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snRNP

Small nuclear ribonucleoproteins (snRNPs) are ribonucleoprotein complexes consisting of small nuclear RNAs (snRNAs) and associated proteins that serve as core components of the spliceosome, the molecular machine responsible for removing introns from pre-messenger RNA (pre-mRNA) in eukaryotic cells to produce mature mRNA.^[1] These particles are highly conserved across eukaryotes and are indispensable for accurate gene expression, as splicing errors can lead to diseases such as spinal muscular atrophy.^[2] snRNPs were discovered in the late 1970s by Michael R. Lerner and Joan A. Steitz, who identified the associated proteins with previously known snRNAs (U1 and U2, first detected in 1968), and named additional snRNAs as U4, U5, and U6 based on their electrophoretic mobility. In 1980, Lerner, Steitz, and colleagues proposed that snRNPs function in pre-mRNA splicing, a hypothesis later confirmed.^[3] The major spliceosomal snRNPs include U1, U2, U4, U5, and U6, each characterized by a specific snRNA (typically 100–200 nucleotides long) that is rich in uridine and post-transcriptionally modified with a trimethylguanosine cap or γ-monomethyl phosphate cap.^[2] The protein components comprise a common set of seven Sm proteins (B/B′, D1, D2, D3, E, F, G) that form a heteroheptameric ring binding the snRNA's Sm site in U1, U2, U4, and U5 snRNPs, while U6 associates with LSm proteins (LSm2–8); additionally, each snRNP harbors unique proteins that confer specificity, such as U1-70K in U1 snRNP.^[1] Minor snRNPs, like U11 and U12, handle splicing of rare AT-AC introns.^[2]

Introduction

Definition and Composition

Small nuclear ribonucleoproteins (snRNPs) are ribonucleoprotein complexes composed of small nuclear RNAs (snRNAs) and associated proteins that serve as essential building blocks of the spliceosome in eukaryotic cells, facilitating the removal of introns from pre-mRNA transcripts.^[4] These complexes are highly structured, with the snRNA providing the RNA scaffold and the proteins conferring stability, specificity, and functional interactions.^[5] The core composition of most snRNPs (U1, U2, U4, and U5) includes a single snRNA molecule, typically 100–300 nucleotides long and rich in uridines, bound to a heteroheptameric ring of seven Sm proteins: SmB/SmB′, D1, D2, D3, E, F, and G.^[6] These Sm proteins assemble in a specific order (D1, D2, F, E, G, D3, B/B′) around a conserved Sm binding site (PuAU3-6GPu) at the 3′ end of the snRNA, forming a stable, doughnut-shaped core structure approximately 110–120 kDa in mass.^[7] In addition to this shared core, each snRNP incorporates type-specific proteins that confer unique functions; for instance, the U1 snRNP includes U1-70K, U1A, and U1C proteins, which together contribute to an overall molecular mass of around 250 kDa for the mature complex.^[8] The U6 snRNP variant deviates from this architecture, associating instead with a heteroheptameric ring of Sm-like (LSm) proteins (Lsm2–Lsm8) bound to its 3′ end, lacking the canonical Sm site.^[5] In mammalian cells, snRNPs exhibit varying abundance, with U1 and U2 being the most prevalent at approximately 10^6 copies per nucleus, reflecting their central roles in spliceosome assembly.^[9] Overall, snRNP complexes range in size from 150 to 400 kDa, depending on the number and size of associated proteins.^[10] snRNPs are evolutionarily conserved across all eukaryotes, with the Sm and LSm protein families displaying high sequence similarity from yeast to humans, underscoring their fundamental importance in RNA processing.^[11]

Discovery and Nomenclature

Small nuclear RNAs (snRNAs) were first identified in 1968 during gel electrophoresis experiments on eukaryotic cell extracts, where unexpected RNA species migrating between 5S and 18S rRNAs were observed.^[12] These RNAs, initially termed "U" RNAs due to their uridylic acid content, were characterized as abundant nuclear components. Studies by researchers such as Harris Busch and Sheldon Penman identified U1 and U2 snRNAs in 1968 based on their electrophoretic mobility in polyacrylamide gels under denaturing conditions.^[3] Michael Lerner and Joan Steitz later identified U4, U5, and U6 snRNAs in 1979 using autoantibodies from patients with systemic lupus erythematosus.^[3] The U designation reflected their localization to the nucleus and distinctive gel positions, with U1 exhibiting the slowest migration and U6 the fastest among the major snRNAs.^[3] The association of these snRNAs with proteins to form small nuclear ribonucleoproteins (snRNPs) was established in the late 1970s through immunological and biochemical approaches. In 1979, Michael Lerner and Joan Steitz utilized autoantibodies from patients with systemic lupus erythematosus to immunoprecipitate RNA-protein complexes, revealing that U1, U2, U4, U5, and U6 snRNAs were tightly bound to common proteins, including those recognized by anti-Sm antibodies.^[3] This work marked the first isolation of intact snRNPs, demonstrating their stability and nuclear enrichment. A pivotal 1980 proposal by Lerner, Steitz, and colleagues suggested snRNPs' involvement in pre-mRNA splicing, based on sequence complementarity between U1 snRNA and intron-exon boundaries.^[13] In the 1980s, Joan Steitz's group advanced snRNA characterization by cloning genes for U1-U6, enabling functional studies that confirmed their roles in spliceosome assembly.^[3] The nomenclature "snRNP" derives from "small nuclear ribonucleoprotein," emphasizing the RNA-protein composition, with the U-series retained for specific snRNAs based on their original electrophoretic ordering. During the 1990s, Reinhard Lührmann's laboratory elucidated the Sm core structure common to most U snRNPs (U1, U2, U4, U5) through immunoprecipitation and protein sequencing, identifying seven Sm proteins (B/B', D1, D2, D3, E, F, G) that form a ring around the snRNA's Sm site. Concurrently, a distinction emerged between Sm-class snRNPs and LSm-class (like Sm) for U6, established in the mid-1990s when LSm proteins (Lsm2-8) were identified as forming a similar heteroheptameric ring on U6 snRNA, differing in protein composition and assembly pathway.^[14] Recent advances in the 2020s, leveraging cryo-electron microscopy (cryo-EM), have provided atomic-resolution structures of individual snRNPs and their integration into the spliceosome, validating early biochemical models. For instance, a 2024 cryo-EM structure of the human 20S U5 snRNP at 3.1 Å resolution revealed detailed interactions of U5-specific proteins with the Sm core, confirming its role in splice site recognition.^[15] These findings build on foundational work, including the 1993 Nobel Prize in Physiology or Medicine awarded to Phillip Sharp and Richard Roberts for discovering split genes, which indirectly underscored snRNPs' essential contributions to splicing machinery.^[16]

