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Spliceosome
Spliceosome
Spliceosome
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A spliceosome is a large ribonucleoprotein (RNP) complex found primarily within the nucleus of eukaryotic cells. The spliceosome is assembled from small nuclear RNAs (snRNA) and numerous proteins. Small nuclear RNA (snRNA) molecules bind to specific proteins to form a small nuclear ribonucleoprotein complex (snRNP, pronounced "snurps"), which in turn combines with other snRNPs to form a large ribonucleoprotein complex called a spliceosome. The spliceosome removes introns from a transcribed pre-mRNA, a type of primary transcript. This process is generally referred to as splicing.[1] An analogy is a film editor, who selectively cuts out irrelevant or incorrect material (equivalent to the introns) from the initial film and sends the cleaned-up version to the director for the final cut.[citation needed]

However, sometimes the RNA within the intron acts as a ribozyme, splicing itself without the use of a spliceosome or protein enzymes.[citation needed]

Spliceosomal splicing cycle

History

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See also: Splicing (genetics)

In 1977, work by the Sharp and Roberts labs revealed that genes of higher organisms are "split" or present in several distinct segments along the DNA molecule.[2][3] The coding regions of the gene are separated by non-coding DNA that is not involved in protein expression. The split gene structure was found when adenoviral mRNAs were hybridized to endonuclease cleavage fragments of single stranded viral DNA.[2] It was observed that the mRNAs of the mRNA-DNA hybrids contained 5' and 3' tails of non-hydrogen bonded regions. When larger fragments of viral DNAs were used, forked structures of looped out DNA were observed when hybridized to the viral mRNAs. It was realised that the looped out regions, the introns, are excised from the precursor mRNAs in a process Sharp named "splicing". The split gene structure was subsequently found to be common to most eukaryotic genes. Phillip Sharp and Richard J. Roberts were awarded the Nobel Prize in Medicine 1993 for the discovery of introns and the splicing process.

Composition

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Each spliceosome is composed of five small nuclear RNAs (snRNA) and a range of associated protein factors. When these small RNAs are combined with the protein factors, they make RNA-protein complexes called snRNPs (small nuclear ribonucleoproteins, pronounced "snurps"). The snRNAs that make up the major spliceosome are named U1, U2, U4, U5, and U6, so-called because they are rich in uridine, and participate in several RNA-RNA and RNA-protein interactions.[1]

The assembly of the spliceosome occurs on each pre-mRNA (also known as heterogeneous nuclear RNA, hn-RNA) at each exon:intron junction. The pre-mRNA introns contains specific sequence elements that are recognized and utilized during spliceosome assembly. These include the 5' end splice site, the branch point sequence, the polypyrimidine tract, and the 3' end splice site. The spliceosome catalyzes the removal of introns, and the ligation of the flanking exons.[citation needed]

Introns typically have a GU nucleotide sequence at the 5' end splice site, and an AG at the 3' end splice site. The 3' splice site can be further defined by a variable length of polypyrimidines, called the polypyrimidine tract (PPT), which serves the dual function of recruiting factors to the 3' splice site and possibly recruiting factors to the branch point sequence (BPS). The BPS contains the conserved adenosine required for the first step of splicing.[citation needed]

Many proteins exhibit a zinc-binding motif, which underscores the importance of zinc in the splicing mechanism.[4][5][6] The first molecular-resolution reconstruction of U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) complex was reported in 2016.[7]

Figure 1. Above are electron microscopy[8] fields of negatively stained yeast (Saccharomyces cerevisiae) tri-snRNPs. Below left is a schematic illustration of the interaction of tri-snRNP proteins with the U4/U6 snRNA duplex. Below right is a cartoon model of the yeast tri-snRNP with shaded areas corresponding to U5 (gray), U4/U6 (orange) and the linker region (yellow).

Cryo-EM has been applied extensively by Shi et al. to elucidate the near-/atomic structure of spliceosome in both yeast[9] and humans.[10] The molecular framework of spliceosome at near-atomic-resolution demonstrates Spp42 component of U5 snRNP forms a central scaffold and anchors the catalytic center in yeast. The atomic structure of the human spliceosome illustrates the step II component Slu7 adopts an extended structure, poised for selection of the 3'-splice site. All five metals (assigned as Mg2+) in the yeast complex are preserved in the human complex.[citation needed]

Alternative splicing

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Main article: Alternative splicing

Alternative splicing (the re-combination of different exons) is a major source of genetic diversity in eukaryotes. Splice variants have been used to account for the relatively small number of protein coding genes in the human genome, currently estimated at around 20,000. One particular Drosophila gene, Dscam, has been speculated to be alternatively spliced into 38,000 different mRNAs, assuming all of its exons can splice independently of each other.[11]

Location of splicing

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Pre-mRNA splicing factors were originally found to be concentrated in nuclear bodies known as nuclear speckles.[12] It was originally postulated that nuclear speckles are either sites of mRNA splicing or storage sites of mRNA splicing factors. It is now understood that nuclear speckles help concentrate splicing factors near genes that are physically located close to them. Genes located farther from speckles can still be transcribed and spliced, but their splicing is less efficient compared to those closer to speckles.[13] RNA splicing is a biochemical reaction, and like all biochemical reactions, its rate depends on the concentration of enzymes and substrates. In this case, the enzymes are the spliceosomes, and the substrates are the pre-mRNAs. By varying the concentration of spliceosomes and pre-mRNAs based on their proximity to nuclear speckles, cells could potentially regulate the efficiency of splicing.[13]

