GSE95844
Argonaute2 and LaminB repress transcription by controlling RNA Pol II recruitment and chromatin topology in Drosophila melanogaster (mRNA)
Although best known as core components of RNA silencing pathways in the cytoplasm, Argonautes have been shown to regulate gene expression by functioning in the nucleus. Previous work showed that Drosophila AGO2 is preferentially associated with active promoters and can activate gene expression by promoting looping to an enhancer. In order to elucidate the genome-wide role of AGO2 in regulating transcription, we performed mass spec analysis of factors that interact with AGO2 in nuclear extracts and found RNA Pol II and LaminB among the top-associated proteins. Using nascent RNA sequencing, we showed that AGO2 and LaminB co-repress transcription at borders between both LaminB-associated domains (LAD) and topologically-associated domains (TADs). Furthermore, LaminB and AGO2 specifically prevent RNA Pol II recruitment at repressed genes, and AGO2 additionally impairs the ability of RNA Pol II to extend into active elongation. Using mRNA-seq profiling, we identified a somatic target of AGO2 repression, nht, which leads to ectopic expression of spermatogenesis genes in AGO2 null mutants. Interestingly, nht is immersed in a LAD located within a repressive TAD flanked by AGO2 binding sites. 4C-seq analysis showed that depletion of either AGO2 or LaminB results in a significant decrease in frequency of interactions within the TAD as well as ectopic inter-TAD interactions. Overall, our findings reveal a coordinated function for AGO2 and LaminB in dictating the overall architecture of the genome to control the recruitment of RNA Pol II and thereby regulate gene expression. Overall design: mRNA-seq from female whole larvae in different AGO2 mutant strains. Two biological replicates were analyzed.