design: mNET-seq was performed with minor modifications. 25 million cells were lysed, and nuclei were isolated and subjected to chromatin precipitation using NUN buffers. Chromatin was digested with MNase, and nascent RNA was immunoprecipitated using antibodies conjugated to protein A/G beads. After washing, RNA was extracted with Trizol, spiked with Drosophila mRNA, and libraries were prepared using the QIA miRNA kit.