SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence

Purpose: It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH-sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in S. cerevisiae. Methods: We performed RNA sequencing analysis to determine the extent of the requirement for theSNF5 QLC in the activation of glucose-repressed genes. Total RNA was extracted from WT, ?Q-snf5 and HtoA-snf5 strains during exponentially growth (+Glu) and after 4 hours of glucose starvation. Next, Poly-A selection was performed using Dynabeads and libraries were performed following manufactures indications. Sequencing of the 32 samples was performed on an Illumina Hi-seq on two lanes. RNA-seq data were aligned to the University of California, Santa Cruz (UCSC), sacCer2 genome using Kallisto (0.43.0,http://www.nature.com/nbt/journal/v34/n5/full/nbt.3519.html) and downstream visualization and analysis was done using R (3.2.2). Differential gene expression analysis, heat maps and volcano plots were created using DESeq2 where a wald test was used to determine differentially expressed genes and Euclidean distance to calculate clustering for heat maps. Conclusions: We found that pH changes and the SNF5 QLC are required for correct transcriptional reprogramming upon carbon starvation, but the dependencies are nuanced. Overall design: S.cerevisiae cells were grown in glucose or starvation conditions with the following genotypes: WT, delta-Q, HtoA-snf5 or starved at pH7. Analysis scripts available: https://github.com/gbritt/Kallisto_DESeq2_Scripts_RNASeq_12.18.17