GSE122804
Integrative analysis from the epigenome to translatome uncovers patterns of dominant nuclear regulation during transient stress
Background: The regulation of gene activity in response to energy availability is an universal phenomenon. When molecular oxygen is limited the production of ATP is inefficient and growth is curtailed. The plant Arabidopsis thaliana rapidly responds to oxygen deprivation (hypoxia) by elevating the abundance of ~50 hypoxia-responsive gene (HRG) transcripts that are prioritized for translation. Many other cellular mRNAs are sequestered in ribonucleoprotein complexes and not translated during hypoxia, including those encoding ribosomal proteins (RPs). Little is known of the effect of hypoxia on nuclear regulatory processes including histone modifications, chromatin accessibility, RNA polymerase II (RNAPII) engagement and nascent transcript production. Here we apply genomic technologies to evaluate epigenetic and transcriptional regulation in response to hypoxia. Results: Hypoxia-induced dynamics in eight chromatin readouts were contrasted to the nuclear, polyadenylated and ribosome-associated mRNAs of Arabidopsis seedlings. This identified patterns of regulatory variation of gene cohorts including the HRGs and RPs. HRGs were characterized by increased chromatin accessibility in their promoters, as well as eviction of the Histone 2A.Z variant, elevation of Histone 3-lysine 9 acetylation, and engagement of RNAPII-Ser2P active in elongation. Following short term stress, over half of the HRGs promoters were bound by the Ethylene Responsive Factor group VII transcription factor, HYPOXIA-RESPONSIVE ERF 2 (HRE2), encoded by an HRG.  Prolonged stress maintained  RP transcription, accompanied by elevated Histone 3-lysine 14 acetylation (H3K14ac) and nuclear RNA retention. The stress-induced activation of genes associated with heat stress was distinct from the HRGs. These had high RNAPII-Ser2P engagement and nuclear accumulation after short term hypoxia without accumulation of higher levels of polyA RNA. These more progressively upregulated genes were enriched for cis-elements recognized by HEAT SHOCK FACTOR transcriptional activators and had more 5' biased histone marks on their gene bodies They had less H2A.Z eviction, Histone 3-lysine 4 trimethylation and H3K9ac than genes with promoters bound by HRE2 and coordinately upregulated from RNAPII-Ser2P engagement to translation. Genes associated with the circadian cycle, photosynthesis and development were also temporally regulated by hypoxia. Conclusions: Hypoxic stress triggers dynamic epigenetic and transcriptional regulatory variations that differentiate rapid versus more progressive activation of stress-gene transcripts that are destined for translation. Growth-associated genes continue to be transcribed but their nascent transcripts are retained in the nucleus. Overall design: Examination of four histone modifications, one histone variant, chromatin accessibility, RNAP Ser2P association, nuclear RNA, poly(A)+ RNA, and TRAP-RNA in control and hypoxia stressed Arabidopsis seelings.  RNA-seq based data was performed in triplicate.  ChIP-seq and ATAC-seq data were performed in duplicate.  In total: 17 ChIP-seq, 4 ATAC-seq, 4 nRNA-seq, 4 poly(A)+ mRNA-seq, and 2 TRAP-seq datasets were generated Condition - All initated at Zeitgeber time 16 (end of light cycle) 2h non-stress - 2NS - harvest after 2h darkness 2h hypoxic stress - 2HS - harvest after 2h darkness and hypoxia 9h non-stress - 9NS - harvest after 9h darkness 9h hypoxic stress - 9HS- harvest after 9h darkness and hypoxia 2h hypoxic stress + 1h reoxygenation - 1R - harvest after 2h darkness and hypoxia followed by 1h reoxygenation 2h hypoxic stress + 2h reoxygenation - 2R - harvest after 2h darkness and hypoxia followed by 2h reoxygenation HRE2 ChIP- 2HS - harvest after 2h darkness and hypoxia