Biology subjects

Mangone, M.

Publications and source records attributed to Mangone, M..

8 recordsLinked to original sources

bioRxiv2025

Exploring MicroRNA Strand Selection: Insights into Gene Regulation and Development

MicroRNAs (miRNAs) are central regulators of gene expression, yet how cells choose between the two strands (5p or 3p) of a miRNA duplex during biogenesis remains unresolved. Here, we present a comprehensive, experimentally grounded framework that decodes the logic of miRNA strand selection. Using Caenorhabditis elegans as a model system, we developed a high-throughput qPCR platform enabling precise quantification of strand usage across developmental stages and in specific somatic tissues. To uncover the molecular grammar guiding this process, we built a predictive machine learning model trained on experimentally validated strand usage data. This AI-driven model, integrating 77 biologically informed features, accurately predicts strand preference not only in nematodes but also across vertebrates, including humans, revealing compositional and structural biases that are conserved yet functionally repurposed. Our analysis shows that strand selection is not stochastic but follows conserved, context-dependent rules shaped by cellular and developmental cues. To support the research community, we provide open-access resources: a database of strand usage profiles, predictive scores across species, and code and protocols via GitHub. This work offers the first unified, generalizable model for miRNA strand selection, establishing a paradigm that combines large-scale experimentation with AI to reveal a conserved, programmable layer of gene regulation.

molecular biology↗

bioRxiv2024

A Comprehensive Analysis of 3-UTRs in Caenorhabditis elegans

Summary/Abstract3Untranslated Regions (3UTRs) are essential portions of genes containing elements necessary for pre-mRNA 3end processing and are involved in post-transcriptional gene regulation. Despite their importance, they remain poorly characterized in eukaryotes. Here, we have used a multi-pronged approach to extract and curate 3UTR data from 11,533 publicly available datasets, corresponding to the entire collection of C. elegans transcriptomes stored in the NCBI repository from 2009 to 2023, and present its complete 3UTRome dataset sequenced at single-base resolution. This updated C. elegans 3UTRome is the most comprehensive resource in any metazoan, covering 97.4% of the 20,362 experimentally validated protein-coding genes with refined and updated 3UTR boundaries for 23,489 3UTR isoforms. We also used this novel dataset to identify and characterize sequence elements involved in pre-mRNA 3end processing and update miRNA target predictions. This resource provides important insights into the 3UTR formation, function, and regulation in eukaryotes.

genomics↗

bioRxiv2022

Multifunctional requirements for ERK1/2 signaling in the development of ganglionic eminence derived glia and cortical inhibitory neurons

The RAS/RAF/MEK/ERK1/2 intracellular signaling pathway is activated by numerous cues during brain development and dysregulated in neurodevelopmental syndromes, particularly the RASopathies and certain forms of autism. Cortical excitatory/inhibitory imbalance is thought to be critical in the neuropathogenesis of these conditions. However, the developmental functions of ERK1/2 signaling in cortical inhibitory neurons (CINs) and other medial ganglionic eminence (MGE)-derived non-neuronal cells are poorly understood. Here, we genetically modulated ERK1/2 signaling in mouse MGE neural progenitors or GABAergic neurons in vivo. We find that MEK-ERK1/2 signaling is essential for regulating MGE-derived oligodendrocyte number in the anterior commissure. While Erk1/2 inactivation does not alter CIN number, we discovered a significant and persistent reduction in somatostatin, but not parvalbumin, expression in a subset of CINs. ERK1/2 signaling is also necessary for chemogenetic activity-dependent FOSB expression in CINs in vivo. Interestingly, one week of chronic chemogenetic stimulation in juvenile or adult animals partially rescues the decrease in somatostatin expression in Erk1/2 mutant CINs. Our data demonstrate ERK1/2 signaling is required for the establishment of MGE-derived glia, whereas in CINs, ERK1/2 drives activity dependent-responses and the expression of somatostatin in a subset of neurons.

neuroscience↗

bioRxiv2022

An updated C. elegans body muscle transcriptome for studies in muscle formation and function

The body muscle is an important tissue used in organisms for proper viability and locomotion. Although this tissue is generally well studied and characterized, and many pathways have been elucidated throughout the years, we still lack a comprehensive understanding of its transcriptome and how it controls muscle development and function. Here, we have updated a nuclear FACS sorting-based methodology to isolate and sequence a high-quality muscle transcriptome from C. elegans mixed-stage animals. We have identified 2,848 muscle-specific protein-coding genes, including 78 transcription factors and 206 protein-coding genes containing an RNA binding domain. We studied their interaction network, performed a detailed promoter analysis, and identified novel muscle-specific cis-acting elements. We have also identified 16 high-quality muscle-specific miRNAs, studied their function in vivo using fluorochrome-based analyses, and developed a high-quality C. elegans miRNA Interactome incorporating other muscle-specific datasets produced by our lab and others. Our study expands our understanding of how muscle tissue functions in C. elegans and in turn, provide results that can in the future be applied to humans to study muscular-related diseases.