Assembly

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The model for formation of the spliceosome active site involves an ordered, stepwise assembly of discrete snRNP particles on the pre-mRNA substrate. The first recognition of pre-mRNAs involves U1 snRNP binding to the 5' end splice site of the pre-mRNA and other non-snRNP associated factors to form the commitment complex, or early (E) complex in mammals.[14][15] The commitment complex is an ATP-independent complex that commits the pre-mRNA to the splicing pathway.[16] U2 snRNP is recruited to the branch region through interactions with the E complex component U2AF (U2 snRNP auxiliary factor) and possibly U1 snRNP. In an ATP-dependent reaction, U2 snRNP becomes tightly associated with the branch point sequence (BPS) to form complex A. A duplex formed between U2 snRNP and the pre-mRNA branch region bulges out the branch adenosine specifying it as the nucleophile for the first transesterification.[17]

The presence of a pseudouridine residue in U2 snRNA, nearly opposite of the branch site, results in an altered conformation of the RNA-RNA duplex upon the U2 snRNP binding. Specifically, the altered structure of the duplex induced by the pseudouridine places the 2' OH of the bulged adenosine in a favorable position for the first step of splicing.[18] The U4/U5/U6 tri-snRNP (see Figure 1) is recruited to the assembling spliceosome to form complex B, and following several rearrangements, complex C is activated for catalysis.[19][20] It is unclear how the tri-snRNP is recruited to complex A, but this process may be mediated through protein-protein interactions and/or base pairing interactions between U2 snRNA and U6 snRNA.[citation needed]

The U5 snRNP interacts with sequences at the 5' and 3' splice sites via the invariant loop of U5 snRNA[21] and U5 protein components interact with the 3' splice site region.[22]

Upon recruitment of the tri-snRNP, several RNA-RNA rearrangements precede the first catalytic step and further rearrangements occur in the catalytically active spliceosome. Several of the RNA-RNA interactions are mutually exclusive; however, it is not known what triggers these interactions, nor the order of these rearrangements. The first rearrangement is probably the displacement of U1 snRNP from the 5' splice site and formation of a U6 snRNA interaction. It is known that U1 snRNP is only weakly associated with fully formed spliceosomes,[23] and U1 snRNP is inhibitory to the formation of a U6-5' splice site interaction on a model of substrate oligonucleotide containing a short 5' exon and 5' splice site.[24] Binding of U2 snRNP to the branch point sequence (BPS) is one example of an RNA-RNA interaction displacing a protein-RNA interaction. Upon recruitment of U2 snRNP, the branch binding protein SF1 in the commitment complex is displaced since the binding site of U2 snRNA and SF1 are mutually exclusive events.[citation needed]

Within the U2 snRNA, there are other mutually exclusive rearrangements that occur between competing conformations. For example, in the active form, stem loop IIa is favored; in the inactive form a mutually exclusive interaction between the loop and a downstream sequence predominates.[20] It is unclear how U4 is displaced from U6 snRNA, although RNA has been implicated in spliceosome assembly, and may function to unwind U4/U6 and promote the formation of a U2/U6 snRNA interaction. The interactions of U4/U6 stem loops I and II dissociate and the freed stem loop II region of U6 folds on itself to form an intramolecular stem loop and U4 is no longer required in further spliceosome assembly. The freed stem loop I region of U6 base pairs with U2 snRNA forming the U2/U6 helix I. However, the helix I structure is mutually exclusive with the 3' half of an internal 5' stem loop region of U2 snRNA.[citation needed]

Minor spliceosome

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See also: Minor spliceosome

Some eukaryotes have a second spliceosome, the so-called minor spliceosome.[25] A group of less abundant snRNAs, U11, U12, U4atac, and U6atac, together with U5, are subunits of the minor spliceosome that splices a rare class of pre-mRNA introns, denoted U12-type. The minor spliceosome is located in the nucleus like its major counterpart,[26] though there are exceptions in some specialised cells including anucleate platelets[27] and the dendroplasm (dendrite cytoplasm) of neuronal cells.[28]

References

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Further reading

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Spliceosome

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The spliceosome is a large, dynamic ribonucleoprotein complex essential for pre-messenger (pre-mRNA) splicing in eukaryotic cells, where it precisely excises non-coding introns and ligates coding exons to produce mature mRNA. Composed of five small nuclear ribonucleoproteins (snRNPs)—U1, , U4/U6 di-snRNP, and U5—along with more than 150 associated proteins in humans, the spliceosome forms a multi-megadalton machine that assembles de novo on each . This assembly is ATP-dependent and involves sequential recruitment of components, driven by DExD/H-box helicases that facilitate extensive conformational rearrangements. The splicing process proceeds through distinct intermediates: the early (E) complex for splice site recognition, the pre-spliceosome (A complex) with U1 and snRNPs binding the 5' and branch-point sites, respectively, followed by the pre-catalytic B complex upon tri-snRNP (U4/U6·U5) integration, and activation to the catalytic B* and C states for intron removal. Catalysis occurs via two reactions: the first forms a lariat intermediate by attacking the 5' splice site with the branch-point , and the second ligates the exons while releasing the intron lariat. The spliceosome's dynamic nature ensures fidelity through proofreading mechanisms, such as those involving the Prp16 and G-patch protein SUGP1, which discard aberrant intermediates to prevent faulty mRNA production. Beyond the major spliceosome, a minor spliceosome processes a subset of U12-type introns using analogous but distinct snRNPs (U11, U12, U4atac/U6atac, U5). By enabling , the spliceosome vastly expands diversity from a limited , playing a pivotal role in gene regulation and cellular function. Dysregulation of spliceosomal components is linked to diseases including cancers and neurodegenerative disorders, underscoring its therapeutic relevance. Recent advances in have provided near-atomic resolution structures of spliceosomal intermediates, revealing intricate RNA-protein interactions and catalytic core details conserved from to humans, including a 2024 blueprint of the human spliceosome's core 150 proteins.

