RNA Processing Research Articles

Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes

While all native tRNAs undergo extensive post-transcriptional modifications as a mechanism to regulate gene expression, mapping these modifications remains challenging. The critical barrier is the difficulty of readthrough of modifications by reverse transcriptases (RTs). Here we use Induro—a new group-II intron-encoded RT—to map and quantify genome-wide tRNA modifications in Induro-tRNAseq. We show that Induro progressively increases readthrough over time by selectively overcoming RT stops without altering the misincorporation frequency. In a parallel analysis of Induro vs. a related RT, we provide comparative datasets to facilitate the prediction of each modification. We assess tRNA modifications across five human cell lines and three mouse tissues and show that, while the landscape of modifications is highly variable throughout the tRNA sequence framework, it is stabilized for modifications that are required for reading of the genetic code. The coordinated changes have fundamental importance for development of tRNA modifications in protein homeostasis.

Deployment and transcriptional evaluation of nitisinone, an FDA-approved drug, to control bed bugs.

Bed bugs are blood-feeders that rapidly proliferate into large indoor infestations. Their bites can cause allergies, secondary infections and psychological stress, among other problems. Although several tactics for their management have been used, bed bugs continue to spread worldwide wherever humans reside. This is mainly due to human-mediated transport and their high resistance to several classes of insecticides. New treatment options with novel modes of action are required for their control. In this study, we evaluated the use of nitisinone (NTBC), an FDA-approved drug, for bed bug control in an insecticide-susceptible (HH) and an insecticide-resistant (CIN) population. Although NTBC was lethal to both populations when administered orally or applied topically in very low doses, we observed a slight but significant resistance in the CIN population. Transcriptomic analysis in both populations indicated that NTBC treatment elicited a broad suppression of genes associated with RNA post-transcriptional modifications, translation, endomembrane system, protein post-translational modifications and protein folding. The CIN population exhibited higher adenosine triphosphate (ATP) production and xenobiotic detoxification. Feeding studies on a mouse model suggest that NTBC could be used as a control method of bed bugs by host treatment. The results indicate that NTBC can be used as a new active ingredient for bed bug control by topical or oral treatment and shed light on the molecular mechanisms of suppressed tyrosine metabolism following NTBC treatment. © 2025 Society of Chemical Industry.

Identification of core biomarkers for tuberculosis progression through bioinformatics analysis and in vitro research

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant global public health issue with high mortality rates and challenges posed by drug-resistant strains, emphasizing the continued need for new therapeutic targets and effective treatment strategies. Transcriptomics is a highly effective tool for the development of novel anti-tuberculosis drugs. However, most studies focus only on changes in gene expression levels at specific time points. This study screened for genes with altered expression patterns from available transcriptomic data and analysed their association with the TB progression. Initially, a total of 1228 genes with altered expression patterns were identified through two-way analysis of variance (ANOVA). We define genes with a P-value less than 0.05 for the combined effect of infection and time on gene expression as those with altered expression patterns. Gene Ontology (GO) enrichment analysis revealed that the biological functions of these genes mainly involve DNA translation, RNA processing, and transcriptional regulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that these genes are primarily associated with fatty acid degradation, pyruvate metabolism, arginine and proline metabolism, as well as cholesterol metabolism signaling pathways. Subsequent Protein-protein interaction (PPI) analysis and Receiver Operating Characteristic (ROC) curve analysis identified four core genes closely associated with TB progression, namely Rac Family Small GTPase 1 (RAC1), Ring-Box 1 (RBX1), Mitochondrial Ribosomal Protein L33 (MRPL33), and ELAV Like RNA Binding Protein 1 (ELAVL1). Q-PCR experiments confirmed that Mtb infection led to changes in the gene expression patterns of RAC1, RBX1, MRPL33, and ELAVL1 in THP-1 cells. These four genes may serve as core biomarkers for TB progression and can be utilized in the development of more effective anti-tuberculosis drugs and host therapy.

