A Core Issue for Understanding DM—How MBNL Interacts with RNA

Given the disease mechanisms that are operative in DM, an understanding of how the RNA-binding protein, Muscleblind (MBNL), interacts with pre-mRNA to regulate alternative splicing is essential. Recent studies have shown that MBNL exhibits differential dose-response relationships across the various gene translation events that it regulates in health and disease. It is as yet unclear precisely how the structure of the pre-mRNA itself contributes to patterning of MBNL-dependent alternative splicing.

RNA Structural Properties May Impact MBNL Binding and Functionality

MBNL’s normal function in alternative splicing, and perturbations of those functions in DM, is governed in part by the tissue-specific distribution and expression levels of its three isoforms (MBNL1, MBNL2, and MBNL3) during pre- and post-natal development. Yet, the structural properties of the pre-mRNAs that MBNL regulates may, themselves, play critical roles in the binding affinity and efficiency of MBNL-directed alternative splicing. A new publication looks at the MBNL—pre-mRNA interactions with the goal of understanding how transcript properties influence alternative splicing.

While the nature of MBNL-binding motifs has been well-characterized previously, Dr. Krzysztof Sobczak’s group (Adam Mickiewicz University—Poland) and their colleagues at the University of Florida show here the structural organization of the RNA regulatory elements in target pre-mRNA may play a more important role. An MDF fellow, Lukasz Sznajder, contributed to this work.

The team demonstrated the importance of target RNA structure in showing that both MBNL binding and splicing activity are regulated by the number and structural arrangement of UGCU motifs, but, while splicing regulation is affected by the distance between UGCU motifs, that outcome is not a function of differences in binding efficiency. MBNL binding patterns are altered, however, when the MBNL binding sites are included in an RNA hairpin. Furthermore, modifications of target RNA secondary structure showed that structuring the same RNA binding site differently leads to altered MBNL1 binding and splicing regulation activity. In tissues expressing multiple MBNL paralogs, the team detected competitive interactions that influenced splicing events.

Modeling Regulation of Alternative Splicing by MBNL

The modeling of MBNL regulation of alternative splicing now has at least two components. Component 1—it has already been clear that the spectrum of MBNL-modulated alternative splicing events are differentially sensitive to free MBNL levels. Component 2—these latest findings extend understanding of regulatory control by showing that structural properties of the pre-mRNA targets also represent a key determinant of splicing event sensitivity to free MBNL. Moreover, tissue specificity in alternative splicing is now seen to derive from the MBNL paralogs that are expressed and interactions among those paralogs. An understanding of MBNL protein interactions and of how pre-mRNA structure impacts binding and functional activity of the MBNL paralogs may be critical in efforts to design effective therapeutic strategies for DM.

Reference:

MBNL splicing activity depends on RNA binding site structural context.
Taylor K, Sznajder LJ, Cywoniuk P, Thomas JD, Swanson MS, Sobczak K.
Nucleic Acids Res. 2018 Jun 28. doi: 10.1093/nar/gky565. [Epub ahead of print]