Discovery and History

Early Observations

In the early 1970s, heterogeneous nuclear RNA (hnRNA) was identified as a class of large, rapidly labeled RNA molecules in eukaryotic cell nuclei, distinct from cytoplasmic mRNAs in size and stability, leading to the hypothesis that hnRNA serves as a precursor to mature mRNA through post-transcriptional processing. Experiments using pulse-chase labeling in cells demonstrated that newly synthesized hnRNA undergoes rapid size reduction and to yield mRNA-like molecules, suggesting the removal of extraneous sequences during maturation. These observations, initially made with viral systems like adenovirus, highlighted discrepancies between nuclear transcripts and final mRNAs, setting the stage for investigations into the nature of this processing. Electron microscopy of RNA-DNA hybrids provided the first visual evidence of interrupted gene structures in 1977, revealing looped-out regions in adenovirus transcripts that corresponded to non-coding intervening sequences, or introns, between coding exons. In one seminal study, hybrids of adenovirus 2 late mRNA with viral DNA showed branched structures with loops at specific genomic positions (e.g., 2.90%, 6.70%, and 23.0%), indicating that mRNA segments were derived from discontinuous DNA regions and joined post-transcriptionally. Independently, similar electron micrographs of adenovirus 2 early mRNA hybrids displayed an "amazing sequence arrangement" at the 5' ends, with multiple non-contiguous segments annealed to separated DNA strands, confirming the split gene configuration and intron excision. These parallel discoveries by Phillip A. Sharp and Richard J. Roberts in 1977 fundamentally altered the understanding of eukaryotic gene organization, demonstrating that genes are split into exons and introns, with splicing required to assemble functional mRNAs from pre-mRNA precursors. For their identification of split genes and RNA splicing, Sharp and Roberts shared the 1993 Nobel Prize in Physiology or Medicine, recognizing the profound implications for gene expression and evolution. Early biochemical assays in the late 1970s further supported intron removal by demonstrating processing of viral transcripts in cell-free systems. In 1981, nuclear extracts from cells were shown to accurately transcribe injected adenovirus DNA and process the resulting transcripts into polyadenylated, capped mRNAs of correct size, implying the removal of non-coding sequences similar to introns observed . These experiments by Walter Keller and colleagues provided the first evidence of splicing activity , using viral templates to mimic nuclear processing and laying groundwork for isolating the responsible machinery.

Key Milestones and Advances

In the 1980s, significant progress was made in isolating the core components of the spliceosome, with Reinhard Lührmann's group achieving the purification of individual small nuclear ribonucleoproteins (snRNPs) such as U1, U2, U5, and the U4/U6 di-snRNP from HeLa cell extracts using immunoaffinity chromatography techniques. These efforts built on earlier observations of snRNP particles and enabled detailed biochemical characterization, revealing their RNA-protein architecture essential for splicing activity. During the late 1980s and 1990s, the specific roles of the major snRNAs—U1, , U4/U6, and U5—in spliceosome function were elucidated through genetic and biochemical studies in and mammalian systems. U1 snRNA was shown to recognize the 5' splice site via base-pairing, initiating spliceosome assembly, while snRNA binds the branchpoint sequence to facilitate lariat formation. The U4/U6 di-snRNA complex was identified as undergoing structural rearrangements to form the catalytic core, with U6 snRNA playing a central role in cleavage, and U5 snRNA aiding 3' splice site alignment and ligation. These discoveries established the stepwise recruitment model of snRNPs during splicing. The concept of RNA catalysis within the spliceosome gained foundational support from the 1989 Nobel Prize in Chemistry awarded to and Thomas R. Cech for discovering the catalytic properties of , initially demonstrated through self-splicing group I introns and RNase P. This work highlighted 's ability to act as a , directly influencing subsequent models of the spliceosome's U2-U6 RNA network as the for reactions, rather than relying solely on protein enzymes. Advances in from 2015 onward revolutionized understanding of spliceosome dynamics, with cryo-electron microscopy (cryo-EM) providing near-atomic resolution snapshots of and complexes. Pioneering structures included the B complex at 3.6 Å in 2015, revealing snRNP arrangements and protein-mediated rearrangements, followed by B^act and C complexes in 2017-2018 that visualized the catalytic core and branch helix formation. These studies demonstrated the spliceosome's conformational plasticity, with over 300 proteins stabilizing transient interactions during assembly and catalysis.30047-3) Recent cryo-EM resolutions have further refined these insights, including a 2.6 structure of the step II catalytically activated C* complex from the green alga in 2024, which captured the post-first-step intermediate with U6 snRNA positioned for ligation and highlighted species-specific protein variations. Concurrently, 2024-2025 structures of aberrant spliceosome intermediates from at resolutions around 3 illustrated mechanisms, showing how stalled post-B^act complexes recruit disassembly factors to discard suboptimal substrates and prevent splicing errors. In 2025, structural studies illuminated checkpoints involving the DEAH-box DHX35 and its activator GPATCH1, with cryo-EM structures from thermophilic fungi at 3.2-3.5 Å resolving their interactions in aberrant B* complexes to unwind mismatched 5' splice sites and trigger rejection pathways. These findings underscore a dual- system (with Prp2) that ensures splicing accuracy by discriminating weak substrates early in assembly. Additionally, 2025 cryo-EM analysis of the human U12 minor spliceosome at 3.3 Å revealed non-canonical base-triple interactions between U11 snRNA and U12-type 5' splice sites, explaining their distinct recognition and lower efficiency compared to the major spliceosome.

