Biology subjects

Scott, M. S.

Publications and source records attributed to Scott, M. S..

At least 19 recordsLinked to original sources

bioRxiv2026

A Ribosomal RNA modification regulates translation of PI3K/AKT activators in high-grade serous ovarian carcinoma

PI3K/AKT signalling is a key driver of ovarian cancer progression and an important therapeutic target. Its deregulation is usually explained by genetic changes and altered signalling at the cell surface. Here, we identify an additional layer of pathway control, in which a change in the level of a cancer-associated ribosomal RNA modification alters the translation of proteins that regulate PI3K/AKT activity. SNORA81 is a high-grade serous ovarian carcinoma-associated H/ACA small nucleolar RNA that directs pseudouridylation of 28S ribosomal RNA at position U4636. Integration of tumour transcriptomes with independent SNORA81-depletion datasets identified 22 SNORA81-linked transcripts with reversed disease-associated expression, 19 of them linked to PI3K/AKT signalling. SNORA81 depletion reduced AKT phosphorylation, impaired cell growth, migration, and altered cell-cycle distribution. Molecularly, polysome profiling following SNORA81 depletion identified 524 mRNAs with altered ribosome association, 485 of which changed independently of RNA abundance and included 29 PI3K/AKT regulators. SNORA81 depletion reduced ribosome association of ITGB4, RASGRP2, IGF1 and FGF18 transcripts, and reduced ITGB4 and RASGRP2 protein abundance. IRAK1 and SPC24 acted as downstream RNA-response genes contributing to selected SNORA81-associated phenotypes. ITGB4 expression partially restored cell growth and restored downstream RNA responses after SNORA81 depletion. These findings identify rRNA modification as a translational regulator of PI3K/AKT signalling in ovarian cancer.

cancer biology↗

bioRxiv2026

A ribosomal pseudouridine drives an oncogenic translation program

Dynamic ribosome heterogeneity has emerged as a potential layer of translational regulation, but whether variation in ribosomal RNA (rRNA) modification stoichiometry can selectively control the translation of mRNAs with shared encoded features remains unclear. Here we show that SNORA81-guided pseudouridylation at U4636 controls a selective translational program in ovarian cancer cells. U4636 is partially pseudouridylated and lies within 28S rRNA near eL31 and the peptide exit tunnel. Depletion of SNORA81 reduces pseudouridylation at U4636 without broadly perturbing rRNA processing or bulk translation. Instead, it remodels codon-specific and nascent-peptide-associated pausing and the polysome association of SNORA81-dependent translationally altered mRNAs. These mRNAs display characteristic GC content and amino-acid composition, are enriched in cancer-related functions and show corresponding changes in protein levels. Our findings support a model in which a change in the abundance of a single snoRNA propagates from rRNA-modification stoichiometry through ribosome dynamics and selective mRNA translation to protein output and cancer cell proliferation. We term this multilevel amplification cascade the "sno-balling" effect.

cancer biology↗

bioRxiv2026

A starvation-remodeled pre-mRNA structure controls U1 recruitment and nutrient-stress adaptation in yeast

Recognition of 5' splice sites by the U1 small nuclear ribonucleoprotein commits pre-mRNAs to splicing, yet splice-site complementarity alone cannot predict productive U1 engagement. Whether dynamic pre-mRNA structure regulates this early spliceosome assembly step remains unclear. Here, we identify a 5'UTR-intron base-pairing interaction positioned near the 5' splice site that acts as an inducible structural gate for U1 engagement. In budding yeast, this element is enriched among introns required for adaptation to nutrient depletion, and in vivo DMS-MaPseq shows that starvation remodels its structure. Structure-guided disruption of pairing impairs adaptation, whereas compensatory mutations restoring pairing without restoring sequence rescue the phenotype, establishing RNA fold as the critical determinant. U1 association decreases when the gate is disrupted and recovers when pairing is restored, and increased Nam8 levels can compensate for gate disruption by stabilizing U1 engagement under stress. Thus, dynamic pre-mRNA folding gates U1 recognition, revealing how transcript architecture converts physiological state into selective splice-site choice.

molecular biology↗

bioRxiv2026

Nanopore Direct RNA Sequencing Enables Reproducible, Site-Resolved Pseudouridine Quantification in Human Ribosomal RNA

