Studying gene expression scaling with cell size in Arabidopsis thaliana : the role of the nuclear RNA exosome complex

Abstract: The scaling of organ size with body size - known as morphological allometry - is a fundamental mechanism observed in all organisms (Mirth et al. 2016). Scaling mechanisms have also been shown at a cellular level, with mRNA levels linearly scaling with cell size, but knowledge about the cellular processes controlling it has been limited (Berry et al. 2022). However, recent evidence in human cells suggest that nuclear mRNA transcripts - through a negative feedback mechanism - inhibit transcription of Pol II, so that Pol II concentrations remain constant in relation to cell size (Berry et al. 2022b). Here, we applied this hypothesis to plants by studying how transcription scaling was affected by mutations disrupting the nuclear RNA exosome complex in A. thaliana. We performed smFISH, and compared the mutants hen2-4 and rrp4-2 with Col-0. We found that the mutants accumulated more transcripts with increasing cell size than WT, but remarkably, the increased number of transcripts in the mutants were found in the cytoplasm and not in the nucleus. This suggests that loss of nuclear exosome functionality - meaning decreased mRNA decay - results in an increased nuclear mRNA export. This could mean that the cell is trying to minimize nuclear transcript accumulation to prevent inhibition of synthesis of new mRNAs, indicating that a negative feedback of nuclear mRNA is also operating in plants.