Genome architecture shapes transcriptional responses to topoisomerase depletion in C. elegans.

DNA supercoiling is an intrinsic consequence of transcription that must be resolved to maintain proper gene expression. How supercoiling shapes transcription dynamics in animal genomes remains unclear. Here, we acutely depleted topoisomerases in Caenorhabditis elegans and applied nascent transcription profiling, nuclear RNA sequencing (RNA-seq), histone modification mapping, and long-read sequencing to capture the transcriptional and chromatin responses to topological stress. We find that topoisomerase depletion preferentially inhibits and uncouples expression of convergent genes, while transcription initiation and coordinated expression of divergent genes are comparatively maintained. Topoisomerase degradation hinders transcription elongation globally, resulting in reduced production of longer transcripts and overall shortening of poly(A) tails. These elongation defects are not accompanied by global changes in elongation-associated histone modifications but coincide with modest reductions in promoter and enhancer marks. Our results indicate that genome architecture shapes transcriptional responses to DNA supercoiling, uncovering a topological basis for coordinated gene expression in a multicellular organism.