Pseudouridine is the most abundant post-transcriptional modification in human ribosomal RNA, with over 110 annotated sites and variable stoichiometry across biological contexts. Existing quantification methods are low-throughput or constrained to predefined panels. We benchmarked nanopore direct RNA sequencing using the Dorado v5.1 model against mass spectrometry-validated sites in human liver tissue, induced pluripotent stem cells, and HeLa cells. Nanopore sequencing detected 95 of 117 validated sites and accurately quantified stoichiometry at 85% of sites with high reproducibility. Low GC-content environments were the primary source of failure. These results establish nanopore sequencing as a scalable tool for epitranscriptomic pseudouridine profiling.

biochemistry↗

bioRxiv2026

snoFlake: A network model for snoRNA-RBP complexes reveals SNORD22 as a U5 snRNP-associated splicing regulator

Small nucleolar RNAs (snoRNAs) are canonically viewed as stable components of ribonucleoprotein complexes dedicated to RNA modification. Here, we developed snoFlake, a snoRNA-centric interaction network integrating physical and functional associations between box C/D snoRNAs and RNA-binding proteins (RBPs), challenging this narrow view. Using snoFlake, we systematically identified snoRNAs predicted to form noncanonical complexes with diverse RBPs, extending their roles into post-transcriptional regulation. We found 23 high-confidence network motifs enriched for RNA-processing functions, including a top-ranked module linking SNORD22 to U5 snRNP components PRPF8 and EFTUD2. SNORD22 co-binds with these spliceosomal RBPs at splice sites showing reduced U5 snRNP occupancy, suggesting a role in reinforcing spliceosomal engagement at suboptimal exons. Consistently, SNORD22 depletion promotes exclusion of weak cassette exons, altering transcript isoform composition and predicted coding output. Beyond SNORD22, snoFlake reveals snoRNAs with similar network profiles, providing a resource for uncovering previously uncharacterized snoRNA-RBP complexes and expanding the functional snoRNome.

bioinformatics↗

bioRxiv2025

SnoBIRD: A tool to identify C/D box snoRNAs and refine their annotation across all eukaryotes

Small nucleolar RNAs (snoRNAs), a group of noncoding RNAs present amongst all eukaryotes, are most extensively characterized for their regulation of ribosome biogenesis and splicing. Despite their central roles, current snoRNA annotations remain incomplete. Several eukaryote genome annotations contain few or no snoRNAs, and none distinguish expressed snoRNAs from their pseudogenes--a recently characterized snoRNA subclass with distinct features and expression levels. To address this, we developed SnoBIRD, a BERT-based C/D box snoRNA predictor trained on snoRNAs spanning all eukaryote kingdoms. We show that SnoBIRD outperforms existing tools and is the only predictor capable of identifying snoRNA pseudogenes using biologically relevant signal. Applied on the fission yeast and human genomes, we demonstrate that only SnoBIRD scales well with genome size in terms of runtime, and we identify and experimentally validate several new SnoBIRD-predicted C/D box snoRNAs. By running SnoBIRD on multiple eukaryote genomes, we identify hundreds of novel snoRNA candidates and highlight SnoBIRDs usefulness to determine the evolutionary paths of snoRNAs distributed across different species. Overall, SnoBIRD represents a user-friendly and efficient tool for reliably predicting C/D box snoRNAs and their pseudogenes across any eukaryote genome. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/646650v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@99b390org.highwire.dtl.DTLVardef@dbe375org.highwire.dtl.DTLVardef@32358aorg.highwire.dtl.DTLVardef@58fb3a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

RNase III cleavage signals spread across splice junctions enforce sequential processing of co-hosted snoRNAs.

Small nucleolar RNAs (snoRNAs) are a class of non-coding RNA molecules whose precursor transcripts are capped and polyadenylated. However, these end modifications are detrimental to snoRNA function and must be removed, a process typically involving excision from introns and/or endonucleolytic cleavage. In the case of polycistronic RNA precursors that host multiple snoRNAs, the sequence of maturation events is not well understood. Here we report a new mode of maturation concerning snoRNA pairs that are co-hosted in the intron and the adjacent 3 exon of a precursor transcript. For such a pair in the model eukaryotic species Schizosaccharomyces pombe, we identified a double-stranded RNA hairpin folding across the exon-exon junction. The hairpin recruits the RNase III Pac1 that cleaves and destabilizes the precursor transcript while participating in the maturation of the downstream exonic snoRNA, but only after splicing and release of the intronic snoRNA. We propose that such RNase III degradation signal hidden in an exon-exon junction evolved to enforce sequential snoRNA processing. Sequence analysis suggest that this mechanism is conserved in animals and plants.

molecular biology↗

bioRxiv2024

The Pseudogene RPS27AP5 Reveals Novel Ubiquitin and Ribosomal Protein Variants Involved in Specialised Ribosomal Functions.

