The U2AF2 splicing factor, made of two tandem RNA recognition
motifs
(RRMs) joined by a flexible linker, selects the intronic polypyrimidine
sequence of premature mRNA, thus ensuring splicing fidelity. Increasing
evidence links mutations of key splicing factors, including U2AF2,
to a variety of cancers. Nevertheless, the impact of U2AF2 cancer-associated
mutations on polypyrimidine recognition remains unclear. Here, we
combined extensive (18 μs-long) all-atom molecular dynamics
simulations and dynamical network theory analysis (NWA) of U2AF2,
in its wild-type form and in the presence of the six most frequent
cancer-associated mutations, bound to a poly-U strand. Our results
reveal that the selected mutations affect the pre-mRNA binding at
two hot spot regions, irrespectively of where these mutants are placed
on the distinct U2AF2 domains. Complementarily, NWA traced the existence
of cross-communication pathways, connecting each mutation site to
these recognition hot spots, whose strength is altered by the mutations.
Our outcomes suggest the existence of a structural/dynamical interplay
of the two U2AF2’s RRMs underlying the recognition of the polypyrimidine
tract and reveal that the cancer-associated mutations affect the polypyrimidine
selection by altering the RRMs’ cooperativity. This mechanism
may be shared by other RNA binding proteins hallmarked, like U2AF2,
by multidomain architecture and high plasticity.
The U2AF2 splicing factor is involved
in the RNA recognition of
the pre-mRNA poly-pyrimidine signaling sequence. This protein contains
two RRM domains connected by a flexible linker, which ensure the preferential
selection of a poly-uridine sequence over a poly-cytosine one. In
this work, all-atom simulations provide insights into the U2AF2 recognition
mechanism and on the features underlying its selectivity. Our outcomes
show that U2AF2’s RNA recognition is driven by cooperative
events modulated by RNA–protein and RNA–ion interactions.
Stunningly, monovalent ions contribute to mediating the binding of
the weakly binding polyC strand, thus contributing to the selection
of suboptimal poly-pyrimidine tracts. This finding broadens our understanding
of the diverse traits tuning splicing factors’ selectivity
and adaptability to precisely handle and process diverse pre-mRNA
sequences.
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