Direct and indirect effects of spliceosome disruption compromise gene regulation by Nonsense-Mediated mRNA Decay DOI Creative Commons
Caleb M. Embree, Andreas Stephanou, Guramrit Singh

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 28, 2024

ABSTRACT Pre-mRNA splicing, carried out in the nucleus by a large ribonucleoprotein machine known as spliceosome, is functionally and physically coupled to mRNA surveillance pathway cytoplasm called nonsense mediated decay (NMD). The NMD monitors for premature translation termination signals, which can result from alternative relying on exon junction complex (EJC) deposited exon-exon junctions spliceosome. Recently, multiple genetic screens human cell lines have identified numerous spliceosome components putative factors. Using publicly available RNA-seq datasets K562 HepG2 cells depleted of 18 different components, we find that natural targeted isoforms are upregulated when members catalytic reduced. While some this increase could be due widespread pleiotropic effects dysfunction (e.g., reduced expression factors mis-splicing their mRNAs), identify AQR, SF3B1, SF3B4 CDC40 may more direct role NMD. We also test hypothesis increased production novel substrates overwhelm correlation between amount detected degree inhibition observed. Finally, similar transcriptome alterations substrate upregulation observed treated with inhibitors derived retinitis pigmentosa patients mutations PRPF8 PRPF31 . Overall, our results show regardless cause, disruption upregulates broad set targets, contribute cellular spliceosomopathies. AUTHOR SUMMARY During gene expression, removes extraneous non-coding sequences precursor RNAs produce messenger RNA (mRNA) contiguous code protein sequence. To guard against splicing errors interrupt coding sequence, linked In work, follow up recent findings several necessary efficient Our analysis transcriptomes lymphoblast based regulation compromised lacking proteins. Four these proteins effect even though general causes other changes indirectly affect suggest defective contributes spliceosomopathies, collection disorders caused

Язык: Английский

Translation of the downstream ORF from bicistronic mRNAs by human cells: Impact of codon usage and splicing in the upstream ORF DOI Creative Commons
Philippe Paget‐Bailly,

Alexandre Helpiquet,

Mathilde Decourcelle

и другие.

Protein Science, Год журнала: 2025, Номер 34(2)

Опубликована: Янв. 22, 2025

Abstract Biochemistry textbooks describe eukaryotic mRNAs as monocistronic. However, increasing evidence reveals the widespread presence and translation of upstream open reading frames preceding “main” ORF. DNA RNA viruses infecting eukaryotes often produce polycistronic have evolved multiple ways manipulating host's machinery. Here, we introduce an experimental model to study gene expression regulation from virus‐like bicistronic in human cells. The consists a short ORF reporter downstream encoding fluorescent protein. We engineered synonymous variants explore large parameter space, including codon usage preferences, mRNA folding features, splicing propensity. show that machinery can translate mRNAs, albeit protein levels are thousand times lower than those Furthermore, recoding exclusively during elongation significantly influences its own efficiency, cryptic splice signals, modulates probability translation. Our results consistent with leaky scanning mechanism facilitating cells, offering new insights into role ORFs regulation.

Язык: Английский

Процитировано

2
Connecting genotype and phenotype in minor spliceosome diseases DOI Open Access
Antto J. Norppa, Mariia Shcherbii, Mikko J. Frilander

и другие.

RNA, Год журнала: 2025, Номер 31(3), С. 284 - 299

Опубликована: Янв. 6, 2025

Minor spliceosome is responsible for recognizing and excising a specific subset of divergent introns during the pre-mRNA splicing process. Mutations in unique snRNA protein components minor are increasingly being associated with variety germline somatic human disorders, collectively termed as spliceosomopathies. Understanding mechanistic basis these diseases has been challenging due to limited functional information on many components. However, recently published cryo-electron microscopy (cryo-EM) structures various assembly intermediates have marked significant advancement elucidating roles splicing. These structural breakthroughs not only enhanced our comprehension spliceosome's functionality but also shed light how disease-associated mutations disrupt its functions. Consequently, research focus now shifting toward investigating defects translate into broader pathological processes within gene expression pathways. Here we outline current knowledge spliceosome, explore consequences mutations, discuss emerging challenges connecting molecular dysfunctions clinical phenotypes.

