Gene Arrangement Shapes Transcriptional Responses to DNA Supercoiling in a Multicellular Organism [CUT&Tag]

ABSTRACT: DNA supercoiling is an intrinsic consequence of transcription that must be resolved to maintain proper gene expression, yet how supercoiling shapes transcription dynamics in chromatinized genomes remains unclear. Here, we acutely depleted topoisomerases I and II in Caenorhabditis elegans and applied nascent transcription profiling, nuclear and total RNA-seq, histone modification mapping, and long-read sequencing to capture the immediate transcriptional and chromatin responses to topological stress. We show that the genomic context influences the effect of supercoiling on transcription initiation, elongation and coordinated expression of adjacent genes. The impact of supercoiling on transcription initiation is not uniformly repressive but instead depends on the orientation and proximity of neighboring genes. DNA supercoiling hinders transcription elongation globally resulting in reduced production of longer transcripts and overall shortening of poly(A) tails. In contrast to transcription initiation, transcription elongation defects are not driven by neighboring transcription but by local supercoiling generated by the gene’s own transcription. These elongation effects are not accompanied by global changes in elongation-associated histone modifications but coincide with modest reductions in promoter and enhancer marks. We find that negative supercoiling promotes coordinated expression of divergent gene pairs, while positive supercoiling uncouples expression of convergent genes. Our results indicate that the relative orientation and spacing between genes modulate how DNA supercoiling propagates through chromatin, revealing a directional mechanism by which genome architecture contributes to coordinated expression of genes in a multicellular eukaryotic genome.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE309620 | GEO | 2026/09/18

REPOSITORIES: GEO