RBM15B

RBM15B (OTT3) is a non-shuttling nuclear SPEN-family RNA-binding protein, with N-terminal RNA recognition motifs and a C-terminal SPOC domain, that operates at the interface of mRNA processing, nuclear export, and m6A deposition (PMID:16129689). Through its C-terminal region it directly engages the mRNA export receptor NXF1 and the export factor Aly/REF, and it self-associates and localizes to the splicing factor compartment and nuclear envelope, linking it to post-transcriptional regulation (PMID:19586903). As a splicing regulator, RBM15B competes with SR proteins, co-elutes with CDK11p110, cyclin L2α, and SR proteins in a ~1-MDa nuclear complex, and inhibits formation of the functional spliceosomal E complex, thereby antagonizing CDK11p110-cyclin L2α-dependent splicing (PMID:21044963). Its defining recent role is as a component of the m6A methyltransferase writer machinery: RBM15B reads the H3K79me2 histone mark via residue H47 to guide selective m6A deposition into 5'UTRs and around start codons of transcripts from H3K79me2-marked loci, enhancing translation of oncogenic mRNAs and sustaining MLL-rearranged leukemia stem cells (PMID:41629530). This chromatin-coupled m6A-writing activity stabilizes diverse target mRNAs through IGF2BP- and YTHDF-family readers — for example PCNA via YTHDF1 (PMID:39361104) and ITSN2 via IGF2BP1 (PMID:41795047). RBM15B is also exploited by viruses, acting with RBM15/SPEN to bind incoming viral RNA and support infection (PMID:21106733, PMID:20828777).

1. 2005 Medium

   Established RBM15B/OTT3 as a SPEN-family nuclear RNA-binding protein with a distinct domain architecture and a function in splicing regulation, defining the protein's basic identity.

   Evidence Yeast two-hybrid, co-localization, domain mapping, and beta-globin/beta-thalassemia splicing reporter assays

   PMID:16129689

   Open questions at the time

   • No genome-wide RNA targets identified
   • SPOC domain partners only partially mapped (EBV EB2; weak SMRT)
   • Catalytic or scaffolding role within any complex undefined
2. 2009 High

   Connected RBM15B to the mRNA export machinery, showing its C-terminus directly binds NXF1 and Aly/REF, positioning it as a post-transcriptional/export cofactor rather than a splicing factor alone.

   Evidence Reciprocal co-immunoprecipitation, mutational mapping, and subcellular fractionation/microscopy

   PMID:19586903

   Open questions at the time

   • Specific exported mRNA cargoes not defined
   • Functional consequence of export-factor binding on endogenous transcripts unresolved
3. 2010 High

   Defined a mechanism by which RBM15B negatively regulates splicing — competing with SR proteins and blocking spliceosomal E complex assembly within a ~1-MDa CDK11p110/cyclin L2α complex.

   Evidence Size exclusion chromatography, co-IP, in vitro pulldown, domain mapping, in vitro and in vivo splicing assays

   PMID:21044963

   Open questions at the time

   • Endogenous splicing targets not enumerated
   • How splicing role integrates with later m6A-writing role unknown
4. 2010 Medium

   Showed RBM15B/RBM15 are co-opted in herpesvirus gene expression and that viral proteins (KSHV ORF57, EBV EB2) target the SPOC domain, revealing the protein as a node hijacked for viral RNA fate.

   Evidence RNAi knockdown, nuclear RNA fractionation export assays, ectopic expression, direct interaction assays

   PMID:20828777 PMID:21106733

   Open questions at the time

   • Mechanism of RNA export deficiency on knockdown not fully resolved
   • RBM15B-specific (vs RBM15) contribution not separated
5. 2025 Low

   Extended RBM15B's pro-viral role to direct binding of incoming viral RNA and m6A deposition, implicating the SPEN/RBM15/RBM15B writer complex in modifying viral transcripts during early infection.

   Evidence VIR-CLASP, direct RNA sequencing for m6A, SPEN depletion, infection assays (preprint); plus CVB3 cardiomyocyte knockdown phenotyping

   PMID:40546402 PMID:bio_10.1101_2025.11.21.689838

   Open questions at the time

   • RBM15B-specific contribution not separated from SPEN/RBM15
   • Preprint, not peer-reviewed
   • Direct enzymatic step not reconstituted
6. 2025 Medium

   Placed RBM15B as an m6A writer that stabilizes specific oncogenic mRNAs through defined reader proteins, establishing a recurrent RBM15B→m6A→reader→mRNA-stability axis across cancers.

   Evidence MeRIP/m6A-RIP, RIP, actinomycin D stability assays, knockdown/overexpression, and xenografts across PCNA-YTHDF1, FNBP1-IGF2BP2, ITSN2-IGF2BP1, and KMT2C-IGF2BP3 studies

   PMID:39361104 PMID:41086050 PMID:41161249 PMID:41795047

   Open questions at the time

   • Direct catalytic activity of RBM15B not reconstituted in most studies
   • Target selectivity rules not defined per study
   • Most chains involve single labs and indirect readouts
7. 2026 High

   Resolved how RBM15B achieves m6A target selectivity — H47-dependent recognition of H3K79me2 couples chromatin state to 5'UTR/start-codon m6A deposition and translational enhancement, defining a chromatin-reading/m6A-writing mechanism.

   Evidence H3K79me2 recognition assays, MeRIP-seq, H47 active-site mutagenesis, translation efficiency assays, leukemic stem cell functional assays

   PMID:41629530

   Open questions at the time

   • Structural basis of H3K79me2 recognition not detailed
   • Relationship between this chromatin-coupled writing and the earlier splicing/export roles unresolved
8. 2026 Low

   Mapped upstream transcriptional and epigenetic control of RBM15B (YY1 activation, FOXP2 repression, CAF-lactate-driven histone lactylation) feeding into m6A stabilization of FOXM1, KDM4C, ITGA1, and ANLN, embedding RBM15B in tumor regulatory circuits.

   Evidence ChIP/promoter and dual-luciferase assays, histone lactylation ChIP, MeRIP, mRNA stability assays, and functional/xenograft models

   PMID:35494016 PMID:41661469 PMID:42020859 PMID:42148505 PMID:42227273

   Open questions at the time

   • Single-lab studies with limited direct enzymatic characterization
   • Multiple intermediaries inferred rather than reconstituted
   • Direct vs indirect RBM15B effects on each target not separated

• How RBM15B's distinct activities — splicing antagonism, mRNA export, and chromatin-guided m6A writing — are coordinated on shared transcripts, and the structural and biochemical basis of its direct catalytic contribution to the methyltransferase complex, remain unresolved.
• No structural model of RBM15B within the METTL3/METTL14 writer complex
• Direct catalytic vs scaffolding role not reconstituted in vitro
• Integration of splicing/export and m6A functions on the same RNAs untested