Biology subjects

Mariotti, M.

Publications and source records attributed to Mariotti, M..

12 recordsLinked to original sources

bioRxiv2026

Regulatory landscape of widespread stop codon readthrough in Drosophila

In stop codon readthrough (SCR), ribosomes continue to translate past the stop. While programmed SCR is rare in mammals, it appears remarkably widespread in insects, yet its regulation and biological significance remain poorly understood. Here, we systematically characterize SCR in Drosophila melanogaster by integrating ribosome profiling, comparative genomics, proteomics, and functional screening. We identify [~]1,400 SCR genes, reveal sequence features associated with programmed SCR, and distinguish constitutive and tissue-restricted modes. We identify conserved cis-elements sufficient to stimulate constitutive SCR and demonstrate that many remain functional in mammalian cells. Unexpectedly, the major distinction between insect and mammalian cells was not termination efficiency, but insect responsiveness to SCR-promoting regulatory elements. SCR was further associated with increased overall protein output, suggesting a function beyond proteome diversification. Our results establish SCR as a pervasive regulatory mechanism in Drosophila and provide a new framework for its study through the Drosophila Stop Codon Readthrough Atlas.

genomics↗

bioRxiv2025

Pyranges v1: a Python framework for ultrafast sequence interval operations

Sequence interval algebra is key to modern bioinformatics. Pyranges v1 offers a Python Pandas-based interface to a comprehensive palette of Rust-powered operations (e.g., overlap, count, slice intervals), enabling the intuitive development of efficient pipelines for diverse sequence data, including gene annotations, mapped reads, and protein domains. Pyranges is faster, consumes less memory, and offers more functionalities than alternative tools including BEDTools, emerging as an innovative one-stop shop for omics analysis.

bioinformatics↗

bioRxiv2025

An updated view of the vertebrate selenoproteome reveals convergent depletions in tetrapods and expansions in ray-finned fishes

Selenoproteins incorporate the rare selenium-containing amino acid selenocysteine (Sec) and play crucial roles for redox homeostasis, stress response, and hormone regulation. Sec is inserted by co-translational recoding of the UGA codon, normally a stop. As a consequence, selenoproteins are often misannotated in public databases and require specialized bioinformatic methods and resources. Here, we present a refined characterization of the composition and evolution of the vertebrate selenoproteome. Based on analyses of 19 gene families across hundreds of genomes, we show that extant selenoproteomes were shaped by extensive gene duplications (56 selenoproteins), losses (50), and Sec-to-cysteine (Cys) conversions (21). Tetrapods including mammals encode 24-25 selenoproteins, with variations in 6 families. Notably, the same genes underwent convergent evolutionary events in multiple tetrapods, namely Sec-to-Cys substitutions (SELENOU1, GPX6) and gene losses (SELENOV). In contrast, ray-finned fish exhibit larger and more dynamic selenoproteomes, reinforcing the hypothesis that the selective advantage of Sec is stronger in aquatic environments. We detected selenoprotein duplications spread across the actinopterygian clade involving 13 families, mainly involved in antioxidant defense. The richest selenoproteomes were found in Salmonidae and Cyprinoidei fish with 56 and 44 selenoproteins, respectively, owing to whole genome duplications. Among our findings, the SELENOP family stands out in lampreys, carrying up to an unprecedented 162 UGAs putatively recoded to Sec. Our study presents the most comprehensive evolutionary map of vertebrate selenoproteins to date and delineates the specific selenoproteome of each lineage, establishing a foundational framework for selenium biology research in the era of biodiversity genomics.

evolutionary biology↗

bioRxiv2024

Overcoming the widespread flaws in the annotation of vertebrate selenoprotein genes in public databases

