A sequential binding mechanism for 5′ splice site recognition and modulation for the human U1 snRNP

Splice site recognition is essential for defining the transcriptome. Drugs like risdiplam and branaplam change how human U1 snRNP recognizes particular 5 ' splice sites (5 ' SS) and promote U1 snRNP binding and splicing at these locations. Despite the therapeutic potential of 5 ' SS modulators, the complexity of their interactions and snRNP substrates have precluded defining a mechanism for 5 ' SS modulation. We have determined a sequential binding mechanism for modulation of -1A bulged 5 ' SS by branaplam using a combination of ensemble kinetic measurements and colocalization single molecule spectroscopy (CoSMoS). Our mechanism establishes that U1-C protein binds reversibly to U1 snRNP, and branaplam binds to the U1 snRNP/U1-C complex only after it has engaged with a -1A bulged 5 ' SS. Obligate orders of binding and unbinding explain how reversible branaplam interactions cause formation of long-lived U1 snRNP/5 ' SS complexes. Branaplam targets a ribonucleoprotein, not only an RNA duplex, and its action depends on fundamental properties of 5 ' SS recognition. Splice sites must be correctly identified for introns to be removed from pre-mRNAs and for expression of the correct mRNA isoforms. Here, the authors elucidate how the human U1 snRNP splicing factor recognizes 5 ' splice sites and how a splicing modulating drug can enhance splice site recognition.