PRPF38A

PRPF38A (yeast Prp38) is an essential pre-mRNA splicing factor required for the catalytic activation of the spliceosome (PMID:1508195). It is recruited to the assembling spliceosome as part of a B-complex protein (BCP) subcomplex together with Snu23 and MFAP1 (metazoan ortholog of yeast Spp381), the three proteins binding and releasing as a unit after tri-snRNP association and dissociating predominantly after U4 snRNP release and NTC recruitment (PMID:39995036). Its N-terminal domain is built from three pairs of antiparallel α-helices and functions as a multi-interface protein–protein interaction hub that engages at least twelve other spliceosomal proteins through four distinct surfaces; excess of this domain stalls splicing at a pre-catalytic stage, whereas an interaction-deficient mutant does not (PMID:26673105). Within the assembled B complex, Prp38 contacts the Prp8 N-terminal domain and stabilizes the U6 ACAGAGA stem–pre-mRNA and Brr2–U4 snRNA interactions prior to catalytic activation, and in human B complex it contacts SNU23 and FBP21 around the U6/5' splice site helix (PMID:28530653, PMID:38383864). The Snu23–Prp38–MFAP1/Spp381 architecture is built on ER/K motif–stabilized single α-helices whose binding strength is tunable by helix stabilization, and is conserved across species (PMID:27773687, PMID:28335716). Functionally, loss of PRPF38A causes widespread intron retention and altered splicing of transcripts controlling protein homeostasis, mitosis, and apoptosis (PMID:28878028), and correct spatial positioning of PRPF38A within nuclear speckles is itself required for normal splicing, since mislocalization to the nuclear lamina induces intron retention (PMID:32609799, PMID:35869234). Independently, the ubiquitin-like protein Hub1/UBL5 binds non-covalently to a conserved HIND element in Prp38 to modulate splice-site usage and alternative splicing (PMID:21614000, PMID:36480405).

1. 1992 High

   Established that Prp38 is an essential splicing factor acting specifically at the first catalytic step rather than during early assembly, defining its functional stage in the pathway.

   Evidence Temperature-sensitive genetic screen with in vitro splicing inactivation and complementation in yeast

   PMID:1508195

   Open questions at the time

   • Molecular mechanism by which Prp38 promotes the first cleavage-ligation step not defined
   • Connection between Prp38 loss and reduced U6 snRNA levels unexplained at the time
2. 1999 High

   Identified Spp381 (MFAP1 ortholog) as a direct binding partner of the Prp38 C-terminal half and placed both in the tri-snRNP, linking Prp38 to U4 snRNA release.

   Evidence Dosage suppressor screen, yeast two-hybrid, co-immunoprecipitation, and in vitro splicing in yeast

   PMID:9858581

   Open questions at the time

   • Structural basis of the Prp38–Spp381 interface not resolved
   • Whether the interaction is direct in the assembled spliceosome not shown
3. 2011 High

   Revealed a regulatory layer in which the ubiquitin-like Hub1 binds a conserved HIND element in Prp38, modulating alternative splice-site usage without disrupting the spliceosome.

   Evidence NMR/biochemical binding, domain mapping, and splicing assays in Hub1-deficient yeast and plants

   PMID:21614000

   Open questions at the time

   • Mechanism by which HIND binding alters splice-site selection not defined
   • Conservation in animals addressed only later
4. 2015 High

   Defined the human PRPF38A N-terminal domain as a multi-interface interaction hub whose contacts are required to progress past a pre-catalytic stage, explaining how it organizes B-complex protein assembly.

   Evidence Crystal structure, alanine surface-scanning two-hybrid, in vitro binding, and splicing inhibition with domain mutants

   PMID:26673105

   Open questions at the time

   • Functional role of each of the four surfaces in vivo not dissected
   • Identities of all twelve binding partners not individually validated functionally
5. 2016 High

   Showed the Snu23–Prp38–MFAP1 subcomplex is held together by ER/K-stabilized single α-helices whose affinity is tunable by helix stabilization, revealing a biophysical principle of its assembly.

