The spliceosome is a colossal ribonucleoprotein assembly, built from five small nuclear RNAs and well over a hundred proteins. It assembles anew on every single intron in every pre-messenger RNA molecule, and once it has excised the intron as a looped structure called a lariat, the ligated mRNA is released. But the excised intron-lariat stays wedged inside the RNA-based active site of the machine, forming a stable complex known as the intron-lariat spliceosome. This state is a dead end. To sustain the relentless pace of splicing in a growing cell, the intron-lariat spliceosome must be dismantled so that its proteins and small nuclear RNAs can be reused, and the trapped intron must be ejected, straightened out at its branch point, and ultimately degraded. These combined events constitute spliceosome termination, and until now the molecular details of how they unfold have been largely unknown.

A team led by researchers at the Research Institute of Molecular Pathology in Vienna, working with colleagues in the Netherlands and Spain, set out to catch the spliceosome in the act of terminating. Their strategy combined cryo-electron microscopy of spliceosomes purified directly from human cells with biochemistry, RNA sequencing and genetic experiments. By tagging the proteins DHX35 and YJU2B in human K562 cells and purifying the spliceosome complexes associated with them, the researchers obtained two distinct molecular snapshots. The first, resolved at a remarkable 2.4 angstrom resolution, captured a state they named the ILS-AQR complex. The second, at 3.2 angstroms, revealed an entirely new intermediate that they called the debranched intron spliceosome, or DIS. Together, these structures trace the sequential stages through which the spliceosome passes as it winds down its work.

The ILS-AQR structure revealed several surprises. The team identified a previously uncharacterized termination factor, YJU2B, bound to the spliceosome alongside the known termination factors TFIP11, C19L1, C19L2 and the RNA helicase DHX15. More strikingly, they found that the RNA helicase Aquarius, a protein already known for its role in spliceosome activation, was gripping the circular portion of the intron-lariat RNA in its active site. Aquarius belongs to a family of helicases that move along single-stranded RNA in a defined direction, and the structure showed it poised to pull on the intron-lariat branch point adenosine, the chemical knot that holds the lariat loop together. The researchers propose that Aquarius, guided by the RNA-binding protein PPIE, tugs the branch point out of the spliceosomal RNA network, while DHX15 simultaneously unwinds a different RNA element on the opposite side. Two RNAs pulled in opposite directions, the authors suggest, begin to unravel the intricate RNA architecture that holds the spliceosome together.

Extracting the branch point serves a second critical purpose: it exposes the knot so that it can be cut open. The enzyme responsible is DBR1, a debranching enzyme whose action is essential for intron turnover and for maintaining the balance of RNA in the cell nucleus. The new study provides the first molecular evidence that debranching happens directly on the spliceosome. Through a combination of proximity labelling, protein interaction predictions and biochemical validation, the researchers showed that DBR1 is tethered to the spliceosome through two conserved peptide segments in its tail. One of these peptides binds the termination factor C19L1, anchoring the catalytic domain of DBR1 within reach of the extracted branch point. Experiments in human cells confirmed the biological importance of this connection: DBR1 lacking the peptide could not rescue the growth defect caused by acute depletion of the endogenous enzyme, whereas the full-length protein could.

Once the branch point has been cut and the early termination factors have been displaced, the spliceosome enters the newly discovered DIS state. In this complex, the RNA network is almost completely dismantled. The U2 snRNP, the ESS2 protein and all six ILS-specific termination factors are gone, and the excised intron, now linearized, remains attached only through a short duplex between the U6 small nuclear RNA and the 5-prime splice site. RNA sequencing of the introns associated with each complex confirmed that the vast majority of DIS-bound introns had indeed been debranched, and that nearly all introns found in the ILS-AQR state were also detected in the DIS, indicating that passage through these two states is the predominant termination pathway for human introns.

The final blow is delivered by the RNA helicase DHX35, recruited to the DIS together with its cofactors GPATCH1 and WDR83. The structure shows DHX35 anchored on the spliceosome through extensive contacts with GPATCH1, which itself winds around the PRP8 protein at the heart of the machine. The U6 snRNA regions just downstream of the splice-site pairing are positioned to dock into the DHX35 active site, and the authors propose that DHX35 translocates along U6 snRNA, unwinding the remaining helical turn of the U6-intron duplex and ejecting the debranched intron for decay. In support of this model, purified DIS complexes immobilized on beads released their U5 snRNP and associated protein complexes upon addition of ATP, but only when DHX35 was catalytically competent. A mutant version of DHX35 unable to hydrolyse ATP bound the spliceosome normally yet failed to trigger disassembly, demonstrating that the helicase actively drives the final separation.

