A systems view of spliceosomal assembly and branchpoints with iCLIP

Michael Briese, Nejc Haberman, Christopher Sibley, Rupert Faraway, Andrea Elser, Anob Chakrabarti, Zhen Wang, Julian König, David Perera, Vihandha O Wickramasinghe, Ashok R Venkitaraman, Nicholas Luscombe, Luciano Saieva, Livio Pellizzoni, Christopher Smith, Tomaz Curk, Jernej Ule

Research output: Contribution to journalArticlepeer-review

Abstract

Studies of spliceosomal interactions are challenging due to their dynamic nature. Here we used spliceosome iCLIP, which immunoprecipitates SmB along with small nuclear ribonucleoprotein particles and auxiliary RNA binding proteins, to map spliceosome engagement with pre-messenger RNAs in human cell lines. This revealed seven peaks of spliceosomal crosslinking around branchpoints (BPs) and splice sites. We identified RNA binding proteins that crosslink to each peak, including known and candidate splicing factors. Moreover, we detected the use of over 40,000 BPs with strong sequence consensus and structural accessibility, which align well to nearby crosslinking peaks. We show how the position and strength of BPs affect the crosslinking patterns of spliceosomal factors, which bind more efficiently upstream of strong or proximally located BPs and downstream of weak or distally located BPs. These insights exemplify spliceosome iCLIP as a broadly applicable method for transcriptomic studies of splicing mechanisms.
Original languageEnglish
Pages (from-to)930-940
Number of pages11
JournalNature Structural & Molecular Biology
Volume26
Issue number10
Early online date30 Sep 2019
DOIs
Publication statusPublished - 1 Oct 2019

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