RNA Biology最新文献

The epitranscriptome comprises chemical modifications found on RNA molecules that play essential roles in co- and post-transcriptional gene regulation. Dysregulation of these modifications has been implicated in various diseases, fuelling interest in evaluating them as emerging biomarkers and therapeutic targets. Nanopore direct RNA sequencing provides a powerful platform for profiling diverse RNA modifications at single-molecule resolution, but the complexity of the signals requires advanced computational approaches for interpretation. Artificial intelligence, particularly deep learning (DL), has become central to this effort. While classical DL architectures such as convolutional and recurrent neural networks have been widely applied, more recent approaches employ specialized learning frameworks and ensemble strategies to address challenges of data scarcity, noise, and biological variability while providing higher resolution output. In this review, we summarize these developments and highlight future multidisciplinary opportunities at the intersection of artificial intelligence and biology for characterizing the epitranscriptome obtained with direct RNA nanopore sequencing.

Non-coding RNAs (ncRNAs) modulate protein-protein interactions (PPIs) by shaping the structural context in which binding occurs, rather than acting as direct inhibitors or enhancers. Using an integrative framework combining catRAPID RNA-protein interaction prediction and AlphaFold3-based structural modelling, we analysed RNA-dependent modulation of interaction states across physiological and oncogenic protein complexes. At the network level, physiological PPIs exhibit high shared ncRNA buffering capacity, whereas oncogenic interactions are characterized by reduced or absent RNA overlap. AlphaFold3 modelling of mutant IDH1/2 complexes illustrates how loss of RNA buffering permits excessive stabilization of enzyme-associated interfaces, reflected by directional changes in buried surface area (ΔBSA) and contact heterogeneity.

Small non-coding RNAs, such as microRNAs and tRNA-derived fragments, are key regulators of cellular processes, but the functions of small intronic RNAs (sinRNAs), a recently identified RNA class, remain largely unknown. Here, we report that two sinRNAs, sinR-D and sinR-T, are upregulated in pancreatic β-cells of NOD mice, a well-established model of type 1 diabetes. Using in vivo RNA-tagging, we demonstrate that these sinRNAs are packaged into extracellular vesicles released by infiltrating CD4⁺ T lymphocytes and subsequently delivered to β-cells during the early stages of autoimmune attack. Functional analyses revealed that overexpression of sinR-T has little effect on β-cell viability, whereas sinR-D markedly increases β-cell apoptosis. This finding suggests that the transfer of sinR-D contributes to β-cell destruction and the onset of type 1 diabetes. Furthermore, pull-down experiments with biotinylated sinRNAs identified Ago2, a core component of the RNA-induced silencing complex (RISC), as a binding partner of sinR-D, indicating mechanistic parallels with microRNA-mediated regulation. Collectively, our data uncover a novel role for sinRNAs as extracellularly transferred regulators of β-cell fate, expanding the repertoire of small RNAs implicated in the initiation of type 1 diabetes.

In response to stress, cells undergo gene expression reprogramming to cope with external stimuli. Cells utilize a conserved stress response mechanism called global downregulation of translation, leading to the storage of translationally repressed mRNAs in RNA granules. During oxidative stress induced by H2O2, genes responsible for combating oxidative stress, such as catalases, are strongly induced. However, the post-transcriptional regulatory events affecting these genes during H2O2 stress are not well-explored. Scd6, an RGG-motif-containing protein in yeast, acts as a translational repressor through its interaction with eIF4G1. This study identifies the role of Scd6 in oxidative stress response by regulating cytoplasmic catalase T1 (CTT1). We observe that peroxide stress induces the assembly of Scd6 puncta, which do not colocalize with P-bodies or stress granules. Scd6 overexpression increased sensitivity, while deletion enhanced tolerance to H2O2 treatment. Increased ROS accumulation and decreased Ctt1 protein levels were observed upon Scd6 overexpression due to translation repression of CTT1 mRNA. CTT1 mRNA interacts with Scd6. smFISH analysis and RNA immunoprecipitation studies reveal that localization of Scd6 to puncta upon peroxide stress reduces its interaction with CTT1 mRNA, allowing derepression. The role of Scd6 in peroxide stress response is conserved since the human homolog LSm14A also localizes to puncta upon H2O2 stress, and its overexpression reduces survival in response to peroxide stress. Overall, this study identifies a unique example of translation regulation whereby stress-induced localization of the translation repressor protein to puncta leads to derepression of the target mRNA.

Tuberculosis, caused by Mycobacterium tuberculosis, is an infectious disease linked to high mortality and can stay in the host cell longer when inactive. Multiple factors are linked to disease prognosis, including microRNAs. It is a diminutive single-stranded RNA that regulates the expression of its target mRNAs. It consists of a brief nucleotide sequence, often 19-25 nucleotides in length, of non-coding RNA. It is also essential for early embryonic development, invasion, cell migration, apoptosis, and cell death. The review aims to analyse the transcriptome characteristics of various miRNAs in the tuberculosis prognosis. However, miR-155, miR-29, circ-miRNA, and lncRNAs regulate gene expression. In TB patients' serum exosomes, miRNA-146 expression was noticeably higher than in healthy individuals. Drug-resistant tuberculosis was related to miR-548 m, miR-631, miR-328-3p, and miR-let-7e-5p, as well as let-7b-5p, miR-30a-3p, IL-27, and CXCL9/10/11 in TB patients' lesion tissue and peripheral blood. Therefore, further miRNA research will focus on TB progression.

