Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-like MBNL1

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 439 East 67th Street, New York, NY 10021, USA.
Nature Structural & Molecular Biology (Impact Factor: 13.31). 12/2008; 15(12):1343-51. DOI: 10.1038/nsmb.1519
Source: PubMed


Muscleblind-like (MBNL) proteins, regulators of developmentally programmed alternative splicing, harbor tandem CCCH zinc-finger (ZnF) domains that target pre-mRNAs containing YGCU(U/G)Y sequence elements (where Y is a pyrimidine). In myotonic dystrophy, reduced levels of MBNL proteins lead to aberrant alternative splicing of a subset of pre-mRNAs. The crystal structure of MBNL1 ZnF3/4 bound to r(CGCUGU) establishes that both ZnF3 and ZnF4 target GC steps, with site-specific recognition mediated by a network of hydrogen bonds formed primarily with main chain groups of the protein. The relative alignment of ZnF3 and ZnF4 domains is dictated by the topology of the interdomain linker, with a resulting antiparallel orientation of bound GC elements, supportive of a chain-reversal loop trajectory for MBNL1-bound pre-mRNA targets. We anticipate that MBNL1-mediated targeting of looped RNA segments proximal to splice-site junctions could contribute to pre-mRNA alternative-splicing regulation.

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    • "Molecular dynamics simulations suggested that 5 0 CU/3 0 UC internal loops exist in a dynamic equilibrium between two conformations (Childs-Disney et al., 2014). A complex of tetrameric MBNL1 bound to a model RNA recognition site has been characterized by X-ray crystallography (Teplova and Patel, 2008) (Figure 4A); a complex of two MBNL1 zinc fingers with two single-stranded RNAs has also been refined from X-ray crystallographic data (Teplova and Patel, 2008). The specificity of MBNL1 binding to imperfect (with multiple U 3 U or CU 3 UC internal loops) rather than to fully base-paired stem-loop was demonstrated experimentally (Kino et al., 2004; Warf and Berglund, 2007). "
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    • "This question is addressed in a paper reporting the crystallographic complex of zinc finger domains from the alternative splicing regulator protein MBNL1 and CGCUGU (80). The model shows the protein interacting with a short single-stranded RNA, in particular with the GC step in its sequence. "
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    • "First , the N - terminal zinc finger of Pan3 conveys sequence specificity by binding to polyA RNA prefer - entially over other polyribonucleotides ( Supplementary Fig S4 ) . The NMR solution structure of the scPan3 zinc finger ( Fig 2 ) revealed a similarity to other zinc fingers that bind RNA ( Hudson et al , 2004 ; Teplova & Patel , 2008 ; Kuhlmann et al , 2014 ) . Each of these other proteins contains tandem zinc fingers within the same polypeptide chain ( four in MBNL1 , two in TIS11d , and seven in Nab2 ) , probably because the affinity of a single finger is insufficient to provide binding specificity . "
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