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

Nature Structural & Molecular Biology volume 15, pages 1343–1351 (2008)Cite this article

Abstract

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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Figure 1: Domain architecture, sequence alignment and structure of the tandem ZnF domains of human MBNL1.
Figure 2: Crystal packing interactions of the MBNL1 ZnF3/4 in the free state and bound to the r(C1-G2-C3-U4-G5-U6) sequence.
Figure 3: Protein-RNA interactions in the molecule A complex.
Figure 4: Details of intermolecular protein-RNA recognition contacts in the complex.
Figure 5: Binding of GCU-containing RNAs to MBNL1 ZnF3/4.
Figure 6: Comparison of MBNL1 ZnF3/4 and TIS11d19 ZnF1/2 complexes with their respective RNA targets.

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Protein Data Bank

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GenBank/EMBL/DDBJ

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Acknowledgements

This research was supported by the US National Institutes of Health grant CA049982 to D.J.P. We thank S. Ilin for help with NMR data collection and O. Rechkoblit for help with X-ray synchrotron data collection of one of the data sets. We would like to thank the staff of NE-CAT beam line at the Advanced Photon Source, Argonne National Laboratory, supported by the US Department of Energy, for assistance with data collection.

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  1. Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 439 East 67th Street, New York, 10021, NY, USA

    Marianna Teplova & Dinshaw J Patel

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  1. Marianna Teplova
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  2. Dinshaw J Patel
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Contributions

The biochemical and structural research was undertaken by M.T. under the supervision of D.J.P. Both M.T. and D.J.P. contributed to the writing of the paper.

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Correspondence to Dinshaw J Patel.

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Teplova, M., Patel, D. Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-like MBNL1. Nat Struct Mol Biol 15, 1343–1351 (2008). https://doi.org/10.1038/nsmb.1519

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