Distinct regulation across the transcription cycle drives mitotic transcriptional silencing

Abstract In most organisms, as cells enter mitosis, transcription is globally silenced. While individual studies have shown that each stage of the transcription cycle can be modulated during mitosis, how initiation, elongation, and termination are temporally and kinetically regulated to ensure transcriptional silencing remains unclear. Here, we combine real-time quantitative imaging of ongoing transcription in early Drosophila embryos with mathematical modelling to systematically dissect how transcriptional kinetics change as cells progress into mitosis. We found that transcription initiation undergoes a gradual repression starting in prophase, while elongation rates remain unaltered. After nuclear envelope breakdown, an abrupt mechanism causes premature termination of elongating RNA, driven at least in part by the SNF-helicase-like protein Transcription Termination factor 2 / Lodestar (TTF2/Lds). Our study provides a quantitative framework for understanding how transcription is modulated across the cell cycle, demonstrating that mitotic repression arises from multiple processes with different dynamics that collectively ensure the precise shutdown of gene expression.