OP27 Unlocking Inflammatory Bowel Disease subtypes: a deep dive into transcriptomics and Machine Learning

Abstract Background Identifying molecular subtypes of IBD is essential to address inconsistencies in gene expression-based classifications, clinical variability, and treatment responses in Crohn's Disease (CD) and Ulcerative Colitis (UC). Building on prior efforts using different methods and datasets, this study aimed to derive and validate IBD subtypes using transcriptomics data and unsupervised machine learning. Methods This study analysed RNA-sequenced data from inflamed and non-inflamed intestinal biopsies of 2,490 adult IBD patients. K-means clustering, guided by Within Cluster Sum of Squares (WCSS) to determine the optimal ‘K’, identified subtypes within the dataset. Distinct clusters for UC and CD were derived from gene expression, with gene set enrichment and network analysis characterizing their features. Statistical tests (Chi-squared and ANOVA) linked these clusters to clinical data for UC and CD. Results K-means clustering revealed three distinct clusters in UC and CD, whose significant association with IBD severity (UC: p = 0.000263; CD: p = 0.007006) and IBD region (p < 0.000001) was determined by Chi Squared test. ANOVA showed age significantly influenced UC clusters (p = 0.0000345) but not CD clusters (p = 0.285). In UC, Cluster 1 focused on RNA processing, DNA repair, and rapid cell turnover, with upregulation of EXOSC genes and other related genes. Cluster 2 highlighted autophagy, stress response, and signaling processes, with upregulated expression of ATG13, VPS37C, and DVL2. Cluster 3 emphasized cytoskeletal stability over metabolic activity, marked by the upregulation of SRF, SRC, and ABL1. Notably, all UC clusters demonstrated upregulation of COX1, TMSB10, and ACTB. In CD, Cluster 1 was defined by cytoskeletal dynamics and reduced protein synthesis, with upregulated expression of CFL1, F11R, and RAD23A. Cluster 2 exhibited increased protein synthesis and stress response pathways, associated with aggressive disease phenotypes, with upregulation of MTREX, SART3, and GTF3C3. Cluster 3 prioritised cytoskeletal organisation over metabolism, featuring upregulation of TESK1, ABL1, and DVL2, along with other genes. Across all CD clusters, COX1, CDH1, and SF3B1 were consistently up-regulated. Conclusion Despite certain limitations, this study categorizes UC and CD into three transcriptomics-based subtypes, identifying meaningful IBD-associated patterns, key subtyping genes, and insights into the disease's complex pathogenesis. These findings may advance new therapeutic strategies and personalized medicine for patients with distinct IBD subtypes.

Comprehensive analysis of the transcriptome-wide m6A Methylome in sheep testicular development.

N6-methyladenosine (m6A) modification of RNA is a critical post-transcriptional modification, that dynamically contributes to testicular development and spermatogenesis. Nevertheless, the investigation into the role of m6A in testicular development of sheep remains insufficient. Herein, we conducted a comprehensive analysis of the m6A transcriptome landscape in the testes of F1 hybrid Southdown × Hu sheep across M0 (0 months old, newborn), M3 (3 months old, sexually immature), M6 (6 months old, sexually mature), and Y1 (1 years old, adult). By profiling the m6A signatures across the transcriptome, we observed distinct differences in m6A modification patterns during sheep testicular development. Our cross-analysis of m6A and mRNA expression revealed that the expression of 743 genes and their m6A modification were concurrent. Notably, the combined analysis of the two comparative groups, M0 vs. M6 and M0 vs. Y1, exhibited a positive correlation, with 30 candidate genes each located within the largest protein-protein interaction network. Intriguingly, eight key hub genes (VEGFA, HDAC9, ZBTB40, KDM5B, MTRR, EAPS1, TSSK3, and BMP4) were identified to be associated with the regulation of sheep testicular development and spermatogenesis. These findings contribute to a deeper understanding of the dynamic role of m6A modification in sheep testicular biology. This study to map RNA m6A modification in sheep testes at different ages, providing novel insights into m6A topology and the molecular mechanisms associated with spermatogenesis in Southdown × Hu sheep F1 hybrids and laying the foundation for further investigations of mammalian spermatogenesis.

