BEYOND SILENCING: SOS SPLICING AS A TRANSCRIPT-LEVEL DEFENSE AGAINST DNA TRANSPOSONS
 |
| Two nuclei of the one-cell stage of a fertilized mouse embryo showing a transposable element in red. DNA is shown in blue |
Transposable elements (TEs) are mobile genetic elements that can shift their position or copy themself from one place to another in the chromosomes. Naturally, TEs are integrated alongside genes or, in some cases, within the intronic regions of genes. The integration of the TEs leads to gene disruption or functionally incompetent transcripts and proteins, causing diseases like cancer and neurological disorders. To prevent this, prokaryotic and eukaryotic systems use epigenetic silencing to suppress TE replication and expression. Despite the presence of these systems, TE accounts for 3-80% of extant genomes, indicating that the silencing systems are prone to failure or error. However, we are not sure if organisms have any alternative mechanisms to protect the genome after the silencing system fails.
Fortunately, recent research has provided us with some insights into the alternative pathway. A paper titled “An RNA splicing system that excises DNA transposons from animal mRNAs”, published in Nature, has discovered spliceosome-independent machinery called SOS splicing, which recognizes inverted terminal repeat (ITR) elements present in DNA transposons and splices the TEs from the mRNA transcripts.
DNA transposons are class II transposons with a cut-and-paste mechanism. They typically consist of a transposase-encoding gene flanked by inverted terminal repeat elements (ITRs). DNA transposons are inserted into most plant and animal genes; however, they don't always disrupt the host gene, though they can introduce premature stop codons (PTCs). With the knowledge of nonsense-mediated mRNA decay (NMD), which recognizes these PTCs and degrades the mRNA, they wanted to find an explanation for this paradox: can DNA transposons be precisely excised from the mRNAs in animals?
To investigate this, the RSD-3 protein in C. elegans was chosen. The protein contains an epsin N-terminal homology (ENTH) domain and is required for RNA interference (RNAi) in C. elegans. To the rsd-3 first exon, Tc1, an active and abundant DNA transposon, was inserted, which can create a functional RSD-3 protein even when Tc1 is excised. This was introduced into the host, and simultaneously, they looked into genes that normally have Tc1 insertions; 90–100% of the Tc1 was excised from the mRNA in all the cases. Moreover, in all the cases, Tc1 was present in the DNA but not on the mRNAs, concluding that Tc1 excision occurs post-transcriptionally.
Through nanopore long-read sequencing, it was found that excision occurs in or near the ITRs, and mostly doesn't have the typical GU-AG consensus splice sites, indicating it works spliceosome-independent. However, these excisions have led to short indels post-repair of mRNAs, giving rise to the term SOS splicing. Moreover, they also found that SOS splicing can only rescue the gene when it generates an in-frame mRNA, so indels left by the splicing don't disrupt the function of the protein. Moreover, deletion of different domains of Tc1, it was found that ITR, which forms double-stranded RNA (dsRNA), is the signal that induces the SOS splicing.
To further identify the proteins involved in the SOS splicing, they used mutagenesis followed by phenotype-based screening to isolate mutants defective in SOS splicing. 20 mutant animals were identified in screening 100,000 haploid genomes. They identified 11 mutations in sut-2, 8 mutations in the gene C07H6.8, and 1 mutation in F15D4.2. They referred to C07H6.8 and F15D4.2 as akap-17 and caap-1. Moreover, they also found homologs of these proteins in mammals and humans. Further, through an immunoprecipitation followed by mass spectrometry (IP–MS) of CAAP1, they found that the RNA ligase RTCB interacts with CAAP1 in HEK293T cells. These suggested that RTCB might play a role in SOS splicing by ligating the mRNA fragments after SOS splicing.
 |
| CAAP1 IP–MS results from HEK293T cells |
Further, through a combination of loss-of-function and RNA-binding/interaction experiments, they found the role of each protein involved in the SOS splicing. As per the model, AKAP17A binds to the TE::mRNA, CAAP1 recruits the RTCB to AKAP17A in the nuclear foci; however, they couldn't explore the role of MSUT2 in the SOS splicing. Nonetheless, they were unable to find the protein with endonuclease activity that excises TEs from mRNAs. However, the criteria of a protein that has nuclease activity and dsRNA-binding, SON, a protein found in IP–MS analysis of CAAP1, is considered a candidate to further look into.
Even though SOS splicing is efficient, it lacks precision, often leading to indels after excision. Despite that, SOS splicing shows that organisms have a fail-safe system that allows them to tolerate transposable element insertion at the transcriptional level and coexist with TEs. Given the presence of transposable elements across the genome and their significant impact on genome evolution, this study suggests that there might be more TE-coexistence systems that are yet to be discovered.
REFERENCE
Zhao, LW., Nardone, C., Chang, C. et al. An RNA splicing system that excises DNA transposons from animal mRNAs. Nature 649, 496–504 (2026). https://doi.org/10.1038/s41586-025-09853-8
IMAGE CREDIT
LMU München, https://share.google/QCtRSu0y7hAKILYpS
ResearchGate, https://share.google/sMNOH4i2hUPS4FxUp
Comments
Post a Comment