Repurposed hnRNPC binds mature mRNAs and safeguards the mitotic transcriptome

Upon entry to mitosis, RNA metabolism is broadly suppressed. While mechanistic understanding is limited, the mitotic transcriptome is generally preserved, allowing daughter cells an economical start. We used highly effective cell cycle synchronization to specifically characterize mitotic heterogeneous nuclear ribonucleoprotein C (hnRNPC), an abundant nuclear RNA-binding protein known for intron binding and splicing regulation. Mitotic hnRNPC exhibited a density shift, forming low- and high-density (LD and HD) complexes. RNA-seq analysis combined with fluorescent crosslinking and immuno-precipitation (fCLIP) revealed hnRNPC binding to 17.1% and 8.7% of expressed genes in LD and HD complexes, respectively, with most sites mapping to protein-coding genes. Mediated by its known cooperative interaction with U-rich motifs along ≳700 nt-long targets, mitotic hnRNPC acquired prevalent interactions with exons, predominantly within the 3' untranslated region of mature mRNAs. Mitotic hnRNPC also retained intron interactions, predominantly in LD-hnRNPC RNPs, which comigrated with both the spliceosome and mono-ribosomes through a density gradient. HD-hnRNPC, which co-migrated with poly-ribosomes, predominantly interacted with mature mRNA complexes comprising new targets specific to mitosis. Downregulation of hnRNPC elicited a global negative effect on the abundance of its mitotic targets. The data point to the global role of mitotic hnRNPC as a stabilizer of pre-mRNA and mRNA.