Epigenetic coordination of transcriptional and translational programs in hypoxia. [nanocage]

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. Nano-cap analysis of gene expression (nanoCAGE) sequencing for profiling transcription start sites and 5'UTRs in hypoxia and normoxia-treated T47D breast cancer and H9 human embryonic stem cells. Three biological replicates were performed for T47D cells, however one normoxia sample failed and was discarded. Four biological replicates were performed for H9 cells. In addition, 4 biological replicates were also performed for T47D cells treated with compound 48 (C48, 10 uM, 24 hrs), and or DMSO.