Functional RNA Dynamics Are Progressively Governed by RNA Destabilization during the Adaptation to Chronic Hypoxia

Abstract

Previous studies towards reduced oxygen availability have mostly focused on changes in total mRNA expression, neglecting underlying transcriptional and post-transcriptional events. Therefore, we generated a comprehensive overview of hypoxia-induced changes in total mRNA expression, global de novo transcription, and mRNA stability in monocytic THP-1 cells. Since hypoxic episodes often persist for prolonged periods, we further compared the adaptation to acute and chronic hypoxia. While total mRNA changes correlated well with enhanced transcription during short-term hypoxia, mRNA destabilization gained importance under chronic conditions. Reduced mRNA stability not only added to a compensatory attenuation of immune responses, but also, most notably, to the reduction in nuclear-encoded mRNAs associated with various mitochondrial functions. These changes may prevent the futile production of new mitochondria under conditions where mitochondria cannot exert their full metabolic function and are indeed actively removed by mitophagy. The post-transcriptional mode of regulation might further allow for the rapid recovery of mitochondrial capacities upon reoxygenation. Our results provide a comprehensive resource of functional mRNA expression dynamics and underlying transcriptional and post-transcriptional regulatory principles during the adaptation to hypoxia. Furthermore, we uncover that RNA stability regulation controls mitochondrial functions in the context of hypoxia.

Post-transcriptional control contributes to hypoxia-induced tumorigenic phenotypes in macrophages

“…Two other studies have observed widespread hypoxic mRNA decay in generic tissue culture models, supporting our findings in primary human macrophages 68, 69 . Using conventional mRNA lifetime calculations from actinomycinD transcription assays and a s 4 U pull-down approach in HUVECs, Tiana et al find that decay rates are about 1.6 times faster in hypoxia for a dataset of a few hundred genes 69 .…”

“…Our work suggests that either hypoxia alone does not induce these pathways in tumors, or that inflammatory activation is enough to drive gene expression of these factors in the opposite direction. Two other studies have observed widespread hypoxic mRNA decay in generic tissue culture models, supporting our findings in primary human macrophages 68,69 . Using conventional mRNA lifetime calculations from actinomycinD transcription assays and a s 4 U pull-down approach in HUVECs, Tiana et al find that decay rates are about 1.6 times faster in hypoxia for a dataset of a few hundred genes 69 .…”

“…Using conventional mRNA lifetime calculations from actinomycinD transcription assays and a s 4 U pull-down approach in HUVECs, Tiana et al find that decay rates are about 1.6 times faster in hypoxia for a dataset of a few hundred genes 69 . In a study of Thp1 cells, an immortalized leukemic monocyte line, Bauer et al find nearly 600 mRNAs to be differentially degraded using SLAM-seq, a metabolic labeling approach similar to TimeLapse-seq 68, 70 . Our data, produced with TimeLapse-seq and analyzed with bakR, identify thousands of transcripts regulated by post-transcriptional decay in primary human macrophages.…”

Hypoxia-altered cholesterol homeostasis enhances the expression of interferon-stimulated genes upon SARS-CoV-2 infections in monocytes

“…Since hypoxia is a major contributing factor to various immune system-associated diseases, we determined RNA dynamics in human monocytic THP-1 cells in response to acute (8 h 1% O 2 = AH) and chronic (72 h 1% O 2 = CH) hypoxia ( 20 ). In line with the major regulatory impact of hypoxia, 2632 transcripts appeared differentially expressed ( padj < 0.05, |log2FC| > 0.3) between normoxia (21% O 2 = N) and hypoxia (AH and/or CH), however, following different regulatory dynamics ( Figure 1A ).…”

“…Previously, we characterized transcriptome-wide changes in de novo synthesis and RNA stability under hypoxia in monocytes by a metabolic labeling approach. Here, we focused on total mRNA changes within the previously published comprehensive metabolic RNA sequencing data of THP-1 cells incubated for 8 h and for 72 h under hypoxia (acute hypoxia (= AH) and chronic hypoxia (= CH), respectively), or under normoxia (N) (GSM5994456 to GSM5994464) ( 20 ). For differential gene expression analyses, raw reads were quality-, adapter-, and polyA-trimmed using Cutadapt ( 21 ) and unique molecular identifier and linker sequences were removed before the processed reads were aligned to the human genome (GRCh38) with Ensembl gene annotation (release 80) using STAR (version 2.7.6a) ( 22 ).…”