Types

Major snRNPs

The major small nuclear ribonucleoproteins (snRNPs) are essential components of the major spliceosome, which mediates the constitutive splicing of most pre-mRNA introns via the U2-dependent pathway. These include U1, U2, U4, U5, and U6 snRNPs, all of which (except U6) assemble around a core of seven Sm proteins bound to their respective snRNAs, while U6 uniquely utilizes an LSm protein ring. U1 and U2 snRNPs are the most abundant in eukaryotic cells, reflecting their roles in initial splice site recognition, whereas U4, U5, and U6 form dynamic complexes that support catalytic activation.^[1]^[17] The U1 snRNP recognizes the 5' splice site through base-pairing interactions mediated by a stem-loop structure in its U1 snRNA. It contains three specific proteins—U1A, U1C, and U1-70K—that stabilize this recognition and contribute to early spliceosome assembly, with the overall particle exhibiting a doughnut-shaped architecture approximately 245 kDa in size.^[17]^[1] The U2 snRNP identifies the branch point sequence upstream of the 3' splice site via complementary base-pairing with its U2 snRNA, forming a bulged duplex that positions the branch adenosine. It incorporates specific proteins such as U2A', U2B'', and the SF3a and SF3b subcomplexes, which together confer a bivalve-like structure and a total mass of around 200-250 kDa, enabling conformational flexibility during splicing commitment.^[17]^[1] The U4/U6 snRNP exists as a di-snRNP complex in which the U4 and U6 snRNAs are extensively base-paired, masking their catalytic potential until needed. This ~1 MDa particle includes shared proteins like Prp4 and Prp31, which stabilize the U4/U6 duplex and facilitate integration into the U4/U6.U5 tri-snRNP; during splicing, the U4/U6 pairing unwinds, leading to dissociation of U4 and activation of U6.^[18]^[1] The U5 snRNP promotes exon alignment through interactions of its U5 snRNA loop I with splice site sequences, serving as a central scaffold in the spliceosome. It harbors Prp8 as the catalytic core protein and associates with hPrp19, with the particle (~200 kDa) showing high conservation across eukaryotes, underscoring its fundamental role in both transesterification steps.^[18]^[1] The U6 snRNP differs from the others by lacking the Sm core and instead binding an LSm2-8 protein ring at its 3' end, which enhances stability. Transcribed by RNA polymerase III, its U6 snRNA participates in 2'-OH activation at the branch point during the first catalytic step, forming key interactions with U2 snRNA to constitute the spliceosome's active site.^[1]^[17]

Minor snRNPs

The minor spliceosome, distinct from the major spliceosome, processes a rare class of U12-type introns characterized by AT-AC boundaries and comprises four specific snRNPs: U11, U12, U4atac, and U6atac, while sharing the U5 snRNP with the major pathway.^[19] U11 and U12 snRNPs form a di-snRNP complex that initiates recognition, with U11 binding the 5' splice site via base-pairing and protein interactions involving specific factors like U11-35K and U11-48K, while U12 recognizes the branch point sequence, analogous to U2 in the major spliceosome but with greater sequence conservation due to rarity. Recent cryo-EM structures have revealed the atomic details of the U11/U12 di-snRNP and the activated minor spliceosome, highlighting unique protein-RNA interactions that confer specificity to U12-type intron recognition.^[20] These snRNPs possess Sm-like cores bound by heptameric Sm proteins and trimethylguanosine caps, similar to major snRNPs, but incorporate unique proteins such as U11/U12-65K (RNPC3) and U11/U12-31K (ZCRB1) that confer specificity.^[21] U4atac and U6atac snRNPs assemble into a di-snRNP, mirroring the U4/U6 base-paired structure in the major pathway, and further integrate with U5 to form a tri-snRNP that facilitates catalytic activation during splicing; this complex undergoes conformational changes, including unwinding of the U4atac/U6atac helix and base-pairing between U12 and U6atac to form the catalytic core.^[19] The U5 snRNP, though shared, adapts through interactions with minor-specific elements like the CENATAC protein in the tri-snRNP, enabling the two-step transesterification for U12-type intron excision.^[20] In humans, U12-type introns constitute approximately 0.35-0.5% of all introns, affecting around 700-800 genes, many involved in critical cellular processes such as neuronal function and DNA repair; notable examples include the FOXN2 gene (involved in neuronal function and information processing) and DYNC1H1 (encoding a dynein heavy chain for cytoskeletal transport).^[22] These introns are rarer in mammals compared to plants and invertebrates, where minor splicing can process up to 1-2% of introns, reflecting lineage-specific retention.^[23] Evolutionarily, the minor spliceosome traces back to an early eukaryotic ancestor, likely descending from group II self-splicing introns alongside the major pathway, with its components highly conserved in vertebrates but lost in some lineages like nematodes, positioning it as a remnant of ancient splicing machinery.^[24] Defects in minor snRNPs, often hypomorphic mutations in snRNAs like U4atac or U12, disrupt splicing efficiency and are linked to rare disorders known as minor spliceosomopathies, including microcephalic osteodysplastic primordial dwarfism type I (MOPD I)/Taybi-Linder syndrome from U4atac variants, early-onset cerebellar ataxia from U12 mutations, Roifman syndrome, and contributions to neurodegenerative conditions like spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS).^[25]^[26]

