RNA Biology最新文献

Protein kinase R (PKR) is a serine/threonine kinase that recognizes double-stranded RNAs (dsRNAs) to initiate innate immune signalling during viral infection. PKR dimerizes on long dsRNAs and undergoes autophosphorylation. Phosphorylated/Activated PKR then catalyses the phosphorylation of numerous substrates to control global translation, inflammatory response, and cell signalling pathways. While primarily known for its antiviral role, emerging evidence suggests that PKR can play multifaceted roles in uninfected cells by interacting with cellular dsRNAs and protein regulators. The misactivation of PKR in uninfected cells is associated with many degenerative and inflammatory diseases. Even in healthy cells, PKR can affect gene expression by controlling mRNA splicing and gene-specific translation under stress. In addition, PKR can modulate cell cycle progression and promote cellular differentiation in several tissue types. This review explores PKR function in various pathological and physiological contexts in the absence of viral stimuli. By elucidating these diverse functions, we aim to highlight the perspectives in cellular dsRNA research and the therapeutic implications of targeting PKR, stimulating further research into this versatile and essential RNA-dependent kinase.

Dysregulation of RNA binding proteins (RBPs) is a hallmark in cancerous cells. In acute myeloid leukaemia (AML) RBPs are key regulators of tumour proliferation. While classical RBPs have defined RNA binding domains, RNA recognition and function in AML by non-canonical RBPs (ncRBPs) remain unclear. Given the inherent complexity of targeting AML broadly, our goal was to uncover potential ncRBP candidates critical for AML survival using a CRISPR/Cas-based screening. We identified the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a pro-proliferative factor in AML cells. Based on cross-linking and immunoprecipitation (CLIP), we are defining the global targetome, detecting novel RNA targets mainly located within 5'UTRs, including GAPDH, RPL13a, and PKM. The knockdown of GAPDH unveiled genetic pathways related to ribosome biogenesis, translation initiation, and regulation. Moreover, we demonstrated a stabilizing effect through GAPDH binding to target transcripts including its own mRNA. The present findings provide new insights on the RNA functions and characteristics of GAPDH in AML.

Cancer diagnosis at an early stage is crucial for improving overall health outcomes. However, existing cancer diagnostic techniques are mostly invasive and tend to identify the disease only in its advanced stages. MicroRNAs (miRNAs), which are small non-coding RNAs involved in gene expression regulation, are stable in serum as circulating miRNAs and have potential as non-invasive biomarkers. However, their application in pan-cancer diagnostics and therapeutics is still largely unexplored. We developed Serum-MiR-CanPred, a deep learning framework using a multi-layer perceptron (MLP) trained on serum miRNA expression data from 20,271 samples across 12 cancer types and healthy controls from GEO databases. The model achieves robust pan-cancer classification (AUC = 96.87%, accuracy = 96%) with a consensus set of 88 miRNAs. Validation using external datasets demonstrated its generalizability and clinical potential. SHapley Additive exPlanations (SHAP) identified hsa-miR-5100 as a key biomarker, dysregulated in cancers including lung, bladder, and gastric carcinomas. Pathway analysis linked these miRNAs to cancer-related processes like VEGFA-VEGFR2 signalling. Molecular docking of pre-mir-5100 with rDock, identified AC1MMYR2 as a potential high-affinity ligand, with binding stability confirmed by molecular dynamics simulations using GROMACS In conclusion, Serum-MiR-CanPred integrates explainable AI with molecular modelling, advancing miRNA-based diagnostics and drug discovery for precision oncology.

Transfer RNA (tRNA) is one of the most abundant RNA types in cells, acting as an adaptor to bridge the genetic information in mRNAs with the amino acid sequence in proteins. Both tRNAs and small fragments processed from them play many nonconventional roles in addition to translation. tRNA molecules undergo various types of chemical modifications to ensure the accuracy and efficiency of translation and regulate their diverse functions beyond translation. In this review, we discuss the biogenesis and molecular mechanisms of tRNA modifications, including major tRNA modifications, writer enzymes, and their dynamic regulation. We also summarize the state-of-the-art technologies for measuring tRNA modification, with a particular focus on 2'-O-methylation (Nm), and discuss their limitations and remaining challenges. Finally, we highlight recent discoveries linking dysregulation of tRNA modifications with genetic diseases.

This review evaluates the current state of C/D snoRNA databases and prediction tools in relation to 2'-O-methylation (2'-O-Me). It highlights the limitations of existing resources in accurately annotating and predicting guide snoRNAs, particularly for newly identified 2'-O-Me sites. We emphasize the need for advanced computational approaches specifically tailored to 2'-O-Me to enable the discovery and functional analysis of snoRNAs. Given the growing importance of 2'-O-Me in areas such as cancer epitranscriptomics, ribosome biogenesis, and heterogeneity, existing tools remain inadequate. As 2'-O-Me gains recognition as a potential biomarker and therapeutic target, more sophisticated methods are urgently needed to improve snoRNA annotation and prediction, facilitating biomedical advancements.