Pseudogenes, traditionally considered non-functional gene copies resulting from evolutionary mutations, have garnered attention due to recent transcriptomics and proteomics revealing their unexpected expressions and consequential cellular functions. Ubiquitin, transcribed from UBA52 and RPS27A genes, fused to ribosomal proteins eL40 and eS31, and polyubiquitin precursors encoded by UBB and UBC genes, has additional pseudogenes labeled as non-functional. However, recent evidence challenges this notion, demonstrating that these pseudogenes produce ubiquitin variants with minimal differences from the canonical sequence, suggesting a new regulatory dimension in ubiquitin-mediated cellular processes. To systematically catalogue possible Ubiquitin (Ub) and Ubiquitin-like (Ubl) variants from pseudogenes, expression data was compiled, identifying potential functional variants. Among these pseudogenes, RPS27AP5 expresses both Ubiquitin variant (UbP5) and ribosomal protein variant (S27aP5), with precursor proteins maturing through cleavage and exhibiting behavior similar to their counterparts post-translation. Notably, S27aP5 integrates into translating ribosomes, increasing the 80S monosomal ribosomal fraction and indirectly influencing p16INK4A transcriptional activation. The discovery of a functional S27a pseudogene supports the concept that a subset of ribosomes may incorporate diverse subunits for specific translational functions.

cell biology↗

bioRxiv2022

Apelin Stimulation of the Perivascular MuSC Niche Enhances Endogenous Repair in Muscular Dystrophy

Impaired skeletal muscle stem cell (MuSC) function has long been suspected to contribute to the pathogenesis of muscular dystrophy (MD). Here we describe that defects in the endothelial cell (EC) compartment of the perivascular stem cell niche in three different types of MD are associated with inefficient mobilization of MuSCs following tissue damage. Using chemoinformatic analysis, we identified the 13 amino acid form of the peptidic hormone apelin (AP-13) as a candidate for systemic stimulation of skeletal muscle ECs. In dystrophic mice, administration of AP-13 generates a pro-myogenic EC-rich niche that supports MuSC function and markedly improves tissue regeneration, muscle strength, and physical performance. Moreover, we demonstrate that EC specific knockout of the AP-13 receptor leads to regenerative defects that phenocopy major pathological features of MD. Altogether, we provide in vivo proof-of-concept that enhancing endogenous repair by targeting the perivascular niche is a viable therapeutic avenue for MD and characterize AP-13 as a novel drug candidate for systemic treatment of stem cell dysfunction.

cell biology↗

bioRxiv2022

Altered tRNA processing is linked to a distinct and unusual La protein in Tetrahymena thermophila

Nascent pre-tRNAs are transcribed by RNA polymerase III and immediately bound by La proteins on the UUU-3OH sequence, using a tandem arrangement of the La motif and an adjacent RNA recognition motif-1 (RRM1), resulting in protection from 3-exonucleases and promotion of pre-tRNA folding. The Tetrahymena thermophila protein Mlp1 has been classified as a genuine La protein, despite the predicted absence of the RRM1. We found that Mlp1 functions as a La protein through binding of pre-tRNAs and affecting processing in Tetrahymena thermophila and when expressed in fission yeast. However, unlike in other examined eukaryotes, depletion of Mlp1 results in 3-trailer stabilization. We also observed that 3-trailers in Tetrahymena thermophila are uniquely short relative to other examined eukaryotes, and that 5-leaders have evolved to disfavour pre-tRNA leader/trailer pairing. Our data indicate that this variant Mlp1 architecture is linked to an altered, novel mechanism of tRNA processing in Tetrahymena thermophila.

molecular biology↗

bioRxiv2021

Post translational modification of duplicated ribosomal protein paralogs promotes alternative translation and drug resistance

Ribosomes are often seen as monolithic machines produced from uniformly regulated genes. However, in yeast most ribosomal proteins are produced from duplicated genes. Here, we demonstrate that gene duplications may serve as a stress response mechanism that modulates the global proteome through differential post-translational modification of ribosomal proteins paralogs. Our data indicate that the yeast paralog pair of the ribosomal protein L7/uL30 produces two differentially acetylated proteins. Under normal conditions most ribosomes incorporate the hypo-acetylated major form favoring the translation of genes with short open reading frames. Exposure to drugs, on the other hand, increases the production of ribosomes carrying the hyper-acetylated minor paralog that increases translation of long reading frames. Many of these genes encode cell wall proteins that increase drug resistance in a programed change in translation equilibrium. Together the data reveal a mechanism of translation control through the differential fates of near-identical ribosomal protein isoforms.