Biogenesis

snRNA Transcription and Nuclear Export

The biogenesis of small nuclear RNAs (snRNAs) begins with transcription in the nucleus, where U1, U2, U4, and U5 snRNAs are synthesized by RNA polymerase II (Pol II) from gene-specific promoters. These promoters feature a proximal sequence element (PSE), located approximately 40–65 base pairs upstream of the transcription start site (TSS), which recruits the snRNA-activating protein complex (SNAPc) to initiate Pol II assembly. An upstream distal sequence element (DSE), positioned about 180–300 base pairs upstream of the TSS, functions as an enhancer by binding transcription factors such as Oct-1, SP1, and ZNF143 (STAF), thereby stimulating promoter activity and ensuring efficient transcription.^[27]^[28] In contrast, U6 snRNA is transcribed by RNA polymerase III (Pol III) using a distinct promoter architecture that includes a PSE similar to Pol II promoters, a DSE with octamer (OCT) and SPH motifs for enhancement, and an intervening TATA box that recruits the TATA-binding protein (TBP) to direct Pol III specificity.^[27]^[29] This Pol II/Pol III dichotomy is evolutionarily conserved from yeast to humans, reflecting adaptations for differential regulation and processing needs.^[30] Following transcription, nascent Pol II-derived pre-snRNAs (U1–U5) undergo 3′ end processing and 5′ cap modification to prepare for export. The 3′ ends are formed by endonucleolytic cleavage mediated by the Integrator complex, which contains a CPSF73-like catalytic subunit that recognizes a conserved 3′ box sequence downstream of the mature 3′ end, ensuring precise termination independent of polyadenylation. Concurrently, these pre-snRNAs receive a 7-methylguanosine (m⁷G) cap co-transcriptionally at the 5′ end via the cap-binding complex (CBC), which stabilizes the RNA and facilitates downstream interactions. U6 pre-snRNA, transcribed by Pol III, lacks polyadenylation signals and instead undergoes 3′ end maturation via a distinct mechanism involving La protein binding, followed by post-transcriptional addition of a γ-monomethylguanosine (m²,²,⁷G) cap that differs from the m⁷G structure on U1–U5.^[31]^[32] These nuclear modifications distinguish U6, which remains in the nucleus, from the export-competent U1–U5 pre-snRNAs. Nuclear export of U1–U5 pre-snRNAs is a rapid process, occurring within minutes of transcription, and is mediated by the phosphorylated adaptor for RNA export (PHAX). PHAX binds the m⁷G cap through CBC and the RNA's 7S region, forming a pre-export complex that exposes PHAX's leucine-rich nuclear export signal (NES) to recruit the exportin CRM1 in conjunction with RanGTP, enabling translocation through nuclear pore complexes. This CRM1-dependent pathway ensures selective export of properly processed pre-snRNAs while excluding U6 due to its incompatible cap structure. Export failure triggers quality control, where defective pre-snRNAs—such as those with improper 3′ ends or caps—are retained in the nucleus and degraded by exonucleases, including the RNA exosome complex and TOE1, preventing accumulation of aberrant molecules that could disrupt splicing.^[33]^[34]^[35]

