silencing activity compared to RNA interference (RNAi) at several tested loci and facilitates strong phenotypic rescue via unmodified cDNA. Its versatility is demonstrated through the dissection of Hippo pathway interactions and the mitigation of TDP-43-induced neurotoxicity in an amyotrophic lateral sclerosis (ALS) model. These findings position emCRISPRi as a transformative tool for functional genomics, enhancer studies, and disease modeling in Drosophila , with significant potential for cross-species adaptation and therapeutic innovation.