Structural basis of branch site recognition by the human spliceosome

Abstract

Intron recognition in the spotlight Excision of noncoding introns from pre–messenger RNAs is catalyzed by the spliceosome, a large RNA-protein complex that recognizes specific sequences at the exon-intron boundaries (splice sites). These sequences are highly degenerate in humans, and it has remained elusive how they are recognized by the spliceosome. Tholen et al . report a series of high-resolution structures of the human U2 small nucleolar ribonucleoprotein, the component of the spliceosome that recognizes branch sites. The structures explain how SF3B6 helps to stabilize the branch helix in the absence of extensive sequence complementarity. A newly identified spliceosome assembly intermediate suggests a mechanism for fidelity control of branch site recognition. —DJ

Genome-wide detection of human variants that disrupt intronic branchpoints

“…3 C and SI Appendix , Table S5 ). This may imply that the BP–U2 interaction in the major spliceosome can be complemented by other spliceosomal elements (e.g., SF3B1, SF3B6, PHF5A, SFA2, SFA3) ( 6 ), and hence a weaker wobble BP–U2 base pairing could be acceptable. Since the minor spliceosome forms a U11–U12 di-snRNA complex to bind to 5′ss and BP simultaneously, it requires more perfect BP–U12 base pairing, which is also reflected in more conserved 5′ss and BP motifs in minor introns ( Fig.…”

“…The major spliceosome recruits U1, U2, U4, U5, and U6 snRNAs, in which the U1 and U2 snRNAs recognize 5′ss and BP independently ( 1 ). In the interaction between BP and U2 snRNA, the BP nucleotide bulges out to bind into a pocket formed by SF3B1 and PHF5A ( 6 ), and its flanking sequences base-pair with U2 snRNA ( 5 , 7 ), while U2 snRNA is stabilized by SF3B6 ( 6 ). The minor spliceosome recruits U11, U12, U4atac, U5, and U6atac snRNAs, in which the U11 and U12 snRNAs first form a di-snRNA complex before recognizing the 5′ss and BP simultaneously ( 7 , 8 ).…”

Genome-wide detection of human variants that disrupt intronic branchpoints

“…We further estimated the binding energy between BP and snRNA ( Methods ), and found that BP in major introns displayed weaker binding with U2-snRNA than that between BP and U12-snRNA in minor introns ( Figure 4c, Table S5 ). This may imply that the BP-U2 interaction in the major spliceosome can be complemented by other spliceosomal elements (e.g., SF3B1, SF3B6, PHF5A, SFA2, SFA3) (Tholen et al 2022), hence a weaker wobble BP-U2 base-pairing could be acceptable. Since the minor spliceosome forms a U11-U12 di-snRNA complex to bind to 5’ss and BP simultaneously, it requires more perfect BP-U12 base-pairing, which is also reflected in more conserved 5’ss and BP motifs in minor introns ( Figure 4a ).…”

“…The major spliceosome recruits U1, U2, U4, U5 and U6 snRNAs, in which the U1 and U2 snRNAs recognize 5’ss and BP independently (Scotti and Swanson 2016). In the interaction between BP and U2 snRNA, the BP nucleotide bulges out to bind into a pocket formed by SF3B1 and PHF5A (Tholen et al 2022), and its flanking sequences base-pair with U2 snRNA (Turunen et al 2013; Mercer et al 2015), while U2 snRNA is stabilized by SF3B6 (Tholen et al 2022). The minor spliceosome recruits U11, U12, U4atac, U5 and U6atac snRNAs, in which the U11 and U12 snRNAs first form a di-snRNA complex before recognizing the 5’ss and BP simultaneously (Turunen et al 2013; Bai et al 2021).…”

Chemokine Receptor 1 and its associated immune pathway are downregulated in SF3B1MT blood and non-blood cancers

“…Our studies, as well as recent cryo-EM and crystal work, revealed that the SF3B1 component of the SF3b complex binds to pre-mRNA on both sides of the branchpoint sequence (BPS) at the catalytic heart of the spliceosome (Gozani et al 1996; 1998; Reed 2000; Will and Luhrmann 2011; Cretu et al 2016; Finci et al 2018). SF3B1 is recruited to the BPS region via direct interactions with U2AF1, which binds to the pyrimidine tract at the 3’ splice site (Gozani et al 1998; Wang et al 1998; Tholen et al 2022). Additional SF3a/b components bind immediately upstream of the BPS, where they anchor U2 snRNP to the pre-mRNA during spliceosome assembly (Gozani et al 1996, 1998; Wang et al 1998; Will and Luhrmann 2011; Cretu et al 2016; Finci et al 2018).…”