Sm Protein Synthesis and Cytoplasmic Storage

The Sm proteins, comprising the core components B/B', D1, D2, D3, E, F, and G, are encoded by nuclear genes and synthesized via translation of their mRNAs in the cytoplasm.^[30] These proteins form a stable heptameric ring structure essential for binding to the Sm site on snRNAs during subsequent assembly steps.^[36] Unlike snRNAs, which undergo nuclear processing before export, Sm proteins are produced directly in the cytoplasmic compartment, ensuring their availability for the post-export phase of snRNP biogenesis.^[30] In the cytoplasm, Sm proteins accumulate and are stored within the survival motor neuron (SMN) complex, a multi-subunit assembly platform that acts as a molecular chaperone to maintain their solubility and prevent unwanted aggregation.^[30] The SMN complex associates with stable Sm protein subcomplexes—including the D1-D2 heterodimer, the E-F-G heterotrimer, and post-translationally modified D3 and B/B' monomers—to maintain their solubility and facilitate their ordered recruitment during core assembly with snRNAs.^[37] This storage mechanism ensures a regulated pool of Sm proteins, poised for efficient recruitment during core snRNP formation without interfering with other cellular processes.^[30] Prior to their incorporation into the heptamer, certain Sm proteins undergo critical post-translational modifications, including symmetric dimethylation of arginine residues in the C-terminal RG dipeptide repeats of SmB/B', D1, and D3.^[38] This modification is catalyzed by the methyltransferase PRMT5 in a complex with MEP50, and it serves as a recognition signal for the Tudor domain of SMN, enhancing binding affinity and preparing the proteins for nuclear targeting signals.30669-6/fulltext) Such modifications are indispensable for the fidelity of Sm protein maturation and subsequent snRNP functionality.^[38] The cellular levels of Sm proteins are maintained through feedback regulation mediated by the SMN complex and associated factors, which sense assembly demands and adjust protein abundance accordingly.^[30] Excess or unassembled Sm proteins are subject to degradation via the ubiquitin-proteasome pathway, preventing toxic accumulation and ensuring stoichiometric balance with snRNAs.^[39] This degradative control is particularly evident under conditions of disrupted biogenesis, where free Sm proteins are rapidly cleared to preserve proteostasis.^[39] In a parallel but distinct pathway, the LSm proteins (Lsm2 through Lsm8), which form the heteroheptameric ring for U6 snRNP, are also translated in the cytoplasm from nuclear-encoded mRNAs but bypass cytoplasmic storage and instead assemble directly onto U6 snRNA in the nucleus.^[30] This nuclear-specific assembly does not involve the SMN complex or Sm-like modifications, reflecting the unique biogenesis route for U6 that integrates it into the spliceosome without cytoplasmic core formation.

Core snRNP Assembly in the SMN Complex

The core assembly of snRNPs occurs in the cytoplasm and involves the formation of a stable heptameric Sm protein ring around the conserved Sm site of the snRNA, a uridine-rich single-stranded motif with the consensus sequence PuA(U)_nGPu (where n=3–6 and Pu denotes a purine, often PuAUUGG in human U1–U5 snRNAs). This process is mediated by the survival motor neuron (SMN) complex, which serves as a dedicated chaperone platform ensuring specificity and ordered assembly. The SMN complex consists of the core subunit SMN and associated Gemin proteins (Gemin2–8), along with accessory factors like Unrip, and it coordinates the integration of seven Sm proteins (D1, D2, B/B', D3, E, F, G) onto the snRNA to form the protective Sm core domain.^[40]00718-5)^[41] Assembly begins with the recognition of the snRNA precursor by the SMN complex, which binds directly to a specific domain in the 3' stem-loop structure of the snRNA, facilitating initial positioning near the Sm site. Prior to full engagement, Sm proteins undergo symmetric dimethylarginine (sDMA) modification on their C-terminal tails by the PRMT5 complex, which includes WD45 (also known as MEP50) as a scaffold protein that enhances methylation efficiency and promotes transfer to the SMN complex. The ordered addition of Sm proteins proceeds in phases: first, pICln (also called ICln) recruits and stabilizes an early intermediate complex (6S) containing D1, D2, F, E, and G around the nascent Sm site; subsequently, the SMN complex displaces pICln, binds this 5Sm subcomplex via Gemin2, and incorporates the final proteins B/B' and D3 to complete the ring, threading the snRNA through the heptameric structure. This sequential mechanism, driven by conformational changes in the SMN complex (including ATP-dependent unwinding by the Gemin3 helicase to expose the Sm site), ensures high specificity for cognate snRNAs and prevents off-target assembly. While the core assembly reaction itself is ATP-independent in purified systems, cellular extracts reveal ATP dependence due to helicase activity, and GTP hydrolysis by the Ran GTPase supports recycling of import factors post-assembly for sustained biogenesis.^[37]^[40]^[42] Quality control during assembly is stringent, with the SMN complex acting as a proofreading platform that rejects non-cognate RNAs or incomplete intermediates; unassembled or aberrant snRNA-Sm complexes are targeted for degradation, often via Gemin5-mediated recognition and exonucleolytic pathways, preventing accumulation of dysfunctional particles. Recent structural studies have revealed a unique mechanism in human cells, where the SMN complex dynamically displaces pICln from the 5Sm intermediate to enable rapid ring closure, differing from simpler pathways in yeast and highlighting evolutionary adaptations for efficiency in complex metazoan splicing demands. with the completed Sm core providing critical protection against cytoplasmic exonucleases to stabilize the snRNA for subsequent nuclear import.^[43]^[7]^[44]