   Evidence Crystal structure with mutant-peptide binding assays and biophysical characterization (ITC/CD)

   PMID:27773687

   Open questions at the time

   • Whether helix tuning is exploited for regulation in vivo unknown
   • Dynamics of subcomplex assembly during spliceosome maturation not addressed
6. 2017 High

   Placed Prp38 structurally in the pre-catalytic B complex, showing it binds the Prp8 N-terminal domain and stabilizes U6 ACAGAGA stem–pre-mRNA and Brr2–U4 interactions before catalytic activation.

   Evidence Near-atomic cryo-EM of the yeast B complex spliceosome

   PMID:28530653

   Open questions at the time

   • Order of contact formation during assembly not resolved from a static structure
   • How these contacts are remodeled at activation not shown
7. 2017 Medium

   Established evolutionary equivalence of human MFAP1 to yeast Spp381 and conservation of the Snu23-Prp38-MFAP1/Spp381 subcomplex across species.

   Evidence In vitro cross-species binding assays, bioinformatics, and yeast prp38-1 complementation

   PMID:28335716

   Open questions at the time

   • Single-lab study
   • Only partial rescue of yeast growth defects achieved
8. 2017 Medium

   Demonstrated a cellular requirement for PRPF38A in correct splicing of survival-relevant transcripts, linking its loss to intron retention and altered processing of homeostasis, mitosis, and apoptosis genes.

   Evidence siRNA knockdown with RNA-seq splicing analysis in human breast cancer cell lines

   PMID:28878028

   Open questions at the time

   • Direct vs. indirect splicing targets not distinguished
   • No mechanistic follow-up beyond the descriptive phenotype
9. 2020 Medium

   Localized PRPF38A to nuclear speckles and showed it co-localizes with MFAP1 in droplet-like bodies that precede speckle formation during telophase, connecting the subcomplex to speckle biogenesis.

   Evidence Proximity labeling (TSA-MS) with live-cell imaging and telophase co-localization

   PMID:32609799

   Open questions at the time

   • Functional significance of pre-speckle droplet co-localization not tested
   • Whether speckle targeting is required for splicing addressed separately
10. 2022 Medium

    Established that PRPF38A spatial positioning is itself functionally important, as forced re-localization to the nuclear lamina increases intron retention.

    Evidence Reversible chemical-dimerizer re-localization with RNA-seq intron-retention quantification in HEK293T cells

    PMID:35869234

    Open questions at the time

    • Single method, single cell line
    • Whether the effect reflects loss of speckle context or sequestration not distinguished
11. 2022 Medium

    Confirmed the Hub1/UBL5–HIND–Prp38 regulatory axis operates in a multicellular animal, generalizing the splice-site regulation mechanism beyond yeast and plants.

    Evidence Biochemical binding, C. elegans ubl-5 mutant genetics, splicing assays, and yeast complementation

    PMID:36480405

    Open questions at the time

    • Only selected targets analyzed
    • Mechanism of splice-site modulation by the HIND interaction still undefined
12. 2024 High

    Refined the human B-complex contacts of PRPF38A, resolving interactions with SNU23 and FBP21 around the U6/5' splice site helix and a MFAP1/UBL5 5' exon binding channel.

    Evidence Enhanced-resolution cryo-EM of human B complex dimers

    PMID:38383864

    Open questions at the time

    • Functional consequence of each refined contact not individually tested
    • Significance of the dimeric arrangement unclear
13. 2025 High

    Resolved the recruitment dynamics, showing Prp38, Snu23, and Spp381 bind and release as a single BCP subcomplex after tri-snRNP binding, with release after U4 dissociation/NTC association, conserved between yeast and humans.

    Evidence Single-molecule colocalization spectroscopy (CoSMoS) of real-time binding/release dynamics in yeast

    PMID:39995036

    Open questions at the time

    • What triggers coordinated BCP release not defined
    • Human dynamics inferred from conservation rather than directly observed

• How the Hub1/UBL5-HIND regulatory input is integrated with PRPF38A's structural role in B-complex assembly to control specific splice-site choices in human cells remains open.
• No mechanistic link established between HIND-mediated regulation and the multi-interface hub function
• Direct human substrate/target rules for PRPF38A-dependent splicing not defined