Integrated gene expression and alternative splicing analysis in human and mouse models of Rett syndrome

Mutations of the MECP2 gene lead to Rett syndrome (RTT), a rare developmental disease causing severe intellectual and physical disability. How the loss or defective function of MeCP2 mediates RTT is still poorly understood. MeCP2 is a global gene expression regulator, acting at transcriptional and post-transcriptional levels. Little attention has been given so far to the contribution of alternative splicing (AS) dysregulation to RTT pathophysiology. To perform a comparative analysis of publicly available RNA sequencing (RNA-seq) studies and generate novel data resources for AS, we explored 100 human datasets and 130 mouse datasets from Mecp2-mutant models, processing data for gene expression and alternative splicing. Our comparative analysis across studies indicates common species-specific differentially expressed genes (DEGs) and differentially alternatively spliced (DAS) genes. Human and mouse dysregulated genes are involved in two main functional categories: cell-extracellular matrix adhesion regulation and synaptic functions, the first category more significantly enriched in human datasets. Our extensive bioinformatics study indicates, for the first time, a significant dysregulation of AS in human RTT datasets, suggesting the crucial contribution of altered RNA processing to the pathophysiology of RTT.

Mitochondrial mRNA and the small subunit rRNA in budding yeasts undergo 3'-end processing at conserved species-specific elements.

Respiration in eukaryotes depends on mitochondrial protein synthesis, which is performed by organelle-specific ribosomes translating organelle-encoded mRNAs. Although RNA maturation and stability are central events controlling mitochondrial gene expression, many of the molecular details in this pathway remain elusive. These include cis- and trans-regulatory factors that generate and protect the 3' ends. Here, we mapped the 3' ends of mitochondrial mRNAs of yeasts classified into multiple families of the subphylum Saccharomycotina. We found that the processing of mitochondrial 15S rRNA and mRNAs involves species-specific sequence elements, which we term 3'-end RNA processing elements (3'-RPEs). In Saccharomyces cerevisiae, the 3'-RPE has long been recognized as a conserved dodecamer sequence, which recent studies have shown specifically interacts with the nuclear genome-encoded pentatricopeptide repeat protein Rmd9. We also demonstrate that, analogous to Rmd9 in S. cerevisiae, two Rmd9 orthologs from the Debaryomycetaceae family interact with their respective 3'-RPEs found in mRNAs and 15S rRNA. Thus, Rmd9-dependent processing of mitochondrial RNA precursors may be a common mechanism among the families of the Saccharomycotina subphylum. Surprisingly, we observed that 3'-RPEs often occur upstream of stop codons in complex I subunit mRNAs from yeasts of the CUG-Ser1 clade. We examined two of these mature mRNAs and found that their stop codons are indeed removed. Thus, translation of these stop-codon-less transcripts would require a noncanonical termination mechanism. Our findings highlight Rmd9 as a key evolutionarily conserved factor in both mitochondrial mRNA metabolism and mitoribosome biogenesis in a variety of yeasts.

Neurological mechanism-based analysis of the role and characteristics of physical activity in the improvement of depressive symptoms.

Depression is a common mental disorder characterized by a high prevalence and significant adverse effects, making the searching for effective interventions an urgent priority. In recent years, physical activity (PA) has increasingly been recognized as a standard adjunctive treatment for mental disorders owing to its low cost, easyapplication, and high efficiency. Epidemiological data shows positive preventive and therapeutic effects of PA on mental illnesses such as depression. This article systematically describes the prophylactic and therapeutic effects of PA on depression and its biological basis. A comprehensive literature analysis reveals that PA significantly improves depressive symptoms by upregulating the expression of "exerkines" such as irisin, adiponectin, and BDNF to positively impacting neuropsychiatric conditions. In particular, lactate could also play a critical role in the ameliorating effects of PA on depression due to the findings about protein lactylation as a novel protein post-transcriptional modification. The literature also suggests that in terms of brain structure, PA may improve hippocampal volume, basal ganglia (neostriatum, caudate-crustal nucleus) and PFC density in patients with MDD. In summary, this study elucidates the multifaceted positive effects of PA on depression andits potential biological mechanisms with a particular emphasis on the roles of various exerkines. Future research may further investigate the effects of different types, intensities, and durations of PA on depression, as well as how to better integrate PA interventions into existing treatment strategies to achieve optimal outcomes in mental health interventions.