Язык: Английский

Процитировано

0
Exploring the connection between RNA splicing and intellectual disability DOI Creative Commons
Anthony Caputo, Ashleigh E. Schaffer

Current Opinion in Genetics & Development, Год журнала: 2025, Номер 91, С. 102322 - 102322

Опубликована: Фев. 8, 2025

Intellectual disability (ID) is a broad diagnostic category that encompasses individuals with impaired cognitive ability. While these disorders have heterogeneous causes, recent developments in next-generation sequencing (NGS) are revealing the prevalence of genetic etiologies. In particular, germline mutations genes affect RNA splicing increasingly common causes ID disorders. Research to elucidate functional relationship between and neurodevelopment critical since molecular therapeutics require nuanced understanding pathological mechanism. this review, we first summarize trends led discovery splicing-ID relationship, then discuss progress future directions for research surrounding neurodevelopment. Finally, speak on how results may serve as foundation burgeoning therapies.

Язык: Английский

Процитировано

0
Functional inhibition of core spliceosomal machinery activates intronic premature cleavage and polyadenylation of pre-mRNAs DOI Creative Commons
Qiumin Feng,

Zejin Lin,

Danhui Zhao

и другие.

Cell Reports, Год журнала: 2025, Номер 44(3), С. 115376 - 115376

Опубликована: Фев. 27, 2025

Highlights•U6/U2 snRNP inhibits global intronic PCPA (premature cleavage and polyadenylation)•U6/U2 regulates mRNA 3′-UTR (untranslated region) length for a subset of genes•Intronic is positively regulated by the 3′ processing activatorSummaryThe catalytic role U6 in pre-mRNA splicing has been well established. In this study, we utilize an antisense morpholino oligonucleotide (AMO) specifically targeting sites snRNA to achieve functional knockdown HeLa cells. The data show significant increase premature polyadenylation (PCPA) events, similar those observed with U1 AMO treatment, as demonstrated 3′-seq analysis. Mechanistically, provide evidence that AMO-mediated inhibition might be driving force application another specific U2 results effects. Together our recently published findings demonstrate inhibitory effect U4 on PCPA, highlight critical suppressing support model which may compete each other within introns during co-transcriptional processing.Graphical abstract

Язык: Английский

Процитировано

0
Multi-Omics Analysis of Survival-Related Splicing Factors and Identifies CRNKL1 as a Therapeutic Target in Esophageal Cancer DOI Open Access

Tianxiao Gao,

Meiling Fan,

Zhongyuan Zeng

и другие.

Genes, Год журнала: 2025, Номер 16(4), С. 379 - 379

Опубликована: Март 27, 2025

Background: RNA alternative splicing represents a pivotal regulatory mechanism of eukaryotic gene expression, wherein factors (SFs) serve as key regulators. Aberrant SF expression drives oncogenic splice variant production, thereby promoting tumorigenesis and malignant progression. However, the biological functions potential targets SFs remain largely underexplored. Methods: Through multi-omics analysis, we identified survival-related in esophageal cancer elucidated their networks. To further investigate downstream targets, combined events resulting from knockdown with those specific to cancer. Finally, these were validated through full-length sequencing confirmed cells clinical specimens. Result: We six that are highly expressed correlate poor prognosis. Further analysis revealed significantly associated immune infiltration, stemness, tumor heterogeneity, drug resistance. CRNKL1 was hub SFs. The target genes pathways regulated by showed substantial overlap, suggesting coordinated roles stemness metastasis. Specifically, markers, such CD44 CTTN, most correlated Conclusions: Our study unveils contribute aggressiveness CTTN may act common effectors This provides mechanistic insights into SF-mediated highlight novel therapeutic vulnerabilities

Язык: Английский

Процитировано

0
Splicing factor RBM10 loss fuels thyroid cancer metastasis DOI Open Access

Kevin Coughlin,

Ledong Wan

The Journal of Experimental Medicine, Год журнала: 2025, Номер 222(5)

Опубликована: Фев. 24, 2025

In this issue of JEM, Krishnamoorthy et al. (https://doi.org/10.1084/jem.20241029) identify the loss splicing factor RBM10 as a driver metastasis in thyroid cancer through regulation RNA splicing. The synthetic lethal interaction between NF-κB and reveals potential therapeutic vulnerability.

