| Citation | Feng D, Qu L, Powell-Coffman JA. Whole genome profiling of short-term hypoxia induced genes and identification of HIF-1 binding sites provide insights into HIF-1 function in Caenorhabditis elegans. PLoS One, 2024. |
| PubMed ID | 38743782 |
| Short Description | Whole genome profiling of short-term hypoxia induced genes and identification of HIF-1 binding sites provide insights into HIF-1 function in Caenorhabditis elegans. GEO Record: GSE228851 Platform: GPL200 Download gene-centric, log2 transformed data: WBPaper00066920.ce.mr.csv |
| # of Conditions | 24 |
Full Description
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Oxygen is essential to all the aerobic organisms. However, during normal development, disease and homeostasis, organisms are often challenged by hypoxia (oxygen deprivation). Hypoxia-inducible transcription factors (HIFs) are master regulators of hypoxia response and are evolutionarily conserved in metazoans. The homolog of HIF in the genetic model organism C. elegans is HIF-1. In this study, we aimed to understand short-term hypoxia response to identify HIF-1 downstream genes and identify HIF-1 direct targets in C. elegans. The central research questions were: (1) which genes are differentially expressed in response to short-term hypoxia? (2) Which of these changes in gene expression are dependent upon HIF-1 function? (3) Are any of these hif-1-dependent genes essential to survival in hypoxia? (4) Which genes are the direct targets of HIF-1? We combine whole genome gene expression analyses and chromatin immunoprecipitation sequencing (ChIP-seq) experiments to address these questions. In agreement with other published studies, we report that HIF-1-dependent hypoxia-responsive genes are involved in metabolism and stress response. Some HIF-1-dependent hypoxia-responsive genes like efk-1 and phy-2 dramatically impact survival in hypoxic conditions. Genes regulated by HIF-1 and hypoxia overlap with genes responsive to hydrogen sulfide, also overlap with genes regulated by DAF-16. The genomic regions that co-immunoprecipitate with HIF-1 are strongly enriched for genes involved in stress response. Further, some of these potential HIF-1 direct targets are differentially expressed under short-term hypoxia or are differentially regulated by mutations that enhance HIF-1 activity. Experimental Details: WBPaper00066920:JAPC01_N2_BioRep1 WBPaper00066920:JAPC02_N2_BioRep2 WBPaper00066920:JAPC03_N2_BioRep3 WBPaper00066920:JAPC04_N2_hypoxia_BioRep1 WBPaper00066920:JAPC05_N2_hypoxia_BioRep2 WBPaper00066920:JAPC06_N2_hypoxia_BioRep3 WBPaper00066920:JAPC07_hif-1(ia04)_BioRep1 WBPaper00066920:JAPC08_hif-1(ia04)_BioRep2 WBPaper00066920:JAPC09_hif-1(ia04)_BioRep3 WBPaper00066920:JAPC10_hif-1(ia04)_hypoxia_BioRep1 WBPaper00066920:JAPC11_hif-1(ia04)_hypoxia_BioRep2 WBPaper00066920:JAPC12_hif-1(ia04)_hypoxia_BioRep3 WBPaper00066920:JAPC13_vhl-1(ok161)_BioRep1 WBPaper00066920:JAPC14_vhl-1(ok161)_BioRep2 WBPaper00066920:JAPC15_vhl-1(ok161)_BioRep3 WBPaper00066920:JAPC16_rhy-1(ok1402)_BioRep1 WBPaper00066920:JAPC17_rhy-1(ok1402)_BioRep2 WBPaper00066920:JAPC18_rhy-1(ok1402)_BioRep3 WBPaper00066920:JAPC19_egl-9(sa307)_BioRep1 WBPaper00066920:JAPC20_egl-9(sa307)_BioRep2 WBPaper00066920:JAPC21_egl-9(sa307)_BioRep3 WBPaper00066920:JAPC22_swan-1(ok267);vhl-1(ok161)_BioRep1 WBPaper00066920:JAPC23_swan-1(ok267);vhl-1(ok161)_BioRep2 WBPaper00066920:JAPC24_swan-1(ok267);vhl-1(ok161)_BioRep3. |
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