Most m5C modifications in mammalian mRNAs are nonadaptive.

5-methylation (m5C) on mRNA molecules is a prevalent internal posttranscriptional modification in eukaryotes. Although m5C modification has been reported to regulate some biological processes, it is unknown whether most mRNA m5C modifications are functional. To address this question, we analyzed the genome-wide evolutionary characteristics of m5C modifications in protein-coding genes of humans and mice. Our analysis of RNA sequencing data from 13 tissues of both species revealed that (1) the occurrence of m5C modification is exceedingly low, (2) the fraction of m5Cs decreases with the amount of Cs across genes or tissues, (3) m5C modifications are mostly unshared between species, (4) m5C sites and motifs do not exhibit greater evolutionary conservation. Additionally, we estimate that a large fraction of the observed mRNA m5C modifications may be deleterious. Together, these observations suggest that most m5C modifications in mammalian mRNAs are nonadaptive, which has important implications for understanding the biological significance of m5C and other posttranscriptional modifications.

DICER1: The Argonaute Endonuclease Family Member and Its Role in Pediatric and Youth Pathology.

In 2001, two enzyme-encoding genes were recognized in the fruit fly Drosophila melanogaster. The genetic material, labeled Dicer-1 and Dicer-2, encodes ribonuclease-type enzymes with slightly diverse target substrates. The human orthologue is DICER1. It is a gene, which has been positioned on chromosome 14q32.13. It contains 27 exons, which are linking the two enzyme domains. DICER1 is found in all organ systems. It has been proved that it is paramount in human development. The protein determined by DICER1 is a ribonuclease (RNase). This RNase belongs to the RNase III superfamily, formally known as 'endoribonuclease'. It has been determined that the function of RNase III proteins is set to identify and degrade double-stranded molecules of RNA. DICER1 is a vital "housekeeping" gene. The multi-domain enzyme is key for small RNA processing. This enzyme functions in numerous pathways, including RNA interference paths, DNA damage renovation, and response to viruses. At the protein level, DICER is also involved in several human diseases, of which the pleuro-pulmonary blastoma is probably the most egregious entity. Numerous studies have determined the full range of DICER1 functions and the corresponding relationship to tumorigenic and non-neoplastic diseases. In fact, genetic mutations (somatic and germline) have been detected in DICER1 and are genetically associated with at least two clinical syndromes: DICER1 syndrome and GLOW syndrome. The ubiquity of this enzyme in the human body makes it an exquisite target for nanotechnology-supported therapies and repurposing drug approaches.

Dynamic Roles of RNA and RNA Epigenetics in HTLV-1 Biology.

Since the discovery of RNA in the early 1900s, scientific understanding of RNA form and function has evolved beyond protein coding. Viruses, particularly retroviruses like human T-cell leukemia virus type 1 (HTLV-1), rely heavily on RNA and RNA post-transcriptional modifications to regulate the viral lifecycle, pathogenesis, and evasion of host immune responses. With the emergence of new sequencing technologies in the last decade, our ability to dissect the intricacies of RNA has flourished. The ability to study RNA epigenetic modifications and splice variants has become more feasible with the recent development of third-generation sequencing technologies, such as Oxford nanopore sequencing. This review will highlight the dynamic roles of known RNA and post-transcriptional RNA epigenetic modifications within HTLV-1 biology, including viral hbz, long noncoding RNAs, microRNAs (miRNAs), transfer RNAs (tRNAs), R-loops, N6-methyladenosine (m6A) modifications, and RNA-based therapeutics and vaccines.

RAS, a Pentatricopeptide Repeat Protein, Interacts with OsTRX z to Regulate Chloroplast Gene Transcription and RNA Processing.