Structure and Composition

Small Nuclear Ribonucleoproteins (snRNPs)

Small nuclear ribonucleoproteins (snRNPs) are the fundamental RNA-protein complexes that constitute the core of the major spliceosome, each containing a unique uridine-rich (snRNA) associated with a set of common and specific proteins. The U1, , U4, and U5 snRNPs share a conserved Sm core domain, while U6 features a distinct LSm core; these structures enable the snRNPs to recognize pre-mRNA splice sites and facilitate spliceosome assembly. Assembly of Sm-class snRNPs begins in the , where the snRNA is transcribed in the nucleus, exported, and bound by Sm proteins before hypermethylation of the 5' and nuclear reimport. The Sm core domain is a heteroheptameric ring formed by seven Sm proteins—B/B', D1, D2, D3, E, F, and G—that assemble onto a conserved (typically PuAUUUUUUG, where Pu is ) located in the 3' region of U1, U2, U4, and U5 snRNAs. This ring structure stabilizes the snRNA and is mediated by the survival motor neuron (SMN) complex, which chaperones the stepwise binding of Sm proteins in an ATP-dependent manner. Following Sm core formation, the monomethylguanosine (m7G) at the 5' end of the snRNA is hypermethylated to a trimethylguanosine (m3G) cap by the enzyme trimethylguanosine synthase 1 (Tgs1), a modification essential for nuclear import via the import receptors snurportin-1 and importin-β. In contrast, U6 snRNA assembles its core in the nucleus with LSm proteins (LSm2–8) and retains a γ-monomethyl triphosphate . The U1 snRNP comprises U1 snRNA (~165 in humans), which features four stem-loops, including a 5' stem-loop ( 3–11) that base-pairs with the pre-mRNA 5' splice site . Its Sm core is supplemented by U1-specific proteins: U1A, which binds stem-loop II via its RNA recognition motif (RRM); U1C, a zinc-finger protein that interacts with the 5' end and stabilizes 5' splice site recognition; and U1-70K, which associates with stem-loop I. U2 snRNP contains U2 snRNA (~185 ), characterized by stem-loop structures including stem-loop IIb for sequence binding, and its Sm core is augmented by U2-specific proteins U2A' and U2B'', which heterodimerize and bind stem-loop I. The largest associated complex is the SF3 complex, divided into SF3a (subunits of ~60, 62, and 110 kDa) and SF3b (a multiprotein subcomplex including subunits of ~49, 130, 145, and 155 kDa), which together form a ~1 MDa module that interacts with the 3' region of U2 snRNA and supports recognition. The U4/U6 di-snRNP is a pre-assembled unit where U4 snRNA (~145 , Sm core) extensively base-pairs with U6 snRNA (~112 , LSm core) to form a duplex stabilized by magnesium ions, bridging the two snRNAs into a single functional entity. U4/U6-specific proteins include Snu13 (15.5K), which binds the 5' stem-loop of U4 snRNA; Prp31 (61K), which interacts with the U4 3' stem-loop and Snu13; and the Prp3-Prp4 heterodimer, where Prp3 contains a PWI domain for RNA binding and Prp4 features repeats for protein interactions, collectively encircling the U4/U6 duplex. U5 snRNP includes U5 snRNA (~220 in humans), featuring internal loop 1 for positioning splice sites, and its Sm core is associated with U5-specific proteins, most notably Prp8 (220 kDa), a large multifunctional scaffold that forms the catalytic core of the spliceosome and directly contacts the snRNA and pre-mRNA substrates. Additional stable components include Snu114, a that regulates Prp8 conformation.00129-9)

Associated Proteins and Dynamics

The spliceosome's functionality relies on a vast array of non-snRNP associated proteins that facilitate its assembly, remodeling, and , with the active spliceosome comprising over 300 proteins and exhibiting an estimated of approximately 2.5 MDa.00146-9) These proteins, often organized into transient complexes, interact dynamically with the core building blocks to drive conformational changes throughout the splicing cycle.00078-1) A key step in spliceosome maturation involves the formation of the U4/U6.U5 tri-snRNP, which integrates into the pre-catalytic and is stabilized by the Sad1-Prp19 complex (also known as the NTC in or SACY in humans), including core components like Prp19/CDC5L. The Prp19/CDC5L complex recruits additional proteins such as PRL1 and SPF27, promoting ubiquitin-mediated interactions that lock the tri-snRNP in place and enable progression to activation. This modular assembly underscores the spliceosome's transient nature, where the Prp19 complex bridges snRNPs and non-snRNP factors to prevent premature disassembly. Branch point recognition is enhanced by specific RNA-RNA interactions within the spliceosome, notably the EBS1-IBS1-like base-pairing that stabilizes -U6 helix II, positioning the for subsequent catalysis. This pairing, analogous to mechanisms, involves conserved sequences in snRNA that pair with the intron's site region, reinforced by associated proteins that modulate helix II formation for accurate substrate selection. ATP-dependent helicases play crucial roles in and remodeling the spliceosome, with Prp2 promoting destabilization of suboptimal intermediates after the first catalytic step, Prp16 enabling rejection of erroneous choices post-activation, and Prp22 verifying exon ligation fidelity before disassembly.30002-2) These DEAH-box enzymes hydrolyze ATP to unwind RNA duplexes and rearrange protein interfaces, ensuring only viable splicing substrates proceed while discarding aberrant ones. Recent cryo-EM structures from 2024 and 2025 have illuminated dynamic interfaces in spliceosomal , revealing how GPATCH1 modulates the DHX35 to facilitate rejection of error-prone introns during early post-catalytic stages. In these complexes, GPATCH1 binds near DHX35's domain in thermophilic eukaryotic models, allosterically enhancing its activity to unwind mismatched substrates and trigger disassembly pathways, thereby maintaining splicing accuracy. These findings highlight the spliceosome's modular dynamics, where transient protein interactions at interfaces like DHX35-GPATCH1 prevent propagation of splicing errors.