RNA-binding proteins (RBPs) constitute a diverse class of proteins essential for every stage of the gene expression process. Many RBPs are also linked to human diseases and pathologies. Understanding the molecular grammar of RNA-protein interactions is critical for deciphering the regulatory RNA code. This review provides a comprehensive overview of Massively Parallel Binding Assays (MPBAs), high-throughput techniques that use large libraries of RNA or protein variants to systematically investigate RNA-protein interactions. We describe the underlying principles of both in vitro and in vivo approaches, their applications, as well as their strengths and weaknesses. We conclude by outlining future directions and challenges in the field that will help drive the development of novel methods to better understand the RBP recognition code.

Type III CRISPR systems are defined by the presence of the Cas10 protein and are among the most abundant CRISPR systems in nature. Cas10 forms a complex with crRNA and several Cas proteins that surveils prokaryotic cells for foreign RNA molecules and when they are detected it activates a cascade of interference activities. The synthesis of the cyclic oligoadenylate signalling molecule by Cas10 is a key aspect of the interference cascade. Despite structures of the Cas10 complex bound to target RNAs, the molecular mechanism by which Cas10 senses the bound state to licence interference is lacking. We identified five residues in S. epidermidis Cas10, two in the Cas10 Palm2 domain and three in domain 4, that line the target RNA binding channel. We assessed the contribution of these residues to interference in the context of a cognate or mismatched target RNA. We found that the residues regulate whether a mismatched crRNA-target RNA duplex is able to activate interference in vivo. We purified two site-directed mutants of Cas10-Csm and show with in vitro cOA synthesis assays that they demonstrate enhanced discrimination of cognate versus mismatched target RNAs.

Human papillomaviruses (HPVs) cause diverse cutaneous and mucosal diseases, with several genotypes strongly associated with cervical cancer. Beyond the well-established role of cellular microRNAs (miRNAs) in gene regulation, increasing evidence shows that HPV also encodes its own viral miRNAs (v-miRNAs). These v-miRNAs modulate both viral and host gene expression, influencing key pathways involved in oncogenesis, including cell cycle control, apoptosis, immune evasion, and epithelial - mesenchymal transition. By shaping these regulatory networks, HPV-derived miRNAs promote viral persistence and contribute to malignant transformation. Their stability and specificity also make them promising biomarkers for cervical cancer diagnosis and prognosis, although clinical translation remains challenging. This review provides an updated overview of HPV-encoded miRNAs, their validated molecular targets, and their roles in tumour development. It also highlights emerging therapeutic strategies and future perspectives for integrating miRNA-based approaches into precision oncology for HPV-related cervical cancer.

Despite growing interest in profiling microRNAs (miRNAs) in infant and toddler stool, no studies have compared protocols for preserving and extracting miRNAs from this specimen type.

Three commercially available kits and four preservation methods were compared for their ability to yield high quality RNA from children <2 years of age (infant/toddler).

Of the three RNA extraction kits compared, Zymo BIOMICs yielded the highest RNA Quality Number (RQN) (median (range) RQN 9.4 (5.7-10.0)). Of the four preservation methods tested, RNAlater and Zymo DNA/RNA Shield Faecal Collection Tubes yielded the highest two RQNs (median (range) RQN 9.8 (5.7-10.0) and 9.4 (5.4-10.0), respectively), which did not differ from each other (p = 0.47). Subsequently, miRNA-seq was used to compare miRNA profiles for RNA extracted using the Zymo BIOMICs kit from paired aliquots of the same stool sample (n = 4 infant donors) collected into RNAlater and Zymo DNA/RNA Shield Faecal Collection Tubes. The percentage of reads classified as human and the percentage of human reads aligning to miRBase did not differ for samples collected in RNAlater versus Zymo Shield (p = 0.12 and p = 0.86, respectively). Furthermore, after multiple testing correction, normalized miRNA counts did not differ between the two preservatives for any of the 42 human miRNAs detected across the eight samples (p_FDR ≥ 0.05).

Collecting stool from infants and toddlers <2 years of age in either RNAlater or Zymo DNA/RNA Shield Faecal Collection Tubes, when paired with RNA extraction using the Zymo BIOMICs extraction kit, yielded high-quality RNA with similar human miRNA profiles.

Quaternary assembly of proteins frequently plays essential roles in biological processes. In contrast, natural RNA oligomers have rarely been reported. The majority of observed RNA quaternary structures are symmetric homodimers, while recent studies have also revealed structures of heterodimers and symmetric homooligomers with more than two protomers. These higher-order assemblies adopt various intermolecular motifs including kissing-loops, pseudoknots, palindromic base-pairing, stacking, minor-groove interactions, and metal ion coordination that are found in RNA dimers. The dynamics in oligomerization vary across different segments of a single RNA as well as among different RNAs within the same family, which are primarily enabled by variable secondary structures, intermolecular motifs, and shape complementarity. These structural insights deepen our understanding of RNA multimerization mechanisms, paving the way for potential applications in condensate formation, RNA structure prediction, and therapeutic targeting and delivery.