(42h) 3D Inter-Allelic Competition Can Decrease the Total mRNA Production in Wild Type Embryos

The mechanism by which transcriptional machinery is recruited to specific enhancers and target promoter regions to regulate gene expression is one of the most puzzling and extensively studied questions in modern biology. Here, we ask if inter-allelic interactions between two homologous alleles can affect gene regulation in living Drosophila embryos. Using MS2- and PP7-based, allele-specific live imaging assay, we visualized de novo transcription of the yellow reporter gene in hemizygous and homozygous embryos. To our surprise, we found that each homozygous allele produces fewer RNAs than the hemizygous allele, suggesting the possibility of allelic competition in homozygotes. Moreover, the MS2-yellow reporter gene showed reduced transcriptional activity when a partial transcription unit (enhancer only or promoter only) was located in the homologous position. We propose that the transcriptional machinery that binds to both the enhancer and the promoter region, such as RNA Pol II or preinitiation complexes, may be responsible for the allelic competition. To support this idea, we showed that the homologous alleles did not interfere with each other in earlier nuclear cycles when Pol II is in excess, while the degree of allelic interference gradually increased in nuclear cycle 14, possibly due to the limited number of freely available Pol II in each transcription hub. Our study provides new insights for the role of 3D inter-allelic interactions in gene regulation.