Temporal-iCLIP captures co-transcriptional RNA-protein interactions

Ross A. Cordiner, Yuhui Dou, Rune Thomsen, Andrii Bugai, Sander Granneman, Torben Heick Jensen*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II (RNAPII)-derived transcripts. Yet, our current understanding of this process in vivo primarily stems from steady state analysis. To remedy this, we here conduct temporal-iCLIP (tiCLIP), combining RNAPII transcriptional synchronisation with UV cross-linking of RNA-protein complexes at serial timepoints. We apply tiCLIP to the RNA export adaptor, ALYREF; a component of the Nuclear Exosome Targeting (NEXT) complex, RBM7; and the nuclear cap binding complex (CBC). Regardless of function, all tested factors interact with nascent RNA as it exits RNAPII. Moreover, we demonstrate that the two transesterification steps of pre-mRNA splicing temporally separate ALYREF and RBM7 binding to splicing intermediates, and that exon-exon junction density drives RNA 5′end binding of ALYREF. Finally, we identify underappreciated steps in snoRNA 3′end processing performed by RBM7. Altogether, our data provide a temporal view of RNA-protein interactions during the early phases of transcription.

Original languageEnglish
Article number696
Number of pages16
JournalNature Communications
Issue number1
Publication statusPublished - 8 Feb 2023


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