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Updated: May 29, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
Published on: November 7, 2025
Nuclear quality control of RNA polymerase II transcripts
Manfred Schmid1, Torben Heick Jensen
1Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, Aarhus University, C.F. Møllers Alle, Bldg. 130, 8000 Aarhus C., Denmark.
Abstract:
Eukaryotic RNA polymerase II produces an astounding diversity of transcripts. These may need to be 5(') capped, spliced, polyadenylated, and packaged with proteins before their export to the cytoplasm. Unscheduled accumulation of any RNA species can interfere with normal RNA metabolism and poses a serious hazard to cells. Yet, given the amount of primary transcripts and the complexity of the RNA maturation process, production of aberrant RNA species is unavoidable. Cells, therefore, employ nuclear RNA quality control mechanisms to rapidly degrade, actively retain, or transcriptionally silence unwanted RNAs. Pathways that monitor mRNA production are best understood and similar pathways are employed to destroy transcriptional noise. Finally, related mechanisms also contribute to gene regulation during normal growth.
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