Integration of RNA-Seq and ribosome profiling to characterize transcriptional and translational estrogen responses of protein-coding and non-coding RNA genes in human breast cancer
Here, we report an integrated assessment of both transcription and ribosome binding (as a proxy for translation) of all protein-coding and lncRNA transcripts in the same hormone-responsive human cancer model before and after hormone treatment, and identify lncRNAs that exhibit estrogen-induced translational regulation, often in the absence of transcriptional regulation. We also identify a large collection of expressed, and in some cases translated pseudogenes with robust responses to estrogen, independent of their parent genes. These findings point to new potential biomarkers for estrogen-responsive breast cancers, as well as potential therapeutic targets, particularly for emerging immunotherapies.