Splicing Mechanism

Assembly Pathway

The spliceosome assembles de novo on pre-mRNA through a series of ordered, ATP-dependent steps that recruit small nuclear ribonucleoproteins (snRNPs) and associated proteins to specific splice sites, culminating in the formation of a catalytically active complex. This pathway ensures precise recognition and removal, with each intermediate complex representing a checkpoint for fidelity. The initial commitment complex, known as the E complex, forms in an ATP-independent manner. U1 snRNP binds via base-pairing of its U1 snRNA to the 5' splice site, while SF1 (also called mammalian branchpoint binding protein, mBBP) recognizes the sequence and U2AF associates with the adjacent polypyrimidine tract, collectively committing the pre-mRNA to splicing. This early recognition is dynamic, allowing frequent redefinition of splice sites to accommodate variability in pre-mRNA sequences. Progression to the pre-spliceosome, or A complex, requires . U2AF facilitates the stable, ATP-dependent recruitment of to the through the action of helicases like Prp5 and Sub2/UAP56, enabling base-pairing between U2 snRNA and the branch point sequence with a characteristic bulged . This step pairs the branch point with the 5' splice site bound by U1 snRNP, forming a network essential for subsequent integration. The assembles when the preformed U4/U6.U5 tri-snRNP—comprising U4, U6, and U5 snRNPs with their core Sm proteins and numerous specific factors—joins the A complex in an ATP-dependent process involving additional helicases. Base-pairing rearrangements between U6 snRNA and the 5' splice site occur, stabilized by B-specific proteins such as Prp38, Snu23, and Spp381, which are conserved from to humans and critical for tri-snRNP docking. This pre-catalytic intermediate positions the reactive sites for activation. Activation to the B* complex involves extensive remodeling driven by the DEAH-box Prp2 in an ATP-dependent manner. Prp2 promotes the release of U1 and destabilizes U4/U6 base-pairing, repositioning U6 snRNA to form new interactions with U2 snRNA and exposing the for nucleophilic attack. This transition also involves ejection of U4 and SF3a/b components, priming the . Recent 2025 cryo-EM structures at near-atomic resolution have illuminated aberrant B complex intermediates that arise from suboptimal 5' splice sites, such as those with bulged loops or single-nucleotide insertions, leading to stalled assembly and discard to maintain splicing fidelity. In these defective states, like DHX35 (activated by GPATCH1) target the U2/ for dissociation, while complexes involving Prp43 and G-patch proteins (e.g., Gih35–Gpl1) block the and prime disassembly via the Ntr1 pathway, preventing progression of faulty substrates. These mechanisms, conserved across eukaryotes, highlight during B-to-B* transition.

Catalytic Steps and Fidelity

The spliceosome catalyzes pre-mRNA splicing through two sequential reactions, ensuring precise removal and ligation. In the first step, which occurs within the activated C complex, the 2'-OH group of the (A) acts as a to attack the at the 5' splice site. This reaction breaks the 5' splice site, forming a lariat intermediate where the intron's 5' end is covalently linked to the via a 2'-5' , while releasing the upstream with a free 3'-OH group. The kinetics of this step involve rapid cleavage facilitated by the spliceosomal , with the reaction rate enhanced by conformational rearrangements that position the substrates optimally. In the second transesterification step, the 3'-OH of the upstream nucleophilically attacks the at the 3' splice site within the C* complex. This ligates the two exons into a mature mRNA and excises the lariat, transitioning the spliceosome to a post-catalytic state. The bond formation here proceeds with high efficiency, driven by similar dynamics as the first step, but with additional to verify 3' splice site alignment before completion. Structural studies reveal that these reactions maintain overall through kinetic discrimination, where suboptimal alignments lead to slower bond breakage or formation rates, allowing discard pathways to intervene. At the core of both catalytic steps, Prp8 serves as the central scaffold, organizing the RNA active site composed primarily of U2 and U6 snRNAs. Prp8's reverse transcriptase/endonuclease-like domain positions key RNA elements and coordinates two magnesium ions (Mg²⁺) essential for catalysis, with conserved aspartate residues stabilizing the ions to activate the nucleophilic attacks. These Mg²⁺ ions facilitate general acid-base chemistry in the RNA-centered active site, polarizing the scissile phosphates for efficient transesterification without requiring protein-based catalysis. Spliceosomal fidelity is maintained by multiple checkpoints that discard aberrant substrates, preventing errors in splice site selection. The DEAH-box Prp16 plays a key role post-first step by ATP-dependently unwinding suboptimal lariat intermediates, rejecting those with mismatched branch points or slow reaction kinetics to favor accurate splicing. This mechanism ensures that only properly formed C complexes proceed, with Prp16's discard activity reversible and coordinated with downstream factors like Prp43 for 5' splice site verification. More recently, structural insights have revealed that the DEAH-box DHX35, activated by its cofactor GPATCH1, senses and rejects aberrant substrates during early catalytic activation. Cryo-EM structures from 2025 show DHX35-GPATCH1 binding to distorted pre-mRNA conformations in the , triggering helicase-mediated disassembly of error-prone spliceosomes to enhance overall splicing accuracy.

