Biology subjects

Finazzi, V.

Publications and source records attributed to Finazzi, V..

5 recordsLinked to original sources

bioRxiv2026

Benchmarking computational tools for locus-specific analysis of transposable elements in single-cell RNA-seq datasets

BackgroundTransposable elements (TEs) are increasingly recognized as regulators of gene expression and cellular identity in development and disease. Single-cell RNA-sequencing (scRNA-seq) enables the analysis of their transcription at cellular resolution, but the repetitive nature of TEs and their frequent overlap with genes create substantial mapping ambiguity. Although several tools quantify TE expression, few support locus-specific analysis, and their performance in single-cell data has not been systematically evaluated. ResultsWe present a comprehensive benchmarking framework for locus-level TE quantification in short-read scRNA-seq, combining real datasets with simulations that provide read-level ground truth. TE-derived reads constitute a considerable fraction of the transcriptome and capture meaningful biological structure. Our simulations reveal that older, sequence-diverged insertions can be quantified with relatively high accuracy, whereas young TEs remain intrinsically difficult to resolve due to unreliable assignment of multi-mapping reads. We observe pronounced family-specific biases and identify gene-TE disambiguation as a major unresolved challenge. Among evaluated methods, SoloTE (unique-mapper mode) and Stellarscope (with an expectation-maximization-based reallocation of multi-mappers) showed comparable performance, while including multi-mappers generally increased false positives without substantially improving locus-level accuracy. ConclusionsOur benchmark delineates the fundamental limits imposed by short-read scRNA-seq on locus-specific TE quantification, providing practical guidance for prospective users. Suggested best practices include focusing locus-level analyses on older insertions, applying unique-mapper strategies to improve precision, aggregating counts at the subfamily level for young TEs, and explicitly checking for gene-TE overlaps. Our workflow is fully reproducible and extensible, providing a foundation for evaluating emerging methods aimed at resolving TE transcription at single-locus resolution.

bioinformatics↗

bioRxiv2025

Methionine synthase reductase regulates heterochromatin independently of methionine synthesis through mitochondrial homeostasis

Metabolic enzymes can influence chromatin organization by modulating the availability of key metabolites, yet how specific metabolic reactions affect chromatin function remains poorly understood. Here, we show that in Caenorhabditis elegans, the methionine-cycle enzyme methionine synthase reductase (MTRR-l/MSR) regulates heterochromatin independently of methionine synthesis. Loss of MTRR-1, but not of the methionine synthase METR-l/MS, specifically reduces heterochromatic histone methylation, derepresses repetitive elements, and causes developmental delay. Multi-omics profiling revealed that mtrr-1 mutants activate transcriptional programs associated with mitochondrial stress and accumulate long-chain acylcamitines, indicating disrupted mitochondrial homeostasis. Functional assays confirmed altered mitochondrial respiration in mtrr-1 mutants, while genetic suppression of the PMK-3/MAPK mitochondrial retrograde signaling pathway partially restored repeat silencing. Consistently, direct perturbation of mitochondrial function was sufficient to induce heterochromatin derepression in wild type animals. Together, our results reveal a previously unrecognized mitochondria-to-chromatin axis controlled by the methionine-cycle enzyme MTRR-l/MSR, demonstrating that mitochondrial homeostasis is required for heterochromatin maintenance independently of canonical methionine metabolism.

cell biology↗

bioRxiv2025

Regulatory logic of human cortex evolution by combinatorial perturbations

Comparative genomic studies between contemporary and extinct hominins revealed key evolutionary modifications, but their number has hampered a system level investigation of their combined roles in scaffolding modern traits. Through multi-layered integration we selected 15 genes carrying nearly fixed sapiens-specific protein-coding mutations and developed a scalable design of combinatorial CRISPR-Cas9 bidirectional perturbations to uncover their regulatory hierarchy in cortical brain organoids. Interrogating the effects of overexpression and downregulation for all gene pairs in all possible combinations, we defined their impact on transcription and differentiation and reconstructed their regulatory architecture. We uncovered marked cell type-specific effects, including the promotion of alternative fates and the emergence of interneuron populations, alongside a core subnetwork comprising KIF15, NOVA1, RB1CC1 and SPAG5 acting as central regulator across cortical cell types.

systems biology↗

bioRxiv2025

Disruption of ADNP-KDM1A-GTF2I complex drives neural differentiation imbalance in Helsmoortel-Van der Aa syndrome

Mutations in ADNP (Activity-Dependent Neuroprotective Protein) are among the most frequent monogenic causes of autism spectrum disorder (ASD) and lead to Helsmoortel-Van der Aa syndrome (HVDAS). Yet how ADNP dysfunction leads to HVDAS is unclear. We employed patient-derived induced pluripotent stem cells, cortical organoids and ADNP KO human neural stem cells (hNSCs) to clarify the cellular and molecular mechanism of HVDAS onset. We purified an ADNP-KDM1A-GTF2I (AKG) protein complex from hNSCs and show that it targets transposable elements (TEs) to repress nearby gene transcription. Upon ADNP KO, KDM1A binding is lost at promoters targeted by AKG, pointing to ADNP as the anchoring subunit of the AKG complex. HVDAS cortical organoids show impaired progenitor proliferation and accelerated neuronal differentiation, coupled with a sustained upregulation of neurogenesis transcriptional programs, including key transcription factors normally repressed by AKG. This work suggests that the AKG complex acts as the relevant ADNP unit in the molecular onset of HVDAS.

neuroscience↗

bioRxiv2024

YY1 mutations disrupt corticogenesis and cytoarchitecture through a cell-type specific rewiring of cell-autonomous and non-cell-autonomous transcriptional programs

Germline mutations of YY1 cause Gabriele-de Vries syndrome (GADEVS), a neurodevelopmental disorder featuring intellectual disability and a wide range of systemic manifestations. To dissect the cellular and molecular mechanisms underlying GADEVS, we combined large-scale imaging, single-cell multiomics and gene regulatory network reconstruction in 2D and 3D patient-derived physiopathologically relevant cell lineages. YY1 haploinsufficiency causes a pervasive alteration of cell type specific transcriptional networks, disrupting corticogenesis at the level of neural progenitors and terminally differentiated neurons, including cytoarchitectural defects reminiscent of GADEVS clinical features. Transcriptional alterations in neurons propagated to neighboring astrocytes through a major non-cell autonomous pro-inflammatory effect that grounds the rationale for modulatory interventions. Together, neurodevelopmental trajectories, synaptic formation and neuronal-astrocyte cross talk emerged as salient domains of YY1 dosage-dependent vulnerability. Mechanistically, cell-type resolved reconstruction of gene regulatory networks uncovered the regulatory interplay between YY1, NEUROG2 and ETV5 and its aberrant rewiring in GADEVS. Our findings underscore the reach of advanced in vitro models in capturing developmental antecedents of clinical features and exposing their underlying mechanisms to guide the search for targeted interventions.

neuroscience↗