Transcriptional repression by a secondary DNA binding surface of DNA topoisomerase I safeguards against hypertranscription

Regulation of global transcription output is important for normal development and disease but only few regulators of the process are known. Here, we describe DNA topoisomerase I (TOP1) as a novel regulator where it exerts transcriptional repression to prevent transcription overdrive. This function requires a conserved secondary DNA binding surface that is distinct from its catalytic pocket. Overall design: RNA-seq of 293T cells transiently overexpressing TOP1 variants (wildtype and mutants at secondary DNA binding surface) or vector control, two mutant mouse embryonic stem cell (mESC) lines homozygous for Top1(R548Q) mutation and their parental wildtype line, and neurons derived from the corresponding mESC lines. For RNA-seq in 293T cells and mESCs, ERCC spike-ins were added to enable cell number normalization. PRO-seq in mutant and wildtype mESC. ChIP-seq of TOP1 and RNAP2S2P in mutant and wildtype mESC.