Induction of a transcriptional adaptation response by RNA destabilization events [dst278]
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, namely whether an mRNA-borne premature termination codon (PTC) or the subsequent mRNA degradation process, and/or its products, elicits TA.  Here, we first established two perturbations leading to mRNA destabilization for mouse Actg1: a Cas9-induced mutation that leads to a PTC, and Cas13d-mediated mRNA cleavage.  We find that both perturbations are effective in degrading Actg1 mRNA and upregulating Actg2.  Notably, increased chromatin accessibility at the Actg2 locus was observed only in the Cas9-induced mutant allele but not in the Cas13d-targeted cells, suggesting that chromatin remodeling is not required for Actg2 upregulation.  We further show that ribozyme-mediated Actg1 pre-mRNA cleavage also leads to a robust upregulation of Actg2.  Together, these data highlight the critical role of RNA destabilization events as a trigger for TA. Overall design: Active (T3H48-aHHR) and inactive (T3H48-iHHR) T3H48-HHR ribozyme was knocked into intron 3 of the Actg1 locus to induce ribozyme-mediated pre-mRNA cleavage.  Stable lines were genotyped and samples were collected for ATAC-Seq.