molecular biology↗

bioRxiv2021

The snoGloBe interaction predictor enables a broader study of box C/D snoRNA functions and mechanisms

Box C/D small nucleolar RNAs (snoRNAs) are a conserved class of RNA known for their role in guiding ribosomal RNA 2-O-ribose methylation. Recently, C/D snoRNAs were also implicated in regulating the expression of non-ribosomal genes through different modes of binding. Large scale RNA-RNA interaction datasets detect many snoRNAs binding messenger RNA, but are limited by specific experimental conditions. To enable a more comprehensive study of C/D snoRNA interactions, we created snoGloBe, a human C/D snoRNA interaction predictor based on a gradient boosting classifier. SnoGloBe considers the target type, position and sequence of the interactions, enabling it to outperform existing predictors. Interestingly, for specific snoRNAs, snoGloBe identifies strong enrichment of interactions near gene expression regulatory elements including splice sites. Abundance and splicing of predicted targets were altered upon the knockdown of their associated snoRNA. Strikingly, the predicted snoRNA interactions often overlap with the binding sites of functionally related RNA binding proteins, reinforcing their role in gene expression regulation. SnoGloBe is also an excellent tool for discovering viral RNA targets, as shown by its capacity to identify snoRNAs targeting the heavily methylated SARS-CoV-2 RNA. Overall, snoGloBe is capable of identifying experimentally validated binding sites and predicting novel sites with shared regulatory function.

bioinformatics↗

bioRxiv2021

High-grade Ovarian Cancer Associated H/ACA snoRNAs Promote Cancer Cell Proliferation and Survival

Small nucleolar RNAs (snoRNAs) are an omnipresent class of non-coding RNAs involved in the modification and processing of ribosomal RNA (rRNA). As snoRNAs are required for ribosome production, the increase of which is a hallmark of cancer development, their expression would be expected to increase in proliferating cancer cells. However, the nature and extent of snoRNAs contribution to the biology of cancer cells remain largely unexplored. In this study, we examined the abundance patterns of snoRNA in high-grade serous ovarian carcinomas (HGSC) and serous borderline tumours (SBT) and identified a subset of snoRNA associated with increased invasiveness. This subgroup of snoRNA accurately discriminates between SBT and HGSC underlining their potential as biomarkers of tumour aggressiveness. Remarkably, knockdown of HGSC-associated H/ACA snoRNAs, but not their host genes, inhibits cell proliferation and induces apoptosis of model ovarian cancer cell lines. Wound healing and cell migration assays confirmed the requirement of these HGSC-associated snoRNA for cell invasion and increased tumour aggressiveness. Together our data indicate that H/ACA snoRNAs promote tumour aggressiveness through the induction of cell proliferation and resistance to apoptosis.

cancer biology↗

bioRxiv2021

Hybridisation boosts dispersal of two contrasted ecotypes in a grass species

O_LIIn the absence of strong reproductive barriers, genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes, and influence rates of hybridisation. How these dynamics affect the emergence and spread of novel ecological strategies remains only partially understood. C_LIO_LIWe use phylogenomics and population genomics to retrace the origin of two geographically overlapping ecotypes of the African grass Alloteropsis angusta. C_LIO_LIWe report the existence of a previously undescribed ecotype inhabiting miombo woodlands and grasslands. The two ecotypes have divergent nuclear genomes. However, the seed-transported chloroplast genomes are consistently shared by distinct ecotypes inhabiting the same region. These patterns suggest that the nuclear genome of one ecotype can reach the seeds of the other via pollen movements, with strong selection subsequently sorting nuclear alleles by habitat. C_LIO_LIThe contrasting ecotypes of A. angusta can use each other as a gateway to new locations across a large part of Africa. Coupled with newly discovered hybridisation with the sister species A. semialata, our results show that hybridisation can facilitate the geographical dispersal of distinct ecotypes of the same grass species. C_LI

evolutionary biology↗

bioRxiv2021

Dynamics and modulation of the human snoRNome

BackgroundSmall nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions. ResultsWe used a low structure bias RNA-Seq approach to accurately quantify snoRNAs and compare them to the entire transcriptome in seven healthy human tissues (breast, ovary, prostate, testis, skeletal muscle, liver and brain). We identified 475 expressed snoRNAs categorized in two abundance classes that differ significantly in their function, conservation level and correlation with their host gene: 390 snoRNAs are uniformly expressed and 85 are enriched in the brain or reproductive tissues. Most tissue-enriched snoRNAs are embedded in lncRNAs and display strong correlation of abundance with them, whereas uniformly expressed snoRNAs are mostly embedded in protein-coding host genes and are mainly non- or anticorrelated with them. 59% of the non-correlated or anticorrelated protein-coding host gene/snoRNA pairs feature dual-initiation promoters, as opposed to only 16% of the correlated non-coding host gene/snoRNA pairs. ConclusionsOur results demonstrate that snoRNAs are not a single homogeneous group of housekeeping genes but include highly regulated tissue-enriched RNAs. Indeed, our work indicates that the architecture of snoRNA host genes varies to uncouple the host and snoRNA expressions in order to meet the different snoRNA abundance levels and functional needs of human tissues.