Thioredoxin z (TRX z) plays a significant role in chloroplast development by regulating the transcription of chloroplast genes. In this study, we identified a pentatricopeptide repeat (PPR) protein, rice albino seedling-lethal (RAS), that interacts with OsTRX z. This interaction was initially discovered by using a yeast two-hybrid (Y2H) screening technique and was further validated through Y2H and bimolecular fluorescence complementation (BiFC) experiments. RAS contains 16 PPR motifs and features a small MutS-related (SMR) domain at its C-terminus. CRISPR/Cas9-generated ras mutants exhibited an albino seedling-lethal phenotype characterized by abnormal chloroplast structures and a significantly reduced chlorophyll content. RAS localizes to the chloroplast and is predominantly expressed in young leaves. Mutations in RAS affect RNA editing at the rpl2, rps14, and ndhA sites, as well as RNA splicing at the rpl2, atpF, and ndhA transcripts within the chloroplast. Furthermore, the expression levels of genes associated with chloroplast formation are altered in the ras mutant. Both OsTRX z and RAS were found to interact with chloroplast signal recognition particle (cpSRP) proteins, indicating that their proper localization within the chloroplast may be dependent on the SRP pathway. Collectively, our findings highlight the critical role of RAS in chloroplast development, as it is involved in RNA processing and the regulation of chloroplast gene expression.

Balancing RNA processing and innate immune response: Possible roles for SMN condensates in snRNP biogenesis.

Biomolecular condensates like U-bodies are specialized cellular structures formed through multivalent interactions among intrinsically disordered regions. U-bodies sequester small nuclear ribonucleoprotein complexes (snRNPs) in the cytoplasm, and their formation in mammalian cells depends on stress conditions. Because of their location adjacent to P-bodies, U-bodies have been considered potential sites for snRNP storage or turnover. SMN, a chaperone for snRNP biogenesis, forms condensates through its Tudor domain. In fly models, defects in SMN trigger innate immune responses similar to those observed with excess cytoplasmic snRNA during viral infection in mammalian cells. Additionally, spinal muscular atrophy (SMA), caused by SMN deficiency, is associated with inflammation. Therefore, SMN may help prevent innate immune aberrant activation due to defective snRNP biogenesis by forming U-bodies to sequester these molecules. Further studies on U-body functions may provide therapeutic insights for diseases related to RNA metabolism.

Multi-omics analysis in inclusion body myositis identifies mir-16 responsible for HLA overexpression

BackgroundInclusion Body Myositis is an acquired muscle disease. Its pathogenesis is unclear due to the co-existence of inflammation, muscle degeneration and mitochondrial dysfunction. We aimed to provide a more advanced understanding of the disease by combining multi-omics analysis with prior knowledge. We applied molecular subnetwork identification to find highly interconnected subnetworks with a high degree of change in Inclusion Body Myositis. These could be used as hypotheses for potential pathomechanisms and biomarkers that are implicated in this disease.ResultsOur multi-omics analysis resulted in five subnetworks that exhibit changes in multiple omics layers. These subnetworks are related to antigen processing and presentation, chemokine-mediated signaling, immune response-signal transduction, rRNA processing, and mRNA splicing. An interesting finding is that the antigen processing and presentation subnetwork links the underexpressed miR-16-5p to overexpressed HLA genes by negative expression correlation. In addition, the rRNA processing subnetwork contains the RPS18 gene, which is not differentially expressed, but has significant variant association. The RPS18 gene could potentially play a role in the underexpression of the genes involved in 18 S ribosomal RNA processing, which it is highly connected to.ConclusionsOur analysis highlights the importance of interrogating multiple omics to enhance knowledge discovery in rare diseases. We report five subnetworks that can provide additional insights into the molecular pathogenesis of Inclusion Body Myositis. Our analytical workflow can be reused as a method to study disease mechanisms involved in other diseases when multiple omics datasets are available.

Dynamic Multilevel Regulation of EGFR, KRAS, and MYC Oncogenes: Driving Cancer Cell Proliferation Through (Epi)Genetic and Post-Transcriptional/Translational Pathways.