Regulation and Alternative Splicing

Core Regulatory Mechanisms

is a fundamental regulatory process in eukaryotic that allows a single pre-mRNA transcript to generate multiple mature mRNA isoforms by varying the inclusion or exclusion of and , thereby expanding diversity from a limited . The primary modes of include cassette exons, where an exon is either included or skipped; mutually exclusive exons, in which one of two or more exons is selected while others are excluded; and retention, where an remains in the mature mRNA rather than being removed. These mechanisms enable fine-tuned control of function, with estimates suggesting that over 90% of multi-exon genes undergo to produce distinct protein variants. Splicing regulation is primarily mediated by cis-acting regulatory elements within the pre-mRNA, such as exonic splicing enhancers (ESEs) and silencers (ESSs), as well as intronic splicing enhancers (ISEs) and silencers (ISSs), which recruit factors to promote or inhibit splice site recognition. , exemplified by SRSF1, bind to ESEs and ISEs to facilitate spliceosome assembly and inclusion by interacting with core splicing factors like U1 . In contrast, heterogeneous nuclear ribonucleoproteins (hnRNPs), such as PTBP1, typically bind to ESSs and ISSs to repress splicing, often by blocking access or competing for splice site binding, thereby promoting or intron retention. These interactions form a combinatorial code that dictates isoform production, with the balance between activators and repressors determining splice site choice. Co-transcriptional splicing integrates spliceosome activity with (Pol II) transcription, ensuring efficient processing as the pre-mRNA emerges from the polymerase. of the Pol II C-terminal domain (CTD), particularly on serine 5 during and serine 2 during elongation, serves as a platform for recruiting splicing factors; for instance, serine 5 by TFIIH promotes early spliceosome assembly, while serine 2 enhances interactions with the U2AF65 splicing factor to stabilize 3' splice site recognition. This dynamic coupling allows splicing decisions to be influenced by transcription rate and context, preventing aberrant isoforms. Recent transcriptome-wide studies have illuminated the intricate roles of spliceosome components in regulating isoform networks, revealing unexpected specialization beyond core catalysis. In a 2024 analysis involving systematic knockdown of 305 spliceosome-associated proteins and regulators in human cells, researchers reconstructed splicing interaction networks showing that many components, including non-catalytic ones, preferentially modulate specific alternative splicing events like cassette exons across thousands of genes, underscoring their roles in maintaining isoform balance. These findings highlight how perturbations in even peripheral factors can propagate through splicing networks, affecting global transcriptome diversity.

Factors Influencing Splice Site Selection

Tissue-specific isoforms of play a crucial role in regulating splice site selection to adapt splicing outcomes to cellular context, particularly in specialized cell types like . For instance, the Nova, a neuron-specific regulator, binds to intronic YCAY clusters near exons to promote or repress inclusion of synaptic protein-encoding exons, thereby fine-tuning neuronal essential for formation and function. This tissue-restricted action of Nova exemplifies how SR-like factors enable cell-type-specific patterns, influencing neuronal development and plasticity. Signaling pathways further modulate splice site selection by post-translationally modifying splicing factors in response to cellular signals, such as those promoting proliferation. The PI3K/AKT pathway, activated by growth factors, phosphorylates SRSF1 at specific serine residues, enhancing its binding to exonic splicing enhancers and shifting splicing toward isoforms that support progression and survival in proliferating cells like those in cancer tissues. This phosphorylation-dependent regulation links extracellular cues to intracellular splicing decisions, amplifying proliferative signals through altered isoform production. Coupling between and (NMD) serves as a mechanism to influence splice site selection by degrading unproductive isoforms, thereby preventing the accumulation of potentially toxic proteins. In this process, splicing events that introduce premature termination codons trigger NMD, which selectively depletes aberrant transcripts while preserving productive ones, thus optimizing the under normal conditions and mitigating errors from mutations or stress. This AS-NMD interplay acts as a regulatory feedback loop, fine-tuning by favoring splice sites that yield stable, functional mRNAs. Environmental stressors like hypoxia also dynamically alter splice site selection through changes in splicing factor activity, adapting cellular responses to low oxygen. Hypoxia upregulates and activates hnRNP A1, which binds to specific intronic sites to promote in genes involved in and , such as Fas and SMN2, thereby generating isoforms that enhance cell survival under oxygen deprivation. This hnRNP A1-mediated shift in splicing supports tumor adaptation in hypoxic microenvironments and illustrates how extrinsic cues reprogram the spliceosome for stress resilience.

Localization and Cellular Dynamics

Nuclear Compartmentalization

The spliceosome primarily functions within the nuclear compartment, where its components are concentrated in distinct subnuclear structures that facilitate efficient pre-mRNA processing. Splicing factors, including small nuclear ribonucleoproteins (snRNPs), are highly enriched in nuclear speckles, also known as SC35 domains, which serve as storage and assembly sites for these macromolecules. These irregular, punctate structures, typically 25-50 per nucleus, are surrounded by perichromatin , dynamic regions associated with active where transcription and splicing occur in close proximity. This spatial organization allows for the rapid recruitment of spliceosomal components to sites of nascent RNA synthesis, optimizing the coupling of transcription and splicing. The biogenesis of snRNPs, the core building blocks of the spliceosome, involves a tightly regulated pathway that spans cytoplasmic and nuclear compartments. snRNAs are initially transcribed in the nucleus and exported to the in a complex involving the cap-binding complex (CBC), the phosphorylated adaptor for RNA export (PHAX), and the exportin CRM1, which facilitates their transit through nuclear pores in a Ran-GTP-dependent manner. In the , the survival motor neuron (SMN) complex mediates the assembly of the Sm core proteins (B/B', D1, D2, D3, E, F, G) onto the Sm site of the snRNA, followed by hypermethylation of the 5' m7G to 2,2,7-trimethylguanosine (TMG) by trimethylguanosine (TGS1). The TMG then acts as a nuclear localization signal, enabling re-import into the nucleus via β, where snRNPs integrate into the nuclear architecture. Upon nuclear entry, spliceosomal components co-localize with nascent transcripts at active transcription sites, supporting co-transcriptional splicing. This association ensures that splice site recognition and spliceosome assembly occur as the pre-mRNA emerges from , minimizing delays in removal and enhancing mRNA . Studies have shown that splicing factors dynamically relocate to perichromatin regions in response to transcriptional activity, underscoring the spliceosome's integration with nuclear machinery. An exception to this general localization pattern is observed in the maturation of snRNPs for the minor spliceosome, which processes U12-type introns. Components of the minor spliceosome, such as U11 and U12 s, are predominantly enriched in , subnuclear organelles that serve as sites for snRNP modification, including pseudouridylation and 2'-O-methylation of snRNAs. This compartmentalization in facilitates the final assembly steps of minor snRNPs before their dispersal to perichromatin sites for splicing activity.