genomics↗

bioRxiv2020

Newfound coding potential of transcripts unveils missing members of human protein communities

Recent proteogenomic approaches have led to the discovery that regions of the transcriptome previously annotated as non-coding regions (i.e. UTRs, open reading frames overlapping annotated coding sequences in a different reading frame, and non-coding RNAs) frequently encode proteins (termed alternative proteins). This suggests that previously identified protein-protein interaction networks are partially incomplete since alternative proteins are not present in conventional protein databases. Here we used the proteogenomic resource OpenProt and a combined spectrum- and peptide-centric analysis for the re-analysis of a high throughput human network proteomics dataset thereby revealing the presence of 280 alternative proteins in the network. We found 19 genes encoding both an annotated (reference) and an alternative protein interacting with each other. Of the 136 alternative proteins encoded by pseudogenes, 38 are direct interactors of reference proteins encoded by their respective parental gene. Finally, we experimentally validate several interactions involving alternative proteins. These data improve the blueprints of the human protein-protein interaction network and suggest functional roles for hundreds of alternative proteins.

systems biology↗

bioRxiv2020

Unsupervised analysis of multi-experiment transcriptomic patterns with SegRNA identifies unannotated transcripts

BackgroundExploratory analysis of complex transcriptomic data presents multiple challenges. Many methods often rely on preexisting gene annotations, impeding identification and characterization of new transcripts. Even for a single cell type, comprehending the diversity of RNA species transcribed at each genomic region requires combining multiple datasets, each enriched for specific types of RNA. Currently, examining combinatorial patterns in these data requires time-consuming visual inspection using a genome browser. MethodWe developed a new segmentation and genome annotation (SAGA) method, SegRNA, that integrates data from multiple transcriptome profiling assays. SegRNA identifies recurring combinations of signals across multiple datasets measuring the abundance of transcribed RNAs. Using complementary techniques, SegRNA builds on the Segway SAGA framework by learning parameters from both the forward and reverse DNA strands. SegRNAs unsupervised approach allows exploring patterns in these data without relying on pre-existing transcript models. ResultsWe used SegRNA to generate the first unsupervised transcriptome annotation of the K562 chronic myeloid leukemia cell line, integrating multiple types of RNA data. Combining RNA-seq, CAGE, and PRO-seq experiments together captured a diverse population of RNAs throughout the genome. As expected, SegRNA annotated patterns associated with gene components such as promoters, exons, and introns. Additionally, we identified a pattern enriched for novel small RNAs transcribed within intergenic, intronic, and exonic regions. We applied SegRNA to FANTOM6 CAGE data characterizing 285 lncRNA knockdowns. Overall, SegRNA efficiently summarizes diverse multi-experiment data.

bioinformatics↗

bioRxiv2020

Cardiomyocyte-specific Srsf3 deletion reveals a mitochondrial regulatory role

Srsf3 was recently reported as being necessary to preserve RNA stability via an mTOR mechanism in a cardiac mouse model in adulthood. Here, we demonstrate the link between Srsf3 and mitochondrial integrity in an embryonic cardiomyocyte-specific Srsf3 conditional knockout (cKO) mouse model. Fifteen-day-old Srsf3 cKO mice showed dramatically reduced (below 50%) survival and reduced left ventricular systolic performance, and histological analysis of these hearts revealed a significant increase in cardiomyocyte size, confirming the severe remodelling induced by Srsf3 deletion. RNA-seq analysis of the hearts of 5-day-old Srsf3 cKO mice revealed early changes in expression levels and alternative splicing of several transcripts related to mitochondrial integrity and oxidative phosphorylation. Likewise, the levels of several protein complexes of the electron transport chain decreased, and mitochondrial complex I-driven respiration of permeabilized cardiac muscle fibres from the left ventricle was impaired. Furthermore, transmission electron microscopy analysis showed disordered mitochondrial length and cristae structure. Together with its indispensable role in the physiological maintenance of mouse hearts, these results highlight the previously unrecognized function of Srsf3 in regulating mitochondrial integrity.

physiology↗