The epidermal growth factor receptor (EGFR) regulates gene expression through two primary mechanisms: as a growth factor in the nucleus, where it translocates upon binding its ligand, or via its intrinsic tyrosine kinase activity in the cytosol, where it modulates key signaling pathways such as RAS/MYC, PI3K, PLCγ, and STAT3. During tumorigenesis, these pathways become deregulated, leading to uncontrolled proliferation, enhanced migratory and metastatic capabilities, evasion of programmed cell death, and resistance to chemotherapy or radiotherapy. The RAS and MYC oncogenes are pivotal in tumorigenesis, driving processes such as resistance to apoptosis, replicative immortality, cellular invasion and metastasis, and metabolic reprogramming. These oncogenes are subject to regulation by a range of epigenetic and post-transcriptional modifications. This review focuses on the deregulation of EGFR, RAS, and MYC expression caused by (epi)genetic alterations and post-translational modifications. It also explores the therapeutic potential of targeting these regulatory proteins, emphasizing the importance of phenotyping neoplastic tissues to inform the treatment of cancer.

The role of CNBP in brain atrophy and its targeting in myotonic dystrophy type 2.

Myotonic Dystrophy type 2 (DM2) is a multisystem disease affecting many tissues, including skeletal muscle, heart, and brain. DM2 is caused by unstable expansion of CCTG repeats in an intron 1 of a gene coding for cellular nuclear binding protein (CNBP). The expanded CCTG repeats cause DM2 pathology due to the accumulation of RNA CCUG repeats, which affect RNA processing in patients' cells. We have previously shown that mutant CCUG repeats reduce CNBP protein in DM2 patients. Reducing Cnbp in Cnbp KO mouse model causes late skeletal muscle atrophy. In this study, we examined if the reduction of Cnbp affects the Central Nervous System (CNS). MRI and DTI analyses showed that total brain volume and grey matter are reduced in Cnbp KO mice, while mean, radial and axonal brain diffusivity is increased. The morphological changes in the brains of Cnbp KO mice are accompanied by reduced stereotypic behavior, anxiety and neuromotor defects. These findings suggest that the reduction of CNBP contributes to CNS pathology in DM2. Since CNBP stability is regulated by pAMPK-dependent phosphorylation, we examined protein levels of pAMPK in DM2 cells and found that the active pAMPK is reduced in DM2. Interaction of CNBP with pAMPK and stability of CNBP protein are also decreased in DM2. Our data show that a small molecule AMPK activator A769662 corrects CNBP stability and normalizes CNBP targets in DM2 fibroblasts. Thus, activators of AMPK could potentially be developed as therapeutics to correct CNBP and reduce muscle and brain atrophies in DM2.

Construction and validation of a diagnostic model for cholangiocarcinoma based on tumor-educated platelet RNA expression profiles

Abstract Objectives We aim to explore the diagnostic value of platelet-based “liquid biopsy” technology for cholangiocarcinoma (CCA), seeking reliable methods for early cancer diagnosis to improve patient prognosis. Methods Bioinformatics methods were utilized to analyze the GEO databases (GSE183635) and (GSE68086), identifying differentially expressed genes and constructing a diagnostic model of CCA using tumor-educated platelet (TEP) RNA expression profiles. GO and KEGG pathway enrichment analysis were performed. Additionally, platelet RNA from CCA patients and controls totaling 60 cases was extracted by qRT-PCR experiments to validate the diagnostic reliability of candidate genes, further confirmed through in vitro experiments. Results A diagnostic model comprising seven platelet genes (CRYM, IFI27, EED, METAP1, RASGRP1, SEC11A, and WDR82) effectively distinguished CCA from controls. Area under curve (AUC) values were 0.862 (training set), 0.875 (internal validation), 0.865 (total internal), and 0.954 (external validation). GO analysis highlighted “non-coding RNA processing,” “nuclear envelope,” and “catalytic activity, acting on RNA.” KEGG pathways included “Ribosome biogenesis in eukaryotes”, “RNA translocation” and “Spliceosome”. qRT-PCR experiments revealed significant differences (p<0.05) in METAP1, SEC11A, WDR82, RASGRP1, and EED gene expression in CCAs, consistent with bioinformatics predictions. CRYM showed significant differences (p<0.001) compared to healthy individuals. WDR82 and CRYM had high diagnostic efficiency (AUC 0.939 and 0.942), surpassing conventional tumor markers (AFP, CEA, and CA19-9). Joint receiver operating characteristics (ROC) analysis yielded an AUC of 0.806, sensitivity of 1.000, and accuracy of 0.833. Conclusions Based on the GEO database, we identified seven TEP RNAs (CRYM, IFI27, METAP1, SEC11A, WDR82, RASGRP1, EED) with strong discriminative ability for CCA, suggesting their potential as reliable non-invasive biomarkers.

