NanoCAGE in ERa knockdown BM67 cells

Estrogen receptor alpha (ERa) activity is associated with increased cancer cell proliferation. Studies aiming to understand the impact of ERa on cancer-associated phenotypes have largely been limited to its transcriptional activity. Herein, we demonstrate that ERa coordinates its transcriptional output with selective modulation of mRNA translation. Importantly, translational perturbations caused by depletion of ERa largely manifest as "translational offsetting" of the transcriptome, whereby amounts of translated mRNAs and corresponding protein levels are maintained constant despite changes in mRNA abundance. Transcripts whose levels, but not polysome-association, are reduced following ERa depletion lack features which limit translation efficiency including structured 5'UTRs and miRNA target sites. In contrast, mRNAs induced upon ERa depletion whose polysome-association remains unaltered are enriched in codons requiring U34-modified tRNAs for efficient decoding. Consistently, ERa regulates levels of U34-modifying enzymes and thereby controls levels of U34-modified tRNAs. These findings unravel a hitherto unprecedented mechanism of ERa-dependent orchestration of transcriptional and translational programs that may be a pervasive mechanism of proteome maintenance in hormone-dependent cancers. Overall design: nanoCAGE sequencing of cytosolic mRNA from shERa BM67 cells was performed on 3 biological replicates. Each biological replicate was prepared with 2 barcodes.