A dual-activity topoisomerase complex promotes both transcriptional activation and repression in response to starvation

Topoisomerases are required to release topological stress generated by RNA polymerase II (RNAPII) during transcription. Here we show that in response to starvation, the complex of topoisomerase 3b (TOP3B) and TDRD3 can promote transcriptional activation or repression. Human HCT116 cells individually inactivated for TOP3B, TDRD3, or TOP3B topoisomerase activity, exhibit similarly disrupted transcription for both starvation-activated genes (SAGs) and starvation-repressed genes (SRGs). Responding to starvation, both TOP3B-TDRD3 and the elongating form of RNAPII exhibit concomitantly increased binding to TOP3B-dependent SAGs, at binding sites that overlap. Strikingly, TOP3B inactivation decreases the binding of elongating RNAPII to TOP3B-dependent SAGs while increased it to SRGs. Furthermore, TOP3B-ablated cells display reduced transcription of several autophagy-associated genes and autophagy per se. Our data suggest that TOP3B-TDRD3 can promote both transcriptional activation and repression by regulating RNAPII distribution. In addition, the findings that it can facilitate autophagy may account for the shortened lifespan of Top3b-KO mice. Overall design: To identify the regulation of the TOP3B-TDRD3 complex on starvation-induced transcription in HCT116 cells, we performed RNA-seq and ChIP-seq (TDRD3, RNAPII and RNAPII-ser2p) using WT and TOP3B-KO/TDRD3-KO/TOP3B-Y336F-KI HCT116 cells under no treatment and starvation condition. We used EBSS medium to starve the cells for 6 hours. Then the RNAs were extracted for RNA-seq. The sonicated chromatins were pulled down by TDRD3, RNAPII or RNAPII-ser2p antibody. Then the DNAs were extracted and generated to Illumina libraries for sequencing. The NGS original reads were mapped to human genome (hg38). Most of the experiments contain two or three replications.