5-Methylcytosine-modified circRNA-CCNL2 regulates vascular remdeling in hypoxic pulmonary hypertension through binding to FXR2.

Pulmonary hypertension (PH) is a malignant cardiovascular disease with a complex etiology. 5-Methylcytosine (m5C) is a post-transcriptional RNA modification identified in both stable and highly abundant RNAs, with a lower frequency of occurrence in circular RNAs (circRNAs). Nevertheless, the function of m5C-modified circRNAs in the pathogenesis of PH remains uncertain. The objective of this study was to investigate the biological role and molecular mechanisms of m5C-modified circRNA-CCNL2 in hypoxic PH pulmonary vascular remodeling. Our findings revealed that hypoxia downregulates circCCNL2 expression, and overexpression of circCCNL2 attenuates PH progression and inhibits the proliferation of pulmonary artery smooth muscle cell (PASMCs). Bioinformatics predictions indicated the presence of m5C modification sites in circCCNL2, which NSUN2 mediated. The downregulation of NSUN2 resulted in a reduction in m5C modification of circCCNL2. It was also observed that the stability of circRNAs was associated with the proliferation of PASMCs. From a mechanistic standpoint, low expression of circCCNL2 resulted in reduced binding of FXR2, while increased association of free FXR2 with CDKL3 led to enhanced proliferation of PASMCs. Notably, circCCNL2 expression was found to be regulated by alternative splicing involving SRSF2, with reduced pre-CCNL2 splicing resulting from low SRSF2 expression, ultimately leading to decreased circCCNL2 expression. This is the first demonstration that m5C-modified circCCNL2 can slow the development of PH and inhibit the proliferation of PASMCs by binding to FXR2. These findings offer new insights into the regulation of circRNAs through m5C modifications and the role of epigenetic reprogramming in PH.

ESRP2-microRNA-122 axis promotes the postnatal onset of liver polyploidization and maturation.

Hepatocyte polyploidy and maturity are critical to acquiring specialized liver functions. Multiple intracellular and extracellular factors influence ploidy, but how they cooperate temporally to steer liver polyploidization and maturation or how post-transcriptional mechanisms integrate into these paradigms is unknown. Here, we identified an important regulatory hierarchy in which postnatal activation of epithelial splicing regulatory protein 2 (ESRP2) stimulates processing of liver-specific microRNA (miR-122) to facilitate polyploidization, maturation, and functional competence of hepatocytes. By determining transcriptome-wide protein-RNA interactions in vivo and integrating them with single-cell and bulk hepatocyte RNA-seq data sets, we delineated an ESRP2-driven RNA processing program that drives sequential replacement of fetal-to-adult transcript isoforms. Specifically, ESRP2 binds the primary miR-122 host gene transcript to promote its processing/biogenesis. Combining constitutive and inducible ESRP2 gain- and loss-of-function mouse models with miR-122 rescue experiments, we demonstrated that timed activation of ESRP2 augments the miR-122-driven program of cytokinesis failure, ensuring the proper onset and extent of hepatocyte polyploidization.

RNA dysregulation in neurodegenerative diseases.

Dysregulation of RNA processing has in recent years emerged as a significant contributor to neurodegeneration. The diverse mechanisms and molecular functions underlying RNA processing underscore the essential role of RNA regulation in maintaining neuronal health and function. RNA molecules are bound by RNA-binding proteins (RBPs), and interactions between RNAs and RBPs are commonly affected in neurodegeneration. In this review, we highlight recent progress in understanding dysregulated RNA-processing pathways and the causes of RBP dysfunction across various neurodegenerative diseases. We discuss both established and emerging mechanisms of RNA-mediated neuropathogenesis in this rapidly evolving field. Furthermore, we explore the development of potential RNA-targeting therapeutic approaches for the treatment of neurodegenerative diseases.