Язык: Английский

Процитировано

0
Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease DOI Creative Commons

Faye Su,

Meng Su,

Wenting Wei

и другие.

Gut Microbes, Год журнала: 2025, Номер 17(1)

Опубликована: Март 10, 2025

Numerous studies have accelerated the knowledge expansion on role of gut microbiota in inflammatory bowel disease (IBD). However, precise mechanisms behind host-microbe cross-talk remain largely undefined, due to complexity human intestinal ecosystem and multiple external factors. In this review, we introduce interactome concept systematically summarize how dysbiosis is involved IBD pathogenesis terms microbial composition, functionality, genomic structure, transcriptional activity, downstream proteins metabolites. Meanwhile, review also aims present an updated overview relevant mechanisms, high-throughput multi-omics methodologies, different types cohort resources, computational methods used understand host-microbiota interactions context IBD. Finally, discuss challenges pertaining integration data order reveal offer insights into future research directions.

Язык: Английский

Процитировано

0
Circular RNA discovery with emerging sequencing and deep learning technologies DOI
Jinyang Zhang, Fangqing Zhao

Nature Genetics, Год журнала: 2025, Номер unknown

Опубликована: Апрель 17, 2025

Язык: Английский

Процитировано

0
TSvelo: Comprehensive RNA velocity inference by jointly modeling Transcription and Splicing DOI Creative Commons
Jiachen Li, Zhe Wang,

Hong-Bin Shen

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 24, 2024

Abstract RNA velocity approaches fit gene dynamics and infer cell fate by modeling the splicing process using single-cell sequencing (scRNA-seq) data. However, due to high noise in unspliced/spliced data for individual genes, existing models often fail accurately capture between unspliced spliced abundance phase portraits of many genes. In addition, optimizing dimensional all genes within a global framework effectively handling multi-lineage still require further exploration modeling. Inspired role transcriptional regulation linking into complex networks providing additional context modeling, we propose TSvelo. TSvelo integrates cross-gene gene-specific processes one neural Ordinary Differential Equation (ODE)-based framework. By incorporating cell-specific rates with unspliced-spliced data, precisely learns pseudotime, can be extended multi-branch datasets. Experiments on six scRNA-seq datasets, including two demonstrate that outperforms methods dynamics, inferring pseudotime trajectories, analyzing expression patterns across branches.

Язык: Английский

Процитировано

0
Direct and indirect effects of spliceosome disruption compromise gene regulation by Nonsense-Mediated mRNA Decay DOI Creative Commons
Caleb M. Embree, Andreas Stephanou, Guramrit Singh

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 28, 2024

ABSTRACT Pre-mRNA splicing, carried out in the nucleus by a large ribonucleoprotein machine known as spliceosome, is functionally and physically coupled to mRNA surveillance pathway cytoplasm called nonsense mediated decay (NMD). The NMD monitors for premature translation termination signals, which can result from alternative relying on exon junction complex (EJC) deposited exon-exon junctions spliceosome. Recently, multiple genetic screens human cell lines have identified numerous spliceosome components putative factors. Using publicly available RNA-seq datasets K562 HepG2 cells depleted of 18 different components, we find that natural targeted isoforms are upregulated when members catalytic reduced. While some this increase could be due widespread pleiotropic effects dysfunction (e.g., reduced expression factors mis-splicing their mRNAs), identify AQR, SF3B1, SF3B4 CDC40 may more direct role NMD. We also test hypothesis increased production novel substrates overwhelm correlation between amount detected degree inhibition observed. Finally, similar transcriptome alterations substrate upregulation observed treated with inhibitors derived retinitis pigmentosa patients mutations PRPF8 PRPF31 . Overall, our results show regardless cause, disruption upregulates broad set targets, contribute cellular spliceosomopathies. AUTHOR SUMMARY During gene expression, removes extraneous non-coding sequences precursor RNAs produce messenger RNA (mRNA) contiguous code protein sequence. To guard against splicing errors interrupt coding sequence, linked In work, follow up recent findings several necessary efficient Our analysis transcriptomes lymphoblast based regulation compromised lacking proteins. Four these proteins effect even though general causes other changes indirectly affect suggest defective contributes spliceosomopathies, collection disorders caused

Язык: Английский

Процитировано

0