Biology subjects

Ballarino, M.

Publications and source records attributed to Ballarino, M..

8 recordsLinked to original sources

bioRxiv2026

nHOTAIRM1 scaffolds ANXA11-dependent assemblies to drive axonal mRNA localization in human motor neurons

Long noncoding RNAs (lncRNAs) are well recognized as regulators of neuronal development and function, yet their integration into canonical axonal transport pathways, an essential component of spatial gene regulation in highly polarized cells, remains incompletely defined. It is still unclear to what extent individual lncRNAs confer cargo selectivity and couple discrete mRNA cohorts to established transport machineries. Here we identify a cytoplasmic role for the neuronal isoform of HOTAIRM1 (nHOTAIRM1) in shaping the axonal RNA landscape of human iPSC-derived spinal motor neurons (spMNs). We show that nHOTAIRM1 associates with Annexin A11 (ANXA11), a factor linked to lysosome-coupled movement of RNA granules and engages a defined subset of MN-relevant mRNAs. Transcriptome-wide and targeted interaction assays, together with computational mapping and steric competition, support direct RNA-RNA pairing between nHOTAIRM1 and mRNAs involved in cytoskeletal organization and synaptic or vesicular functions, while spatial analyses place these RNA pairs in close proximity within the soma and neurites. Loss-of-function experiments further show that nHOTAIRM1 depletion reduces the association of these mRNAs with ANXA11-positive complexes and diminishes their enrichment in neuronal projections, an effect that is recapitulated by ANXA11 depletion. Collectively, these findings support a model in which nHOTAIRM1 contributes to the selective recruitment of cargo mRNAs into ANXA11-associated transport assemblies, thereby promoting their localization within distal neurites. More broadly, our findings provide mechanistic insight into how a lncRNA can regulate mRNA sorting and compartment-specific RNA trafficking in human spMNs.

molecular biology↗

bioRxiv2025

Decoding RNA Triple Helices: Identification from Sequence and Secondary Structure

The discovery of long non-coding RNAs has revealed additional layers of gene-expression control. Specific interactions of lncRNAs with DNA, RNAs, and RNA-binding proteins enable regulation in both cytoplasmic and nuclear compartments; for example, a conserved triple-helix motif is essential for MALAT1 stability and oncogenic activity. Here we present a secondary-structure-based framework to annotate and detect RNA triple helices. First, we extend the dot-bracket formalism with a third annotation line that encodes Hoogsteen contacts. Second, we introduce TripleMatcher, which searches for a triple-helix pattern, filters candidates by C1'-C1' distance thresholds, and merges overlaps into region-level zones. Using telomerase RNAs and RNA-stability elements with experimentally established triple helices (8 RNAs), TripleMatcher localized all annotated regions (structure-wise detection 8/8); geometric filtering removed most spurious candidates and improved precision (PPV from 0.42 to 0.81) and overall accuracy (F1 from 0.42 to 0.62) while maintaining sensitivity. Benchmarking eight predictors showed that pseudoknot-aware methods most reliably reproduce the local architecture required for detection, aligning secondary-structure quality with downstream triple-helix recovery. Applied prospectively, the framework identified candidate regions directly from predicted secondary structures and scaled to a screen of 4,147 RNAs, where distance filtering reduced 150,948 raw candidates to 90 geometrically feasible regions across seven molecules, including human telomerase complexes. Together, the notation and TripleMatcher provide a concise route from secondary structure to a small, interpretable set of triple-helix candidates suitable for targeted experimental validation.

bioinformatics↗

bioRxiv2024

Long noncoding RNA HSCHARME promotes the maturation of stem cells-derived cardiomyocytes by controlling gene regulatory networks altered in human cardiomyopathies

A growing body of evidence suggests that tissue-specific long noncoding RNAs (lncRNA) play pivotal roles in the heart. Here, we exploited the synteny between the mouse and human genomes to identify the novel lncRNA HSCHARME (Human Syntenic CHARME) and combined single-cell transcriptomics, CAGE-seq data, RNA-FISH imaging and CRISPR-Cas9 genome editing to document its role in cardiomyogenesis. By investigating the mechanism of action of HSCHARME in hiPSC-derived cardiomyocytes, we found that the locus produces the major pCHARME isoform that associates with SC35-containing speckles and interacts with the splicing regulator PTBP1. Consistently, the functional inactivation of pCHARME influences the splicing of cardiac-specific pre-mRNAs and impacts their expression, which parallels a decline in cardiomyocyte differentiation and physiology. In line with a possible association with disease, large-scale analysis of the lncRNA expression across cardiomyopathy patients revealed increased levels of pCHARME in hypertrophic (HCM) and dilated (DCM) hearts and identified a subset of disease-associated targets whose expression can be modulated through HSCHARME dosage. By unlocking mechanistic insights into the role of pCHARME in cardiac cells, our data identify a novel non-coding regulator of cardiomyocyte function with potential implications in disease.

molecular biology↗

bioRxiv2024

A circuit involving the lncRNA MB3 and the driver genes MYC and OTX2 inhibits apoptosis in Group 3 Medulloblastoma by regulating the TGF-β pathway via HMGN5

