Journal
NATURE STRUCTURAL & MOLECULAR BIOLOGY
Volume 26, Issue 10, Pages 930-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/s41594-019-0300-4
Keywords
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Funding
- European Research Council [206726-CLIP, 617837-Translate]
- Slovenian Research Agency [P2-0209, Z7-3665, J7-5460]
- Edmond Lily Safra Fellowship - Wellcome Trust
- Sir Henry Dale Fellowship - Wellcome Trust
- Royal Society [215454/Z/19/Z]
- Biotechnology and Biological Sciences Research Council [BB/M009513/1]
- Wellcome Trust [110292/Z/15/Z, FC001002]
- Medical Research Council [MC_UU_12022/1, MC_UU_12022/8]
- National Institute of Neurological Disorders and Stroke of the National Institutes of Health (NIH-NINDS) [R01 NS102451]
- Cancer Research UK [FC001002]
- UK Medical Research Council [FC001002]
- MRC [MC_UU_12022/1, 1764955, MC_U105185858, MC_UU_12022/8] Funding Source: UKRI
- Wellcome Trust [110292/Z/15/Z, 215454/Z/19/Z] Funding Source: Wellcome Trust
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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.
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