Nuclear Import and Final Maturation

Following cytoplasmic assembly of the core domain, the nascent snRNP is transported back into the nucleus through a mechanism involving the trimethylguanosine (TMG) cap on the snRNA, which is recognized by the adaptor protein snurportin 1 (SPN1).^[45] SPN1 then binds importin-β, forming a complex that facilitates translocation across the nuclear pore complex, while the SMN complex contributes by exposing a nuclear localization signal (NLS) on its Gemin3 subunit to enhance import efficiency.^[46] The Ran-GTP gradient, generated by the GTPase Ran, drives the directional import by promoting dissociation of the importin-β-cargo complex in the nucleus upon GTP hydrolysis.^[47] In the nucleus, final maturation occurs primarily in Cajal bodies, subnuclear structures enriched in snRNP biogenesis factors, where snRNP-specific proteins are added to the core domain to confer functional specificity.^[48] For instance, the U1 snRNP incorporates U1C, a protein that stabilizes interactions with pre-mRNA substrates.^[30] Concurrently, U4 and U6 snRNAs anneal to form base-paired structures, and this U4/U6 di-snRNP integrates with U5 to assemble the U4/U6.U5 tri-snRNP, a key intermediate in spliceosome formation, also within Cajal bodies before redistribution to nuclear speckles.^[49] Maturation is marked by extensive post-transcriptional modifications of the snRNA, including 2'-O-methylation and pseudouridylation, which enhance RNA stability and splicing fidelity.^[50] These hypermodifications are guided by small nucleolar RNPs (snoRNPs): box C/D snoRNPs direct site-specific 2'-O-methylation via their fibrillarin subunit, while box H/ACA snoRNPs catalyze pseudouridylation through dyskerin.^[51] Such modifications occur post-import in the nucleolus or Cajal bodies, distinguishing mature from immature snRNPs.^[52] Mature snRNPs are compartmentalized in nuclear speckles, dynamic storage sites that serve as reservoirs for splicing factors, from which they are recruited to active transcription sites upon demand.^[53] For U6 snRNP, which follows a distinct biogenesis path without cytoplasmic export, the LSm ring—a heteroheptameric protein complex analogous to the Sm core—assembles directly in the nucleus to stabilize the U6 snRNA and facilitate its interactions in the spliceosome.^[2] Recent cryo-electron microscopy (cryo-EM) studies have provided structural insights into U5 snRNP maturation, revealing the 20S U5 particle as a late biogenesis intermediate where proteins like CD2BP2 and TSSC4 stabilize the snRNA and core before tri-snRNP integration.^[54]

Recycling and Disassembly

After the completion of pre-mRNA splicing, the spliceosome undergoes disassembly to release the ligated exons as mature mRNA, the excised intron lariat, and the constituent snRNPs for recycling. This process is initiated by the DEAH-box ATPase Prp22 (DHX8 in humans), which facilitates the release of the mRNA and promotes the transition from the postsplicing (P) complex to the intron-lariat spliceosome (ILS) complex in an ATP-dependent manner.^[55] Subsequently, the DEAH-box helicase Prp43 (DHX15), in cooperation with its cofactors Spp382 (Ntr1) and Ntr2 to form the NTR complex, catalyzes the dismantling of the ILS complex, releasing U1 and U2 snRNPs early in the cycle (U1 during B complex formation and U2 post-splicing) while the U4, U5, and U6 snRNPs are initially retained and recycled as a tri-snRNP unit before further separation.^[56] Defects in Prp43 or Prp22 activity lead to spliceosome stalling and accumulation of undissembled complexes, impairing splicing efficiency.^[57] In the recycling pathway, the core Sm rings on U1, U2, U4, and U5 snRNPs remain intact, preserving their structural stability and enabling rapid reincorporation into new spliceosomes without full disassembly.^[41] U6 snRNA, associated with the LSm2-8 ring rather than Sm proteins, is particularly stable and requires re-association with factors like Prp24 and LSm proteins during recycling to reform the U4/U6 di-snRNP.^[58] snRNAs may undergo re-modification, such as restoration of the N6-methyladenosine (m6A) at position 43 on U6, to ensure functionality before reuse; the survival motor neuron (SMN) complex contributes to quality control by facilitating Sm core reassembly or targeting defective snRNPs for degradation if modifications are compromised.^[59] This pathway allows snRNPs to be recycled multiple times per cell cycle, supporting high splicing throughput. snRNPs exhibit overall stability with half-lives on the order of days in human cells, enabling multiple rounds of use, though U6 is the most stable due to its LSm ring association, which protects it from degradation.^[60] The disassembly and recycling processes are energy-intensive, relying on ATP hydrolysis by helicases like Prp43 and, during U4/U6 di-snRNP reformation, the Ski2-like helicase Brr2 for prior unwinding steps that must be reversed.^[61] A comprehensive 2023 atlas of spliceosome biogenesis and recycling factors, known as IARA, catalogs these components, including Prp43, Prp22, and SMN complex elements, highlighting their roles in post-splicing dynamics across human splicing cycles.^[62]