BackgroundGroup 3 (G3) is one of the most common, aggressive and fatal subtypes of the paediatric cerebellar tumour Medulloblastoma (MB), primarily driven by the MYC oncogene. Targeting MYC has long been challenging and this, combined with our incomplete understanding of G3 MB molecular bases, has hindered the development of effective targeted therapies. Long noncoding RNAs (lncRNAs), with their extensive oncogenic roles, cancer-specific expression, and connection to MYC biology, offer opportunities for unravelling this complexity and providing new insights and therapeutic targets. MethodologyUsing genome-wide, molecular and cellular assays, we characterised the activity of the MYC-dependent, anti-apoptotic lncRNA lncMB3 in G3 MB cells. ResultsThrough transcriptomic and interactomic analyses, we clarified lncMB3 function and mode-of-action. LncMB3 controls the TGF-{beta} pathway, critically altered in G3 medulloblastomagenesis. This regulation occurs via the direct coding-noncoding RNA interaction between lncMB3 and the mRNA for the epigenetic factor HMGN5, with both sharing targets in the TGF-{beta} cascade. This axis converges on apoptosis through OTX2, another G3 MB driver gene, and photoreceptor lineage genes. Synergistic effects between lncMB3 targeting and cisplatin treatment underscores the relevance of this regulatory network in vitro. Finally, we propose novel ferritin-based nanocarriers as efficient delivery tools for antisense oligonucleotides targeting lncMB3. ConclusionsLncMB3 emerges as a central node linking MYC amplification to apoptosis inhibition through a circuit involving RNA-based mechanisms, G3 MB key drivers and underexplored factors. This integrated framework deepens our understanding of G3 MB molecular underpinnings and lay the foundation for translating lncRNA research into potential applications.

cancer biology↗

bioRxiv2024

Genome biology of long non-coding RNAs in humans: a virtual karyotype

BackgroundLong non-coding RNAs (lncRNAs) represent a unique and groundbreaking class of RNA molecules that exert regulatory functions with remarkable tissue and cellular specificities. Although the number of identified functional lncRNAs is increasing, comprehensive profiling of lncRNA genomics remains elusive. Creating a virtual lncRNA karyotype is especially important for species whose intrinsic features enable their biosynthesis and function in context-dependent manners. Results and conclusionsTo address this challenge, we employed existing annotation files to create a statistical genomics portrait of lncRNA genes for comparison with protein-coding genes. We provide a foundational reference for exploring the non-coding genome, offering insights into the genomic characteristics of lncRNAs that may enhance understanding of their biological significance and impact.

genomics↗

bioRxiv2024

Transcriptional profiling of human brain cortex identifies novel lncRNA-mediated networks dysregulated in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease for which a comprehensive knowledge about the pathological mechanisms is still lacking. A multitude of dysregulated cellular processes and pathways have been linked to ALS so far, including the recent focus directed toward the implication of several classes of non-coding (nc)RNAs. Within this context, the class of long ncRNAs (lncRNAs), may provide an important contribution to the onset and the severity of ALS pathogenesis, due to their high tissue specificity and their function as gene expression regulators. Nevertheless, their identification in humans often relies on differential expression analyses from bulk RNA-seq, which limits their targeting in the cellular contexts where they may be primarily involved. Here we apply dedicated pipelines to single-nucleus nuclei datasets to study lncRNA from non-pathological and pre-frontal ALS human cortex. We found that in brain, distinct cell subtypes express very different pattern of lncRNAs to suggest possible roles in cellular processes found dysregulated in ALS patients. Moreover, we show the lncRNA involvement in important gene regulatory networks that result differentially regulated in pathological conditions and dissect the genomic organization of differentially expressed lncRNAs.

genomics↗

bioRxiv2022

The long noncoding RNA Charme supervises cardiomyocytes maturation by controlling cell differentiation programs in the developing heart

Long noncoding RNAs (lncRNAs) are emerging as critical regulators of heart physiology and disease, although the studies unveiling their modes-of-action are still limited to few examples. We recently identified pCharme, a chromatin-associated lncRNA whose functional knockout in mice results in defective myogenesis and morphological remodelling of the cardiac muscle. Here, we combined Cap-Analysis of Gene Expression (CAGE), single-cell (sc)RNA sequencing and whole-mount in situ hybridization analyses to study pCharme cardiac expression. Since the early steps of cardiomyogenesis, we found the lncRNA being specifically restricted to cardiomyocytes, where it assists the formation of specific nuclear condensates containing MATR3, as well as important RNAs for cardiac development. In line with the functional significance of these activities, pCharme ablation in mice results in a delayed maturation of cardiomyocytes, which ultimately leads to morphological alterations of the myocardium and ventricular hypo-trabeculation. Since congenital anomalies in myocardium are clinically relevant in humans and predispose patients to major complications, the identification of novel genes controlling cardiac morphology becomes crucial. Our study offers unique insights into a novel lncRNA-mediated regulatory mechanism promoting cardiomyocyte maturation and bears relevance to Charme locus for future theranostic applications.

molecular biology↗

bioRxiv2020

Epigenetic regulation of Wnt7b expression by the cis-acting long noncoding RNA lnc-Rewind in muscle stem cells

Skeletal muscle possesses an outstanding capacity to regenerate upon injury due to the adult muscle stem cells (MuSCs) activity. This ability requires the proper balance between MuSCs expansion and differentiation which is critical for muscle homeostasis and contributes, if deregulated, to muscle diseases. Here, we functionally characterize a novel chromatin-associated lncRNA, lnc-Rewind, which is expressed in murine MuSCs and conserved in human. We find that, in mouse, lnc-Rewind acts as an epigenetic regulator of MuSCs proliferation and expansion by influencing the expression of skeletal muscle genes and several components of the WNT (Wingless-INT) signalling pathway. Among them, we identified the nearby Wnt7b gene as a direct lnc-Rewind target. We show that lnc-Rewind interacts with the G9a histone lysine methyltransferase and mediates the in cis repression of Wnt7b by H3K9me2 deposition. Overall, these findings provide novel insights into the epigenetic regulation of adult muscle stem cells fate by lncRNAs.

cell biology↗