Nuclear speckle periphery organizes stable intron-retained RNAs into a distinct nuclear retention compartment that resolves during mitosis
Intron retention (IR) is an important regulatory mechanism shaping RNA fate, yet its spatial and temporal organization in human cells remain largely unknown. Here, using compartment-resolved transcription-shutdown time course, we uncover and characterize a major class of long-lived intron-retained RNAs (LL-IR-RNAs) that account for nearly half of all IR events in pluripotent stem cells. These RNAs persist for hours in the nucleus, have high nuclear abundance, and derive from genes critical for genome maintenance and mitosis, such as centromere and kinetochore assembly, Fanconi anemia repair, chromatin regulation, telomere maintenance, and m6A RNA methylation.