The study also illuminates how the cell deals with spliceosomes that go wrong. Splicing is not always successful, and defective complexes assembled on aberrant introns must be recognized and dismantled through a quality-control pathway. By revising an existing structure of a defective spliceosome from fission yeast, the researchers identified two additional factors, the YJU2B orthologue Saf4 and an uncharacterized protein called LENG1. LENG1, a paralogue of the essential branching factor CWC25, appears to partner with YJU2B specifically in defective complexes, where it helps guide the DHX35-GPATCH1-WDR83 machinery to the stalled spliceosome. The same helicases, DHX15 and DHX35, therefore serve both routine termination and quality control, but in regular termination they act in two sequential states, whereas in defective complexes they can be deployed simultaneously for a single-step disassembly.

The significance of this work extends beyond the mechanics of one molecular machine. Errors in splicing are implicated in a wide range of human diseases, including cancers driven by mutations in the splicing factor SF3B1, and the factors identified here, several of which rank among each other’s strongest genetic dependencies in human cell screens, may represent new points of vulnerability. By revealing how three RNA helicases, Aquarius, DHX15 and DHX35, orchestrate the gradual dismantling of the spliceosomal RNA network, coupling intron debranching and ejection to machine disassembly, the study closes a long-standing gap in our understanding of gene expression. Every protein-coding message in the human body depends on this final act of molecular housekeeping, and it has now, at last, been caught on camera.

Subject of Research: Structural mechanism of human spliceosome termination and intron-lariat debranching

Article Title: Mechanism of spliceosome termination

Article References: Boreikaite, V., Faraway, R., Vorländer, M. K., Phillips, A. W., Opitz, L., Wanke, M., Yakoub, G., Raffl, G., Fin, L., González-Prieto, R., Luijsterburg, M. S., Ameres, S. L., & Plaschka, C. (2026). Mechanism of spliceosome termination. Nature. https://doi.org/10.1038/s41586-026-11101-6

Image Credits: AI Generated

DOI: 10.1038/s41586-026-11101-6

Keywords: spliceosome, pre-mRNA splicing, cryo-electron microscopy, intron lariat, DHX35, DHX15, Aquarius, DBR1, RNA helicase, spliceosome recycling, RNA quality control, gene expression

The research, led by Lu-Yan Chan, Ming-Kin Wong, and Yong-Hong Yan as co-first authors in the laboratory of Zhongying Zhao at Hong Kong Baptist University, with collaborators at the National Institute of Biological Sciences in Beijing and the University of Science and Technology of China, focuses on CYL-1, the worm counterpart of cyclin L1. Cyclins are best known as the rhythmic partners of cyclin-dependent kinases, the enzymes that drive cells through the phases of the cell cycle. Yet a growing body of work has revealed that many cyclins moonlight in other processes, and cyclin L had previously been implicated in pre-mRNA splicing through its interaction with CDK-11 in cultured cell lines. What remained murky was whether this splicing connection mattered in a living, developing animal—and what else the protein might be doing there.

To find out, the team first established where and when CYL-1 operates. Fluorescently tagged versions of the protein revealed that CYL-1 is expressed ubiquitously, residing in cell nuclei throughout the entire course of worm development. That broad, persistent nuclear presence hinted that the protein is not a niche player confined to one tissue or stage, but a general component of the gene-expression machinery whose loss should ripple across the organism. The next step was to identify who CYL-1 actually works with inside those nuclei.

Using co-immunoprecipitation followed by mass spectrometry—a technique in which a bait protein is pulled down from worm extracts along with everything physically bound to it, and the captured partners are then identified by their peptide fingerprints—the researchers mapped CYL-1’s interaction network in vivo. The results confirmed that CYL-1 forms complexes with two worm CDK-11 isoforms, CDK-11.1 and CDK-11.2, and also identified a highly conserved protein called EELO-1, named for its association with early transcriptional elongation, as a core interactor. Together with the splicing-associated factor SAP30BP highlighted in the study’s title, these proteins define a complex that sits at the junction of transcription and RNA processing.

Genetic analysis then revealed how essential this machinery is. When the researchers interfered with cyl-1, cdk-11.1, cdk-11.2, or eelo-1 using RNA interference, embryos failed to develop normally, and the two CDK-11 paralogs were shown to act redundantly: knocking down either alone was survivable to a degree, but compromising both sharply reduced embryonic viability. This redundancy is a classic signature of duplicated genes that share a critical function, and it means the worm tolerates losing one copy of the kinase only because the other can carry the load. The four proteins, in other words, are not optional accessories but load-bearing pillars of mRNA biogenesis during embryogenesis.

