Neurofibromatosis type 1 (NF1) is one of the most common inherited disorders in humans and is caused by mutations in the NF1 gene. To date, the majority of the reported NF1 mutations are predicted to result in protein truncation, but very few studies have correlated the causative NF1 mutation with its effect at the mRNA level. We have applied a whole NF1 cDNA screening methodology to the study of 80 unrelated NF1 patients and have identified 44 different mutations, 32 being novel, in 52 of these patients. Mutations were detected in 87% of the familial cases, but in 51% of the sporadic ones. At least 15 of the 80 NF1 patients (19%) had recurrent mutations. The study shows that in 50% of the patients in whom the mutations were identified, these resulted in splicing alterations. Most of the splicing mutations did not involve the conserved AG/GT dinucleotides of the splice sites. One frameshift, two nonsense and two missense mutations were also responsible for alterations in mRNA splicing. The location and type of mutation within the NF1 gene, and its putative effect at the protein level, do not indicate any relationship to any specific clinical feature of NF1. The high proportion of aberrant spliced transcripts detected in NF1 patients stresses the importance of studying mutations at both the genomic and RNA level. It is possible that part of the clinical variability in NF1 could be due to mutations affecting mRNA splicing, which is the most common molecular defect in NF1.
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http://dx.doi.org/10.1093/hmg/9.2.237 | DOI Listing |
Mamm Genome
January 2025
Universidade Professor Edson Antônio Velano (UNIFENAS), Rodovia 179, Km 0, Alfenas, MG, 37132440, Brasil.
This study aimed to identify splicing quantitative trait loci (cis-sQTL) in Nelore cattle muscle tissue and explore the involvement of spliced genes (sGenes) in immune system-related biological processes. Genotypic data from 80 intact male Nelore cattle were obtained using SNP-Chip technology, while RNA-Seq analysis was performed to measure gene expression levels, enabling the integration of genomic and transcriptomic datasets. The normalized expression levels of spliced transcripts were associated with single nucleotide polymorphisms (SNPs) through an analysis of variance using an additive linear model with the MatrixEQTL package.
View Article and Find Full Text PDFCommun Biol
January 2025
Shengjing Hospital of China Medical University, Obstetrics and Gynecology Department, NO36. Sanhao Street, Heping district, Shenyang, China.
Circular RNAs (circRNAs) have garnered substantial attention due to their distinctive circular structure and gene regulatory functions, establishing them as a significant class of functional non-coding RNAs in eukaryotes. Studies have demonstrated that circRNAs can interact with RNA-binding proteins (RBPs), which play crucial roles in tumorigenesis, metastasis, and drug response in cancer by influencing gene expression and altering the processes of tumor initiation and progression. This review aims to summarize the recent advances in research on circRNA-protein interactions (CPIs) and discuss the functions and mode of action of CPIs at various stages of gene expression, including transcription, splicing, translation, and post-translational modifications in the context of cancer.
View Article and Find Full Text PDFNat Commun
January 2025
National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
Epitranscriptomic modifications, particularly N6-methyladenosine (mA), are crucial regulators of gene expression, influencing processes such as RNA stability, splicing, and translation. Traditional computational methods for detecting mA from Nanopore direct RNA sequencing (DRS) data are constrained by their reliance on experimentally validated labels, often resulting in the underestimation of modification sites. Here, we introduce pum6a, an innovative attention-based framework that integrates positive and unlabeled multi-instance learning (MIL) to address the challenges of incomplete labeling and missing read-level annotations.
View Article and Find Full Text PDFNat Commun
January 2025
State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China.
Transcription elongation, especially RNA polymerase II (Pol II) pause-release, is less studied than transcription initiation in regulating gene expression during meiosis. It is also unclear how transcription elongation interplays with transcription initiation. Here, we show that depletion of NKAPL, a testis-specific protein distantly related to RNA splicing factors, causes male infertility in mice by blocking the meiotic exit and downregulating haploid genes.
View Article and Find Full Text PDFNat Commun
January 2025
Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France.
Interferon (IFN)-α is the earliest cytokine signature observed in individuals at risk for type 1 diabetes (T1D), but the effect of IFN-α on the antigen repertoire of HLA Class I (HLA-I) in pancreatic β-cells is unknown. Here we characterize the HLA-I antigen presentation in resting and IFN-α-exposed β-cells and find that IFN-α increases HLA-I expression and expands peptide repertoire to those derived from alternative mRNA splicing, protein cis-splicing and post-translational modifications. While the resting β-cell immunopeptidome is dominated by HLA-A-restricted peptides, IFN-α largely favors HLA-B and only marginally upregulates HLA-A, translating into increased HLA-B-restricted peptide presentation and activation of HLA-B-restricted CD8 T cells.
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