SF3B6

SF3B6 (SF3b14a/p14) is an integral component of the human SF3b subcomplex within the 17S U2 snRNP that participates in branch site recognition during spliceosome assembly (PMID:34822310, PMID:16537922). It directly contacts the branch site-interacting region of U2 snRNA, and these RNA-protein interactions are dynamic, changing as the complex transitions between the 17S U2 snRNP and the spliceosomal A and B complexes (PMID:16537922, PMID:17652325). High-resolution cryo-EM of the substrate-bound U2 snRNP shows that SF3B6 stabilizes the branch site:U2 snRNA duplex, a function expected to aid recognition of introns with poor complementarity to U2 snRNA (PMID:34822310), and structural work further localizes SF3B6 to a defined position within the spliceosomal B complex (PMID:38383864). Beyond core splicing, SF3B6 directly binds diverse target mRNAs and regulates their expression and alternative splicing, including oncogene and tumor suppressor transcripts, and its knockdown impairs breast cancer cell proliferation and migration while increasing apoptosis (PMID:41233405).

1. 2006 High

   Established that SF3B6 makes physical contact with U2 snRNA near the branch site and that this contact is not static, framing SF3B6 as a dynamic participant in branch site engagement across assembly stages.

   Evidence Lead(II)-induced RNA cleavage and UV cross-linking of immunoaffinity-purified human 17S U2 snRNPs compared across A and B complexes

   PMID:16537922

   Open questions at the time

   • Did not define the precise residues mediating the contact
   • Functional consequence of the dynamic rearrangement not tested by perturbation
2. 2007 Medium

   Pinpointed the molecular contact, confirming SF3B6 directly cross-links to the branch site-interacting region of U2 snRNA rather than contacting it indirectly.

   Evidence UV cross-linking with IMAC enrichment and MALDI-MS/MS of peptide-RNA heteroconjugates from a partial U2 snRNP

   PMID:17652325

   Open questions at the time

   • No mutagenesis to validate the cross-link contribution to function
   • Single-lab biochemical assignment
3. 2021 High

   Resolved at near-atomic detail how SF3B6 acts within the substrate-bound U2 snRNP, showing it stabilizes the branch site:U2 snRNA duplex and thereby could license introns with weak U2 complementarity.

   Evidence Cryo-EM (2.0–2.2 Å) of in vitro-reconstituted human 17S U2 snRNP during ATP-dependent remodeling and pre-mRNA binding

   PMID:34822310

   Open questions at the time

   • Direct demonstration that SF3B6 loss broadens or restricts branch site usage in cells not shown
   • Does not address regulation of SF3B6 within the complex
4. 2021 Low

   Proposed a regulatory mechanism in which SF3B6 allosterically promotes an open-to-close conformational transition in SF3B1 to influence branch point selection.

   Evidence Comparative homology modeling, anisotropic network model normal mode analysis, and correlated-motion analysis of human vs. yeast SF3b

   PMID:35028595

   Open questions at the time

   • Purely computational with no experimental validation of the predicted allostery
   • Functional inference about residue motions not tested by mutagenesis
5. 2021 Low

   Linked SF3B6 to a cancer-associated regulatory axis, showing a lncRNA binds SF3B6 and promotes its phosphorylation to alter alternative splicing in pancreatic cancer cells.

   Evidence RNA pull-down, RIP, immunofluorescence, western blotting, and xenograft assays in PDAC cells

   PMID:34470609

   Open questions at the time

   • Phosphorylation claim lacks kinase identification and phosphosite mapping
   • No mutagenesis to establish causality of the interaction
6. 2022 Medium

   Tested whether SF3B6 modulates the U2AF2-SF3B1 interface and found it does not, delimiting where SF3B6's influence does and does not lie.

   Evidence Quantitative binding assays of U2AF2 UHM with SF3B1 ULM ± SF3B6

   PMID:35780835

   Open questions at the time

   • Negative result confined to a single interface
   • Does not address SF3B6 effects on other steps of U2 recruitment
7. 2023 Low

   Showed SF3B6 protein stability and SF3B complex incorporation are independent of PHF5A, indicating SF3B6 levels are buffered against loss of another SF3b subunit.

   Evidence Western blotting and SF3B complex analysis in patient-derived fibroblasts with PHF5A LOF variants

   PMID:37422718

   Open questions at the time

   • Indirect observation of SF3B6, no direct test of stability determinants
   • Compensatory mechanism not identified
8. 2024 Medium

   Updated the structural model by localizing SF3B6 to a previously unknown position within the spliceosomal B complex, revealing new contacts at a later assembly stage.

   Evidence Cryo-EM of dimerized human spliceosomal B complexes formed with ATP-γS at improved resolution

   PMID:38383864

   Open questions at the time

   • SF3B6-specific contacts not validated by mutagenesis or function
   • Functional role of the new position inferred from structure alone
9. 2025 Medium

   Extended SF3B6 beyond core splicing, demonstrating it directly binds target mRNAs to regulate their expression and splicing and is required for breast cancer cell proliferation and migration.

   Evidence siRNA knockdown with RNA-seq and iRIP-seq in MDA-MB-231 cells with RT-qPCR target validation

   PMID:41233405

   Open questions at the time

   • Direct regulation of named oncogene/suppressor targets not reconstituted biochemically
   • Mechanism linking SF3B6 to NF-κB-associated transcripts not resolved

• How SF3B6's branch-site duplex stabilization translates into genome-wide branch point and alternative splicing choices, and how its cancer-associated regulation feeds back on this activity, remains unresolved.
• No cell-based perturbation linking SF3B6 structural function to defined branch site usage changes
• Allosteric regulation of SF3B1 lacks experimental confirmation
• Kinase and phosphosites governing SF3B6 regulation unidentified