The mechanistic heart of the study lies in what those pillars actually do to RNA. Immunostaining assays, which use antibodies to visualize the location of specific molecular marks on proteins, showed that loss of CYL-1 disrupts events at the very start of the transcription cycle, affecting transcriptional initiation and the elongation of RNA polymerase along the gene body. RNA sequencing of embryos depleted of each complex member added a genome-wide view: beyond changes in overall transcript levels, the researchers documented widespread defects in pre-mRNA splicing, with alternative splicing patterns shifting substantially and differently depending on which of the four genes—cyl-1, cdk-11.1, cdk-11.2, or eelo-1—had been silenced. That last detail matters. If the four proteins were simply interchangeable parts of one machine, depleting any of them would produce the same splicing fingerprint. Instead, each leaves a distinct signature, suggesting partially specialized roles within a shared complex.

Perhaps the most striking finding came from asking a developmental question rather than a biochemical one. Using established cell fate markers—reporter constructs that fluoresce only when a cell has committed to a particular identity—the team demonstrated that CDK-11.1, CDK-11.2, and EELO-1 are involved in regulating cell fate specification during development. In an embryo, every cell carries the same genome; what distinguishes a muscle cell from a neuron is which subset of genes is transcribed and how those transcripts are processed. A complex that influences both transcriptional output and splicing is therefore ideally positioned to shape that decision, and the new data indicate that it does. The result reframes splicing factors not merely as editors of genetic text but as participants in the regulatory logic that assigns identities to embryonic cells.

Importantly, the study also uncovers an asymmetry within the complex. While CYL-1 is required for transcriptional initiation, elongation, and splicing, its partners CDK-11.1, CDK-11.2, and EELO-1 carry the additional responsibility of governing cell fate determination—a role that CYL-1 itself did not show in these assays. This differential division of labor between a cyclin and its interactors adds a nuanced twist to cyclin biology. It suggests that the familiar cyclin-CDK pairing can be modular: the kinase and its associated factors may perform functions beyond, and independent of, the cyclin that helps recruit or activate them. For an organism as experimentally tractable as C. elegans, whose transparent embryos allow researchers to watch every cell division in real time, such a system offers a powerful platform for dissecting how those roles are partitioned at the molecular level.

The evolutionary implications extend well beyond worms. CDK-11 and cyclin L are conserved across metazoans, including mammals, where CDK11 has been implicated in cell cycle control, apoptosis, and RNA processing, and where splicing deregulation is increasingly recognized as a driver of developmental disorders and cancer. EELO-1’s conservation means the worm findings likely illuminate a broadly shared architecture of gene expression. If a CDK-11-containing complex couples transcriptional elongation and splicing to cell fate decisions in nematodes, the same coupling may operate in vertebrate embryos, stem cells, and disease states where differentiation goes awry. The study does not test these possibilities directly, but it establishes the in vivo framework that such future work in other organisms can build upon.

What makes the work resonate beyond its immediate field is the picture it paints of gene expression as a single, physically continuous process rather than a relay of disconnected stages. The RNA polymerase that reads a gene, the factors that splice its transcript, and the regulatory network that decides a cell’s destiny are, in this emerging view, held together in one macromolecular assembly. A defect anywhere in that assembly—an underactive kinase, a missing cyclin, an absent elongation factor—can propagate outward from a biochemical glitch to a developmental outcome: an embryo that fails to survive, or a cell that adopts the wrong identity. By grounding that logic in the concrete genetics of a living animal, the Hong Kong-led team has turned a splicing complex into a lens on one of biology’s deepest questions—how a genome becomes an organism—and provided a molecular handle that researchers studying development, RNA biology, and disease will now be eager to pull.

Subject of Research: The role of a CYL-1/CDK-11/EELO-1 complex in pre-mRNA splicing and cell fate specification during C. elegans development

Article Title: A CDK-11/SAP30BP/CYL-1 complex links pre-mRNA splicing to developmental cell fate decisions

Article References: Chan, L.-Y., Wong, M.-K., Yan, Y.-H., Ho, V. W. S., Ma, Y., Xie, D., Ye, P., Zeng, J., Dong, M.-Q., Guang, S., & Zhao, Z. (2026). A CDK-11/SAP30BP/CYL-1 complex links pre-mRNA splicing to developmental cell fate decisions. BMC Biology. https://doi.org/10.1186/s12915-026-02734-0

Image Credits: AI Generated

DOI: 10.1186/s12915-026-02734-0

Keywords: CYL-1, CDK-11, EELO-1, pre-mRNA splicing, cell fate determination, C. elegans, embryogenesis, cyclin-dependent kinase, transcriptional elongation, developmental genetics, mRNA biogenesis, BMC Biology