genetics↗

bioRxiv2022

Identifying the C. elegans vulval transcriptome

Development of the C. elegans vulva is a classic model of organogenesis. This system, which starts with six equipotent cells, encompasses diverse types of developmental event, including developmental competence, multiple signaling events to control precise and faithful patterning of three cell fates, execution and proliferation of specific cell lineages, and a series of sophisticated morphogenetic events. Early events have been subjected to extensive mutational and genetic investigations and later events to cell biological analyses. We infer the existence of dramatically changing profiles of gene expression that accompanies the observed changes in development. Yet except from serendipitous discovery of several transcription factors expressed in dynamic patterns in vulval lineages, our knowledge of the transcriptomic landscape during vulval development is minimal. This study describes the composition of a vulva-specific transcriptome. We used tissue specific harvesting of mRNAs via immunoprecipitation of epitope-tagged poly(A) binding protein, PAB-1, heterologously expressed by a promoter known to express GFP in vulval cells throughout their development. The identified transcriptome was small but tightly interconnected. From this data set we identified several genes with identified functions in development of the vulva and validated more with promoter-GFP reporters of expression. For one target, lag-1, promoter-GFP expression was limited but fluorescent tag of the endogenous protein revealed extensive expression. Thus, we have identified a transcriptome of the C. elegans as a launching pad for exploration of functions of these genes in organogenesis.

genetics↗

bioRxiv2019

The C. elegans 3’UTRome V2: an updated genomic resource to study 3’UTR biology

3-Untranslated Regions (3-UTRs) of mRNAs emerged as central regulators of cellular function as they contain important but poorly-characterized cis-regulatory elements targeted by a multitude of regulatory factors. The model nematode C. elegans is ideal to study these interactions since it possesses a well-defined 3-UTRome. In order to improve its annotation, we have used a genomics approach to download raw transcriptome data for 1,088 transcriptome datasets corresponding to the entire collection of C. elegans trancriptomes from 2015 to 2018 from the Sequence Read Archive at the NCBI. We then extracted and mapped high-quality 3-UTR data at ultra-deep coverage. Here we describe and release to the community the updated version of the worm 3-UTRome, which we named 3-UTRome v2. This resource contains high-quality 3-UTR data mapped at single base ultra-resolution for 23,084 3-UTR isoform variants corresponding to 14,788 protein-coding genes and is updated to the latest release of WormBase. We used this dataset to study and probe principles of mRNA cleavage and polyadenylation in C. elegans. The worm 3-UTRome v2 represents the most comprehensive and high-resolution 3-UTR dataset available in C. elegans and provides a novel resource to investigate the mRNA cleavage and polyadenylation reaction, 3-UTR biology and miRNA targeting in a living organism.

genomics↗

bioRxiv2019

Consecutive signaling pathways are activated in progression of Duchenne muscular dystrophy in C. elegans

BackgroundDuchenne muscular dystrophy (DMD) is a lethal, X-linked disease characterized by progressive muscle degeneration. The condition is driven by nonsense and missense mutations in the dystrophin gene, but the resulting changes in muscle-specific gene expression that take place in dystrophins absence remain uncharacterized, as they are potentially obscured by the chronic inflammation elicited by muscle damage in humans. C. elegans possess a mild inflammatory response that allows for the characterization of the transcriptome rearrangements affecting disease progression independently of inflammation. ResultsIn effort to better understand these dynamics we have isolated and sequenced body muscle-specific transcriptomes from C. elegans lacking functional dystrophin at distinct stages of disease progression. We have identified two consecutively altered gene networks, which are also disrupted in the dystrophin deficient mdx mouse model. We found an upregulation of genes involved in mitochondrial function early in disease progression, and an upregulation of genes related to muscle fibre repair in later stages. This suggests that dystrophin may have a signaling role early in development, and its absence may activate compensatory mechanisms that counteract muscle degradation caused by loss of dystrophin. We have also developed a temperature-based screening method for synthetic paralysis that can be used to rapidly identify genetic partners of dystrophin. ConclusionsOur results allow for the comprehensive identification of transcriptome rearrangements that potentially serve as independent drivers of disease progression and may in turn allow for the identification of new therapeutic targets for the treatment of DMD. One Sentence SummaryA tissue specific transcriptome analysis of dystrophin deficient muscle in C. elegans reveals that dystrophin has distinct, dynamic signaling roles in early and late stage progression of Duchenne muscular dystrophy.

genetics↗

bioRxiv2018

MicroRNAs modulate alternative splicing in the C. elegans intestine and body muscle tissues

MicroRNAs (miRNAs) are known to modulate gene expression, but their activity at the tissue-specific level remains largely uncharacterized. In order to study their contribution to tissue-specific gene expression, we developed novel tools to profile miRNA targets in the C. elegans intestine and body muscle. We validated many previously described interactions, and identified ~3,500 novel targets. Many of the miRNA targets curated are known to modulate the functions of their respective tissues. Within our datasets we observed a disparity in the use of miRNA-based gene regulation between the intestine and body muscle. The intestine contained significantly more miRNA targets than the body muscle highlighting its transcriptional complexity. We detected an unexpected enrichment of RNA binding proteins targeted by miRNA in both tissues, with a notable abundance of RNA splicing factors. We developed in vivo genetic tools to validate and further study three RNA splicing factors identified as miRNA targets in our study (asd-2, hrp-2 and smu-2), and show that these factors indeed contain functional miRNA regulatory elements in their 3UTRs that are able to repress their expression in the intestine. In addition, the alternative splicing pattern of their respective downstream targets (unc-60, unc-52, lin-10 and ret-1) is dysregulated when the miRNA pathway is disrupted. A re-annotation of the transcriptome data in C. elegans strains that are deficient in the miRNA pathway from past studies supports and expands on our results. This study highlights an unexpected role for miRNAs in modulating tissue-specific gene isoforms, where post-transcriptional regulation of RNA splicing factors associates with tissue-specific alternative splicing.

molecular biology↗