Epigenetic coordination of transcriptional and translational programs in hypoxia. [RNA-Seq]

Stress adaptation entails perturbations in transcriptional and post-transcriptional mechanisms of regulation of gene expression, but how these programs are coordinated remains largely unknown. To address this, we systematically interrogated the effects of hypoxia on transcriptomes, epigenomes and translatomes of T47D breast cancer cells and H9 human embryonic stem cells. This revealed that hypoxia-induced alterations in H3K4me3 exert unexpectedly minimal effects on transcript abundances. Instead, they were associated with pervasive changes in the transcription start site (TSS) selection, subsequent 5’UTR remodeling, and reshaping of translational landscapes. Importantly, this epigenetically-driven reprograming of translation is distinct from HIF1-dependent transcriptional mechanisms or integrated stress response- or mTOR-guided translational reprogramming. Indeed, comparable effects on TSS selection and 5'UTR remodeling were observed when H3K4me3 was pharmacologically stimulated in the absence of induction of HIF, ISR or modulation of mTOR signaling. These results demonstrate a previously unappreciated physiologically relevant mechanism of translational regulation driven by epigenetic reprograming of the 5’UTRome which is orchestrated with other hypoxia-triggered adaptive mechanisms. Three or four replicates of polysome profiling were performed on hypoxia and normoxia-treated H9 and T47D cells, respectively. Hypoxia treatments were 0.5% oxygen for 24 (H9 cells) or 48 hours (T47D cells). Total cytosolic RNA, and polysome-associated mRNA (mRNA associated with > 3 ribosomes) were isolated and quantified using RNA sequencing.