Structural insights into the targeting of mRNA GU-rich elements by the three RRMs of CELF1

• Published in: Nucleic acids research 2013-08, Vol.41 (14), p.7153-7166
• Main Authors: Edwards, John M, Long, Jed, de Moor, Cornelia H, Emsley, Jonas, Searle, Mark S
• Format: Article
• Language: English
• Subjects: Binding Sites; Electron Spin Resonance Spectroscopy; Guanine - analysis; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Protein Binding; Protein Structure, Tertiary; RNA, Messenger - chemistry; RNA, Messenger - metabolism; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - metabolism; Structural Biology; Uridine - analysis; Xenopus Proteins - chemistry; Xenopus Proteins - metabolism; Yugus
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkt470

The CUG-BP, Elav-like family (CELF) of RNA-binding proteins control gene expression at a number of different levels by regulating pre-mRNA splicing, deadenylation and mRNA stability. We present structural insights into the binding selectivity of CELF member 1 (CELF1) for GU-rich mRNA target sequences of the general form 5'-UGUNxUGUNyUGU and identify a high affinity interaction (Kd ∼ 100 nM for x = 2 and y = 4) with simultaneous binding of all three RNA recognition motifs within a single 15-nt binding element. RNA substrates spin-labelled at either the 3' or 5' terminus result in differential nuclear magnetic resonance paramagnetic relaxation enhancement effects, which are consistent with a non-sequential 2-1-3 arrangement of the three RNA recognition motifs on UGU sites in a 5' to 3' orientation along the RNA target. We further demonstrate that CELF1 binds to dispersed single-stranded UGU sites at the base of an RNA hairpin providing a structural rationale for recognition of CUG expansion repeats and splice site junctions in the regulation of alternative splicing.