Structure

Core Domain Architecture

The core domain of small nuclear ribonucleoproteins (snRNPs) is a highly conserved structural module shared across all spliceosomal snRNPs, consisting primarily of a heteroheptameric ring formed by seven Sm proteins (SmB/B', D1, D2, D3, E, F, and G) that encircles a specific single-stranded Sm site on the snRNA. These Sm proteins each feature a characteristic β-sheet barrel domain, with some incorporating RNA-recognition motifs (RRMs) that facilitate binding; the ring assembles in a specific order (D1, D2, F, E, G, D3, B/B') around the uridine-rich Sm site (typically PuAUUUUGUG), clamping the RNA in a doughnut-like configuration with the RNA threading through the central pore. This architecture was first resolved at atomic detail through X-ray crystallography of the human U1 snRNP core at 5.5 Å resolution, revealing the asymmetric arrangement and intimate RNA-protein contacts essential for stability.^[63] The snRNA within the core domain folds into conserved secondary structures, including stem-loops that flank the Sm site and provide platforms for protein interactions, while single-stranded regions enable direct contacts with Sm proteins. In U1 snRNA, for example, the core encompasses the Sm site positioned between stem-loop 3 (SL3) and stem-loop 4 (SL4), with these elements forming a compact scaffold stabilized by base-pairing and loop interactions. Cryo-electron microscopy (cryo-EM) structures have further illuminated these folds, such as the 3.6 Å resolution model of yeast U1 snRNP core, which shows the snRNA's helical segments protruding from the Sm ring and interacting via hydrogen bonds and stacking with protein side chains.^[64] Overall, the snRNP core domain forms an asymmetric particle approximately 10-15 nm in diameter, with the Sm ring serving as the central hub from which snRNA stems extend like arms. Recent high-resolution cryo-EM studies, including a 3.1 Å structure of human U5 snRNP core, have achieved resolutions below 3.5 Å, enabling visualization of atomic details such as the ring's toroidal shape and RNA trajectory.^[15] Key interactions at the RNA-protein interface are predominantly electrostatic, involving positively charged residues on Sm proteins that neutralize the RNA backbone's negative charge, while magnesium ions coordinate phosphate groups to stabilize RNA folding and maintain the core's compact conformation.^[64] This core architecture exhibits deep evolutionary conservation, with homologs of Sm proteins—known as LSm in eukaryotes for U6 snRNP or SmAPs in archaea—forming similar heptameric or hexameric rings that bind U-rich RNAs, suggesting an ancient prokaryotic origin predating the last eukaryotic common ancestor. Bacterial Hfq proteins, which are LSm-like, further underscore this lineage by forming ring structures that regulate RNA stability through analogous central pore binding.^[65]

snRNP-Specific Features

snRNPs exhibit distinct structural features tailored to their roles in spliceosome assembly and function, extending beyond the conserved Sm core domain. In U1 snRNP, the snRNA contains an extended stem-loop 1 (SL1) region where nucleotides 3–10 form Watson-Crick base pairs that mimic the 5' splice site sequence (AG/GUAAGU) of pre-mRNA, facilitating initial recognition. This interaction is stabilized by the U1-C protein through hydrogen bonds and electrostatic contacts with the RNA backbone. Additionally, the U1-70K protein's RNA recognition motif (RRM) domain binds SL1 in a novel configuration, involving base stacking (e.g., C33 and G34 with Arg191 and Lys138) and hydrogen bonds, which secures the particle's integrity. U2 snRNP incorporates specialized protein complexes for branch point recognition. The SF3b subcomplex features a stalk-like HEAT repeat domain in SF3B1 that encases the branch site:U2 snRNA duplex, positioning the branch point adenosine for subsequent catalysis. Complementing this, the SF3a complex features bidentate interactions between the SURP2 domain of Prp9 (SF3a60) and the N-terminal half of Prp21's αD helix, stabilizing the overall architecture. Prp9's zinc-finger domain binds stem-loop IIa of U2 snRNA. These elements ensure precise intron branch point binding during early spliceosome formation.^[66] The U4/U6 di-snRNP displays unique RNA and protein arrangements for snRNA pairing. The U4 snRNA features a cap-proximal stem-loop structure that serves as the nucleolar localization element (NoLE), binding the NHPX/15.5-kD protein and enabling nucleolar targeting independent of Sm proteins or U6 association. Prp24 acts as a chaperone, bridging U4 and U6 snRNAs via its electropositive groove and RNA recognition motifs (RRMs), which facilitate ATP-independent annealing without forming stable ternary complexes. This bridging is enhanced by interactions between Prp24's RRM4 and the Lsm2–8 ring on U6, promoting di-snRNP stability. U5 snRNP harbors elements critical for exon alignment. Its snRNA includes a large internal loop I with the conserved sequence G1C2C3U4U5U6Y7A8Y9, which directly interacts with the 5' exon before the first splicing step and coordinates both exons for ligation in the second step.^[67] The Prp8 protein's Jab1/MPN domain serves as a central scaffold, interacting with Brr2 helicase to regulate U4/U6 unwinding and maintaining U5 structural integrity during biogenesis. Recent cryo-EM structures from 2024 reveal four states of U5 snRNP bound to chaperones CD2BP2 and TSSC4, showing how CD2BP2 occupies the Prp8 interface to prevent premature tri-snRNP assembly during recycling, with displacement of CD2BP2 facilitated by recruitment of U4/U6 components during tri-snRNP assembly.^[68] Unlike other snRNPs, U6 employs a variant 3' end stabilization and cap. The LSm2–8 heteroheptameric ring encircles the uridine-rich 3' tail of U6 snRNA, enhancing stability and facilitating interactions with Prp24 for U4/U6 annealing. U6 lacks the 2,2,7-trimethylguanosine (TMG) cap, instead featuring a γ-monomethyl phosphate cap (mpppG) on the 5' end, which is added post-transcriptionally by a distinct capping enzyme and supports nuclear retention without influencing transport like TMG caps.