Sorafenib (Sfb) is a multikinase inhibitor regularly used for the management of patients with advanced hepatocellular carcinoma (HCC) that has been shown to increase very modestly life expectancy. We have shown that Sfb inhibits protein synthesis at the level of initiation in cancer cells. However, the global snapshot of mRNA translation following Sorafenib-treatment has not been explored so far. In this study, we performed a genome-wide polysome profiling analysis in Sfb-treated HCC cells and demonstrated that, despite global translation repression, a set of different genes remain efficiently translated or are even translationally induced. We reveal that, in response to Sfb inhibition, translation is tuned, which strongly correlates with the presence of established mRNA cis-acting elements and the corresponding protein factors that recognize them, including DAP5 and ARE-binding proteins. At the level of biological processes, Sfb leads to the translational down-regulation of key cellular activities, such as those related to the mitochondrial metabolism and the collagen synthesis, and the translational up-regulation of pathways associated with the adaptation and survival of cells in response to the Sfb-induced stress. Our findings indicate that Sfb induces an adaptive reprogramming of translation and provides valuable information that can facilitate the analysis of other drugs for the development of novel combined treatment strategies based on Sfb therapy.

Cellular senescence is a stable cell cycle arrest associated with upregulated inflammatory responses. Senescent cells contribute to various pathological and physiological processes including organismal ageing and cancer. Cellular senescence can be induced by various cellular stresses including DNA damage, telomere shortening, oncogene activation, and epigenetic alterations. We have shown that plasma membrane damage can also induce cellular senescence. However, common and specific molecular mechanisms among different senescent cell subtypes remain unknown. MicroRNAs (miRNAs) regulate mRNA and rewire gene expression profiles, contributing to multiple processes including cellular senescence. Here, we performed time-resolved miRNA sequencing and compared the results with mRNA sequencing results using cells experiencing plasma membrane damage-dependent senescence (PMD-Sen) and cells undergoing DNA damage response-dependent senescence (DDR-Sen). We found 65 miRNAs that are differentially regulated in PMD-Sen, contributing to 2,495 miRNA-mRNA pairs. Moreover, PMD-Sen and DDR-Sen shared 41 miRNAs across their sets of miRNA-mRNA pairs. Notably, miR-155-5p emerged as the miRNA with the largest number of shared miRNA-mRNA pairs that exhibit a highly negative correlation. These results highlight miR-155-5p as the potential key regulator of PMD-Sen and DDR-Sen.

Gene expression involves a series of consequential processes, beginning with mRNA synthesis and culminating in translation. Traditionally studied as a linear sequence of events, recent findings challenge this perspective, revealing coupling mechanisms that coordinate key steps of gene expression, even when spatially and temporally distant. In this review, we focus on translation, the final stage of gene expression, and examine its coupling with key stages of mRNA metabolism: synthesis, processing, export, and decay. For each of these processes, we provide an overview of known instances of coupling with translation. Furthermore, we discuss the role of high-throughput technologies in uncovering these intricate interactions on a genome-wide scale. Finally, we highlight key challenges and propose future directions to advance our understanding of how coupling mechanisms orchestrate robust and adaptable gene expression programs.

Neural stem cells (NSCs) are multipotent stem cells with self-renewal capacity, able to differentiate into all neural lineages of the central nervous system, including neurons, oligodendrocytes, and astrocytes; thus, their proliferation and differentiation are essential for embryonic neurodevelopment and adult brain homoeostasis. Dysregulation in these processes is implicated in neurological disorders, highlighting the need to elucidate how NSCs proliferate and differentiate to clarify the mechanisms of neurogenesis and uncover potential therapeutic targets. MicroRNAs (miRNAs) are small, post-transcriptional regulators of gene expression involved in many aspects of nervous system development and function. Multiple studies have shown that miRNAs control the balance between self-renewal and differentiation during development through transcriptional networks and fine-tuned signalling pathways. They also regulate key biological processes, including cell fate determination, developmental timing, neurogenesis, gliogenesis, and apoptosis. Transcriptomic analyses and high-resolution profiling have revealed temporally and spatially restricted miRNA expression patterns in NSCs and their progeny, suggesting highly context-dependent regulatory functions. Here, we provide an integrated overview of recent advances in miRNA biology relevant to NSC maintenance and lineage specification, with a focus on the mechanistic understanding of miRNA roles in neuronal differentiation, glial development, and programmed cell death across neural development.

Small Cajal body-specific RNAs (scaRNAs) are noncoding RNAs involved in the maturation of U-rich small nuclear RNAs. Except for a few that have their own transcription units, most scaRNA genes are embedded in introns and are predicted to be transcribed with host genes. Herein, we report that scaRNA28 is the first scaRNA with a dual synthesis pathway, and that this RNA is transcribed in an independent transcription unit (ITU) by RNA polymerase II while located in intron 2 of the transformation/transcription domain-associated protein (TRRAP) gene. We evaluated the scaRNA28 synthesis pathway using minigenes containing exon 2, intron 2, and exon 3 of TRRAP. A minigene with a mutation preventing 5' splicing recognition of the exon 2/intron 2 junction generated scaRNA28, suggesting a pathway processing unspliced transcripts into scaRNA28. Even promoterless minigenes and DNA fragments with regions from exons 2 to 3 of TRRAP showed RNA polymerase II-dependent synthesis of scaRNA28, indicating a novel synthesis pathway involving an ITU. Linker-scanning mutational analysis revealed that the promoter region required for scaRNA28 expression in the ITU is located within 60 bases including exon 2/intron 2 junction of TRRAP, and especially the first two bases of intron 2 region, a putative part of the MYC-binding (E-box) motif, are essential for scaRNA28 expression in the ITU. MYC promotes scaRNA28 expression by binding to the promoter region in the ITU. Our findings demonstrated a novel transcriptional pathway for the synthesis of scaRNA28, the first scaRNA with a dual synthesis pathway.