A long antisense RNA is transcribed at the 5’ end of the human HIF-1a gene upon drug inhibition of DNA Topoisomerase I.

Hypoxia-inducible factor 1 (HIF-1) is a master regulator of the cell response to oxygen deprivation. We have previously shown that the Topoisomerase I (Top1) inhibitor camptothecin (CPT) modifies RNAPII density along transcribed genes suggesting an involvement of Top1 in RNAPII pausing. Here, we demonstrate that CPT affects RNAPII density at the promoter pause site of HIF-1a gene and increases the transcription of specific regions corresponding to the 5’ end of intron 1 in human HCT 116 cells. The effect requires Top1 and is independent of replication-mediated DNA breaks. Chromatin RNA immpunoprecipitation (RIP) experiments show that CPT increases the amount of specific RNA bound to chromatin in a transcription-dependent manner, thus showing that CPT promotes transcription along the studied regions. Further analyses demonstrated that CPT stimulates the transcription of a long RNA, antisense to HIF-1a mRNA, while decreasing HIF-1a mRNA levels. Thus, despite its transcription inhibitory activity, CPT can trigger the production of an antisense transcript at the 5’ end of the HIF 1a gene, likely suggesting a new regulation mechanism of HIF-1a expression and activity.