Function

Role in Spliceosome Formation

The spliceosome assembles de novo on each intron in a stepwise manner, with snRNPs serving as core components that recognize specific pre-mRNA sequences and drive conformational changes. The initial commitment step forms the E (early prespliceosomal) complex, in which the U1 snRNP binds the 5' splice site via base-pairing between U1 snRNA and the pre-mRNA, marking the intron for splicing. Non-snRNP proteins, including SF1/MBBP (which binds the branch point sequence) and the U2AF65/U2AF35 heterodimer (which interacts with the polypyrimidine tract near the 3' splice site), cooperate to stabilize this early recognition and position the branch point for subsequent U2 snRNP binding. This E complex represents a reversible commitment, ensuring accurate intron identification before further assembly.^[1] The transition to the A complex follows, characterized by ATP-dependent recruitment of the U2 snRNP to the branch point. U2AF facilitates this by bridging the 3' splice site and branch point, while the SF3a and SF3b protein complexes within U2 snRNP promote stable base-pairing of U2 snRNA with the branch point sequence, displacing SF1/MBBP. This step converts the prespliceosome into a more stable intermediate, with U1 and U2 snRNPs positioned at opposite ends of the intron, forming a cross-intron scaffold essential for later rearrangements. The A complex is also reversible but commits the intron more firmly to the splicing pathway.^[69] Subsequent integration of the U4/U6.U5 tri-snRNP generates the B (precatalytic) complex, where the U5 snRNP recognizes the 5' exon through base-pairing between loop I of its snRNA and sequences adjacent to the 5' splice site, and the DEAD-box helicase Prp28 promotes U1 snRNP dissociation to allow U5 repositioning. This tri-snRNP addition bridges the 5' and 3' splice sites, incorporating over 30 additional proteins that stabilize the complex. Activation of the B complex then occurs via release of U1 snRNP and unwinding of the U4/U6 snRNA duplex by the Brr2 helicase, enabling U6 snRNA to base-pair with the 5' splice site and poising the spliceosome for catalytic steps; this activation is often irreversible, as demonstrated by single-molecule studies showing tri-snRNP retention or discard based on proofreading. These dynamics rely on transient protein-RNA interactions mediated by DEAD-box helicases, maintaining a conserved stepwise model across eukaryotes.^[70]^[71]^[72] A parallel pathway exists for the minor spliceosome, which processes rare U12-type AT-AC introns. Here, U11 and U12 snRNPs preassemble into a di-snRNP that cooperatively recognizes the 5' splice site (via U11 base-pairing) and branch point (via U12), combining functions analogous to the E and A complexes without distinct intermediates. The U11-48K protein stabilizes 5' splice site binding, while U11-59K and U11/U12-65K link the snRNPs within the compact di-snRNP. The U4atac/U6atac.U5 tri-snRNP then joins to form a B-like complex, mirroring major spliceosome progression but with intron-specific adaptations for efficiency.^[19]

Contributions to Splicing Catalysis

In the first transesterification step of pre-mRNA splicing, U6 snRNA plays a central role in positioning the 5' splice site through base pairing with its conserved ACAGAG motif, which aligns the phosphodiester bond for nucleophilic attack by the branch point adenosine's 2'-OH group.^[73] Concurrently, the loop I structure of U5 snRNA interacts directly with the 5' exon, tethering it in proximity to the catalytic center to ensure precise alignment before cleavage.^[74] This positioning is facilitated by two catalytic Mg²⁺ ions coordinated within the active site of the Prp8 protein, a core U5 snRNP component that stabilizes the transition state and supports the RNA-based catalysis resembling that of group II introns.^[75] The second transesterification step involves U5 snRNA bridging the 5' and 3' exons via its loop I interactions, which persist from the first step to align the exons for ligation while the lariat intron is released.^[76] U6 snRNA again drives the chemistry, activating the 3'-OH of the freed 5' exon to perform a 3'-5' phosphodiester bond formation at the 3' splice site, with its internal 2'-OH group contributing to metal ion coordination for catalysis.^[1] Proofreading mechanisms ensure fidelity, as the DEAH-box ATPase Prp16 remodels the spliceosome post-first step to reject suboptimal branch sites via ATP-dependent unwinding, while Prp22 similarly verifies 3' splice site selection before exon joining, repressing aberrant intermediates.^[77] U1 and U2 snRNPs contribute indirectly to catalytic efficiency by stabilizing the pre-mRNA substrate during spliceosome maturation; U1 snRNP bridges with U2 via the Prp5 ATPase to promote stable U2 binding at the branch point, preventing dissociation and ensuring substrate availability for catalysis.^[78] Additionally, U1 snRNP suppresses premature cleavage events that could disrupt splicing fidelity, such as off-target polyadenylation of nascent transcripts, thereby maintaining substrate integrity for the catalytic phases.^[79] Recent studies highlight U1C, a U1 snRNP-specific protein, as a modulator of splicing outcomes, where its interaction with U1 snRNA helix H influences the response to small-molecule splicing regulators, potentially fine-tuning catalytic activation in therapeutic contexts. The catalytic contributions of snRNPs enable highly efficient splicing, with eukaryotic cells processing thousands of introns per transcript across the transcriptome to support rapid gene expression.^[80] Variant snRNPs, such as those in the minor U12-dependent spliceosome (e.g., U11/U12), further regulate alternative splicing by recognizing distinct intron motifs, allowing tissue-specific isoform production and enhancing regulatory diversity without altering core catalytic mechanisms.^[81]

