Induction of a transcriptional adaptation response via perturbations at the DNA and RNA levels [dst233]

Transcriptional adaptation (TA) is a cellular process whereby mRNA-destabilizing mutations lead to the transcriptional upregulation of so-called adapting genes. The nature of the TA-triggering factor(s) remains unclear. Here, we first generated Cas9-induced mutations in mouse Actg1, including an mRNA-destabilizing allele and an RNA-less allele. We find in the Actg1 mRNA-destabilizing allele, higher levels of Actg2 mRNA as well as increased chromatin accessibility at the Actg2 locus compared with wild-type and the RNA-less allele. Notably, Cas13d experiments show that Actg1 mRNA cleavage, but not Actg1 pre-mRNA cleavage, also triggers Actg2 upregulation; however, this upregulation is not associated with increased chromatin accessibility at the Actg2 locus. Furthermore, time course experiments show that increased Actg2 expression persists even after Actg1 mRNA degradation by Cas13d ceases. Together, our data highlight the importance of cytoplasmic mRNA degradation as a trigger for the TA response and suggest that chromatin remodeling is not necessary for TA. To investigate the role of mRNA degradation during transcriptional adaptation, we knocked in CRISPR-Cas13d in NIH/3T3 cells and targeted Actg1 mRNA for degradation by transfecting the cells with Actg1-specific guide RNA. Guide RNA targeting GFP was used as control. Then we performed ATAC-seq to detect the changes in chromatin accessibility in Actg1-targeted cells compared with GFP-targeted cells. Three biological replicates were prepared for each condition.