Recycling and Turnover

After the second catalytic step of splicing, the post-spliceosomal complex, also known as the intron-lariat spliceosome (ILS), undergoes remodeling to release the ligated exons as mature mRNA and the lariat intron. The DEAH-box RNA helicase Prp22 plays a central role in this process by unwinding the mRNA from the spliceosome in an ATP-dependent manner, facilitating exon ligation and lariat release. Prp22 binds to the 3' end of the ligated exons, pulling them away from the active site to complete the reaction and enable mRNA export, while also contributing to proofreading by rejecting suboptimal 3' splice sites to ensure fidelity. Subsequent disassembly of the ILS is mediated by the DEAH-box Prp43, often in association with cofactors Ntr1 and Ntr2, which promotes the release of the U2, U5, and U6 s for back to the nucleoplasm. Prp43 translocates along the U6 snRNA from its 3' end, destabilizing interactions within the ILS to dismantle the complex in an ATP-dependent fashion, thereby allowing snRNP reuse in new splicing cycles and preventing accumulation of post-catalytic structures. This step is essential for maintaining spliceosomal efficiency, as defects in Prp43 activity lead to impaired snRNP and splicing defects. To manage stalled or aberrant spliceosomal complexes that fail to progress, mechanisms target their components for degradation. When assembly is impaired, Sm core proteins—essential for stability—are ubiquitinated and degraded by the 26S proteasome, preventing the accumulation of non-functional intermediates and ensuring cellular resource allocation. This ubiquitin-proteasome pathway acts as a system for stalled , linking assembly defects to . Recent 2025 structural studies have elucidated how aberrant post-B^act spliceosome intermediates are directed toward disassembly to avert splicing errors. Cryo-EM analyses of defective complexes in reveal that sensors like the Gih35–Gpl1 pair detect mismatches, such as single-nucleotide insertions at the 5' splice site, blocking and recruiting the Ntr1-Prp43 complex for targeted dismantling. These findings highlight a discard pathway that recycles viable snRNPs while isolating aberrant ones, enhancing overall splicing accuracy and preventing error propagation. Recycled snRNPs are often stored in nuclear speckles before re-engagement in splicing.

Minor Spliceosome

Distinct Components

The minor spliceosome, responsible for splicing U12-type introns, features a distinct set of small nuclear RNAs (snRNAs) that parallel but differ from those in the major spliceosome. Specifically, U11 snRNA replaces U1, U12 replaces , U4atac replaces U4, and U6atac replaces U6, while U5 snRNA is shared between the two machineries. These minor snRNAs assemble into snRNPs with core Sm proteins, which are also common to the major spliceosome, enabling analogous base-pairing interactions with intron elements but tailored to the conserved sequences of U12-type introns. A key distinction lies in U12 snRNA's role in branch point recognition, where it base-pairs with a highly conserved , TCCTTAAC, featuring the bulged essential for the splicing reaction—unlike the more variable YNYURAC motif recognized by snRNA in the major pathway. Overall, the minor spliceosome incorporates more than 100 proteins, fewer than the ~300 associated with the major spliceosome, though it shares many non-snRNP factors while harboring unique components primarily in the U11/U12 di-snRNP. Among these, the U11/U12 di-snRNP includes seven to eight minor-specific proteins, such as the 65K protein (RNPC3), which acts as a molecular bridge between U11 and U12 snRNAs to facilitate dual recognition of the 5' splice site and during early assembly. Other unique factors in this complex encompass ZMAT5 (20K), SNRNP25 (25K), SNRNP35 (35K), SNRNP48 (48K), PDCD7 (59K), and ZCRB1 (31K), alongside the U4atac/U6atac snRNP-specific proteins like U4atac-60K and U6atac-61K. These components ensure precise targeting despite the minor pathway's lower abundance. Recent structural advances, including a 2025 cryo-EM study at atomic resolution (3.4 apo and 3.5 substrate-bound), have illuminated 5' splice site recognition by the minor spliceosome, revealing base-pairing between the U11 snRNA 5' end and the exon-intron junction, stabilized by non-canonical base-triple interactions in U11's stem-loop 3 and contributions from proteins like SNRNP48 and ZMAT5 near the Sm ring. This visualization underscores the architectural adaptations that enable the minor spliceosome's fidelity in processing rare introns.

Processing of U12-Type Introns

U12-type introns, also known as AU-AC introns, represent a minor class of introns characterized by highly conserved 5′ splice site (5′ss) consensus sequences (typically 5′-UAAUUUUAU-3′ or similar) and sequences (BPS) that differ from those of the more abundant U2-type introns. These introns are recognized specifically by the minor spliceosome through base-pairing interactions involving U11 and U12 snRNAs, which form a di-snRNP complex that binds the 5′ss and BPS, respectively, initiating the splicing process. In humans, U12-type introns constitute less than 0.5% of all introns and are found in approximately 700 genes, often embedded within constitutively expressed genes critical for cellular function. These introns are particularly enriched in genes involved in RNA processing, regulation, and , underscoring their role in maintaining fundamental cellular processes. The assembly of the minor spliceosome for U12-type intron processing follows a pathway parallel to that of the major spliceosome but utilizes distinct components, beginning with the U11/U12 di-snRNP binding to initiate E complex formation. Subsequent rearrangements involve the U4atac/U6atac.U5 tri-snRNP, where U4atac and U6atac snRNAs form base-pairing interactions analogous to U4/U6 in the major pathway, enabling activation of the catalytic center for the two steps. This process is less efficient than major spliceosome activity, with splicing rates several-fold slower, partly due to the lower abundance of minor spliceosome components. Mutations in minor spliceosome components, such as those in the RNU4ATAC gene encoding U4atac snRNA, lead to significantly higher error rates in U12-type splicing because these elements lack the genetic seen in the major spliceosome; each minor snRNA is typically encoded by a single genomic locus, making the system more vulnerable to disruption. For instance, recessive mutations in RNU4ATAC associated with microcephalic osteodysplastic type I (MOPD I) reduce splicing efficiency by nearly 10-fold, resulting in intron retention or activation of cryptic splice sites and widespread dysregulation of U12-dependent genes. This reduced fidelity highlights the minor spliceosome's reliance on precise molecular interactions without backup mechanisms. Evolutionarily, U12-type introns trace back to an ancient splicing machinery, likely originating from group II self-splicing introns in the last common eukaryotic ancestor, with their positions showing greater conservation across distant species like humans and compared to U2-type introns. This high positional conservation suggests that U12-type introns were present in the proto-eukaryotic and have been maintained in essential genes due to their functional importance, reflecting a relic of early eukaryotic intron evolution.