Clinical and Biological Significance

Associations with Autoimmune Diseases

Small nuclear ribonucleoproteins (snRNPs) are frequent targets of autoantibodies in systemic autoimmune diseases, particularly systemic lupus erythematosus (SLE) and mixed connective tissue disease (MCTD).^[82] These anti-snRNP antibodies, including anti-Sm and anti-U1-RNP, contribute to immune dysregulation by forming immune complexes that deposit in tissues, leading to inflammation and organ damage such as glomerulonephritis.^[83] In SLE, anti-Sm antibodies are highly specific, occurring in 10-40% of patients, while anti-U1-RNP antibodies are detected in 30-44% of cases.^[84] In MCTD, anti-U1-RNP antibodies are a diagnostic hallmark, present in 95-100% of patients, often at high titers.^[84] The primary immunogenic targets within snRNPs are the Sm proteins, especially B/B', and the U1-specific protein U1-70K in the U1 snRNP particle.^[82] Sm B/B' elicits the strongest antibody response due to its exposed epitopes in the core domain, while U1-70K's RNA-binding domain (residues 100-180) enhances immunogenicity through structural accessibility.^[82] Pathogenesis involves molecular mimicry, where viral infections like Epstein-Barr virus trigger cross-reactive antibodies against snRNP components, initiating epitope spreading and B-cell activation.^[83] Apoptotic modifications, such as caspase-3 cleavage of U1-70K, further expose neoepitopes, promoting autoantibody production via Toll-like receptor 7 (TLR7) signaling and type I interferon amplification.^[82] Diagnosis relies on serological assays, including enzyme-linked immunosorbent assay (ELISA) and immunoblotting, which detect anti-Sm and anti-U1-RNP with high specificity for SLE and MCTD.^[85] These tests are integrated with clinical criteria, as antibody presence alone is not sufficient for diagnosis but correlates with disease activity and prognosis.^[85] Epidemiologically, anti-snRNP antibodies are more prevalent in women, reflecting SLE's 9:1 female-to-male ratio, though some cohorts show higher anti-Sm titers in affected males.^[86] No direct causality exists between these antibodies and disease onset, but their levels often parallel flares in renal and cutaneous involvement.^[87]

Links to Neurodegenerative and Genetic Disorders

Spinal muscular atrophy (SMA) is a hereditary neurodegenerative disorder primarily caused by homozygous mutations in the SMN1 gene, which encodes the survival motor neuron (SMN) protein essential for snRNP core assembly. These mutations lead to reduced SMN protein levels, impairing the formation of the SMN complex and resulting in defective snRNP biogenesis, particularly the Sm core domain shared by U1, U2, U4, and U5 snRNPs. SMA manifests in four types (I-IV) classified by age of onset and severity, with type I (Werdnig-Hoffmann disease) being the most severe infantile form, affecting approximately 1 in 10,000 live births. The SMN2 gene, a paralog of SMN1, partially compensates by producing low levels of functional SMN protein through alternative splicing, but this is insufficient to prevent motor neuron degeneration in severe cases. Beyond SMA, disruptions in snRNP function are implicated in other neurodegenerative and genetic disorders. In amyotrophic lateral sclerosis (ALS), mutations or aggregation of TAR DNA-binding protein 43 (TDP-43) disrupt nuclear speckles, where snRNPs and splicing factors concentrate, leading to impaired spliceosome maintenance and RNA processing defects in motor neurons. Similarly, mutations in pre-mRNA processing factor genes such as PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, and SNRNP200 (encoding proteins in the U4/U6-U5 tri-snRNP complex) cause autosomal dominant retinitis pigmentosa (RP), a retinal degeneration disorder, by inducing generalized splicing defects that preferentially affect photoreceptor-specific transcripts. Recent single-nucleus RNA sequencing atlases from 2025 highlight how snRNP dysregulation contributes to broader neurodegeneration, including altered splicing networks in Alzheimer's disease and ALS brain regions, underscoring shared RNA processing vulnerabilities across these conditions. The core mechanisms linking snRNP defects to these disorders involve reduced snRNP levels causing widespread splicing errors, particularly in genes critical for neuronal survival and function. In SMA, diminished snRNP assembly leads to inefficient splicing of motor neuron transcripts, exacerbating SMN deficiency despite SMN2 compensation, and results in selective vulnerability of spinal motor neurons. Defective snRNP maturation often manifests as accumulation of immature snRNPs in the cytoplasm, as observed in SMA mouse models where Sm core defects correlate with disease severity. Furthermore, deficiencies in U1 snRNP-specific protein U1C, a regulator of SMN complex activity, broaden these impacts by disrupting U1 snRNP formation and potentially amplifying splicing aberrations in neuronal contexts, as detailed in recent biochemical studies. Therapeutic advancements targeting snRNP-related defects in SMA have shown promise. Nusinersen, an antisense oligonucleotide that enhances SMN2 exon 7 inclusion to boost functional SMN production, received FDA approval in 2016 for treating all SMA types. Gene therapies, such as onasemnogene abeparvovec (Zolgensma), deliver a functional SMN1 copy via AAV9 vector and was approved by the FDA in 2019 for children less than 2 years of age with spinal muscular atrophy via intravenous administration. An investigational intrathecal formulation has demonstrated efficacy in clinical trials for broader patient populations, including older children, with regulatory filings submitted in 2025, improving motor outcomes and survival in clinical trials. These interventions indirectly restore snRNP assembly by elevating SMN levels, highlighting the feasibility of addressing snRNP biogenesis in genetic disorders.^[88]^[89]

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Anti-Sm antibodies (60.0% vs 13%, p<0.01) and anti-snRNP antibodies (56% vs 21%, p=0.03) were more prevalent in men. SLICC/ACR mean damage index (2.7 +/- 2.7 ...
[85]
The impact of anti-U1-RNP positivity: systemic lupus erythematosus ...
May 23, 2018 · Thus, the prevalence of 25-30% for anti-RNP was reported in John Hopkins and LUMINA lupus cohorts and also 13% prevalence for the anti-U1-RNP ...