Biological Significance

Role in Disease (Spliceosomopathies)

Mutations in genes encoding spliceosomal components give rise to a class of disorders termed spliceosomopathies, characterized by defective pre-mRNA splicing that leads to tissue-specific pathologies. Autosomal dominant retinitis pigmentosa, a progressive retinal degeneration, is frequently caused by mutations in PRPF31, which encodes a protein essential for the assembly of the U4/U6.U5 tri-snRNP complex. These mutations disrupt tri-snRNP formation, impairing spliceosome function and resulting in haploinsufficiency that selectively affects photoreceptor cells. Similarly, spinal muscular atrophy (SMA), a leading genetic cause of infant mortality, arises from homozygous deletions or mutations in SMN1, leading to reduced levels of the survival motor neuron (SMN) protein critical for snRNP biogenesis. SMN deficiency compromises the assembly and nuclear import of spliceosomal snRNPs, causing widespread splicing defects that particularly impact motor neuron survival and function. Myelodysplastic syndromes (MDS), a group of clonal hematopoietic disorders, commonly feature heterozygous in SF3B1, a core subunit of the snRNP involved in branch point recognition. These , often at hotspot residue K700E, shift branch point usage toward suboptimal sites, promoting aberrant splicing of genes involved in hematopoiesis and , which contributes to ineffective blood cell production and progression to . In contrast to these mutations, somatic alterations in spliceosomal genes are prevalent in various cancers, where they confer a selective advantage through altered splicing landscapes. Therapeutic strategies targeting the spliceosome have gained traction, with 2024 studies highlighting small-molecule inhibitors like sudemycins as promising anticancer agents by exploiting splicing vulnerabilities in tumors with hyperactive or mutant spliceosomes. Sudemycins, analogs of natural product FR901464, bind SF3B1 to block spliceosome assembly, inducing selective toxicity in cancer cells while sparing normal tissues, as demonstrated in preclinical models of hematological malignancies. Emerging 2025 research further implicates minor spliceosome defects in neurodegeneration, particularly in amyotrophic lateral sclerosis (ALS) linked to FUS mutations, where impaired U12-dependent splicing of neuronal transcripts disrupts protein homeostasis and exacerbates motor neuron degeneration.

Evolutionary Conservation

The spliceosome is believed to have emerged in the last eukaryotic common ancestor (LECA), where its core components, including the small nuclear RNAs (snRNAs) U1, U2, U4, U5, and U6, were already established and underwent minimal structural changes throughout eukaryotic evolution. These snRNAs exhibit varying degrees of sequence conservation, with U6 showing high identity (>70%) and core functional regions of others preserved between distant lineages such as budding yeast (Saccharomyces cerevisiae) and humans (Homo sapiens), reflecting their critical catalytic roles in intron removal. This ancient origin traces back to the integration of group II intron-derived elements from prokaryotic ancestors into the emerging eukaryotic genome, forming the foundational ribonucleoprotein machinery for pre-mRNA splicing. Despite this core conservation, spliceosomal variations have arisen across eukaryotic lineages to accommodate diverse transcriptomic needs. In kinetoplastids like trypanosomes (), the spliceosome primarily facilitates trans-splicing, where a short spliced leader is added to the 5' end of polycistronic pre-mRNAs, diverging from the cis-splicing predominant in most eukaryotes while retaining homologous U snRNAs and proteins. , in contrast, display additional integrations of small nucleolar RNAs (snoRNAs), such as expanded U3 snoRNA variants that interact with spliceosomal components to fine-tune rRNA processing and indirectly influence splicing efficiency in intron-rich genomes. These adaptations highlight how the spliceosome's modular architecture allows lineage-specific modifications without disrupting its fundamental mechanism. The minor spliceosome, responsible for excising rare U12-type AT-AC introns, represents a relic of an early, prokaryotic-like splicing system akin to group II self-splicing introns, and its components show patchy distribution across eukaryotes. While present in metazoans and many protists, the minor spliceosome and its specific snRNAs (U11, U12, U4atac, U6atac) have been independently lost multiple times, notably in the fungal lineage including , simplifying splicing to U2-type introns only. This loss underscores evolutionary pressures favoring streamlined major spliceosomes in certain clades. Comparative genomics has illuminated the deep conservation of key spliceosomal proteins, such as Prp8, the largest and most central component of the U5 , which exhibits strong across (encompassing animals and fungi) due to its indispensable role in . Recent 2024 computational models, integrating phylogenomic alignments and structural predictions, reveal divergence patterns in Prp8 domains, with conserved catalytic cores contrasting variable peripheral regions that tolerate lineage-specific adaptations. These analyses affirm Prp8's status as a molecular , preserving traces of the LECA spliceosome amid eukaryotic diversification.

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