Selenocysteine (Sec) is a non-canonical amino acid incorporated into selenoproteins, oxidoreductase enzymes carrying essential roles in redox homeostasis. Sec insertion occurs in response to UGA, normally interpreted as stop codon, but recoded in selenoprotein mRNAs. Owing to the dual function of UGA, the identification of selenoprotein genes poses a challenge. We show that the vertebrate selenoprotein genes are widely misannotated in major public databases. Only 12% and 6% of selenoprotein genes are well annotated in Ensembl and NCBI GenBank, respectively, due to the lack of dedicated selenoprotein annotation pipelines. In most cases (81% and 84%), overlapping flawed annotations are present which lack the Sec-encoding UGA. In contrast, NCBI RefSeq employs a dedicated selenoprotein pipeline, yet with some shortcomings: its selenoprotein annotations are correct in 76% of cases, and most errors affect families with a C-terminal Sec residue. We argue that selenoproteins must be correctly annotated in public databases and that must occur via automated pipelines, to keep the pace with genome sequencing. To facilitate this task, we present a new version of Selenoprofiles, an homology based tool for selenoprotein prediction that produces predictions with accuracy comparable to manual curation, and can be easily deployed and integrated in existing annotation pipelines.

bioinformatics↗

bioRxiv2022

Deterioration of the human transcriptome with age due to increasing intron retention and spurious splicing

Adult aging is characterized by a progressive deterioration of biological functions at physiological, cellular and molecular levels, but its damaging effects on the transcriptome are not well characterized. Here, by analyzing splicing patterns in [~]1,000 human subjects sampled across multiple tissues, we found that splicing fidelity declines with age. Most prominently, genuine introns fail to be spliced out, manifesting as a broad surge in intron retention, and this is exacerbated by the increase in diverse spurious exon-exon junctions with age. Both of these effects are prominently detected in the majority of human tissues. Collectively, they result in the progressive deterioration of the active transcriptome, wherein functional mRNAs are increasingly diluted with non-functional splicing isoforms. We discuss the concept of "splicing damage" and formulate methods to quantify it. Using these tools, we show that splicing damage increases both with age and with the incidence of diseases. Altogether, this work uncovers transcriptome damage as a critical molecular indicator of human aging and healthspan.

genomics↗

bioRxiv2021

TXNRD3 supports male fertility via the redox control of spermatogenesis

Thioredoxin/glutathione reductase (TGR, TXNRD3) is a thiol oxidoreductase of unknown function composed of thioredoxin reductase and glutaredoxin domains. This NADPH-dependent enzyme evolved by gene duplication within the Txnrd family, is expressed in the testes and can reduce both thioredoxin and glutathione in vitro. To characterize the function of TXNRD3 in vivo, we generated a strain of mice with the deletion of Txnrd3 gene. We show that Txnrd3 knockout mice are viable and without discernable gross phenotypes, but TXNRD3 deficiency leads to fertility impairment in male mice. Txnrd3 knockout animals exhibit a lower fertilization rate in vitro, a sperm movement phenotype and an altered redox status of thiols. Proteomic analyses revealed a broad range of substrates reduced by TXNRD3 during sperm maturation, presumably as a part of quality control. The results show that TXNRD3 plays a critical role in male reproduction via the thiol redox control of spermatogenesis.

biochemistry↗

bioRxiv2021

Naked mole-rat hematopoietic stem and progenitors are highly quiescent with an inherent myeloid bias

Naked mole-rats (NMRs) are the longest-lived rodents yet their stem cell characteristics remain enigmatic. Here we comprehensively mapped the NMR hematopoietic landscape and identified unique features likely contributing to longevity. Adult NMRs form red blood cells in spleen and marrow, which is a neotenic trait. A myeloid bias towards granulopoiesis in concert with decreased B-lymphopoiesis defines the marrow composition, resembling fetal leukopoiesis. Very similar to primates, the primitive stem cell compartment is marked by CD34 and THY1. Remarkably, stem and progenitor respiration rates are as low as in human cells, while NMR cells show a strong expression signature for fatty acid metabolism. The pool of quiescent stem cells is higher than in mice, and the cell cycle of hematopoietic cells is prolonged. Our work provides a platform to study immunology and stem cell biology in an animal model of exceptional longevity. TeaserJuvenile features of hematopoiesis shape the blood system of the longest-lived rodent.

cell biology↗

bioRxiv2021

Aging predisposes B cells to malignancy by activating c-Myc and perturbing the genome and epigenome

While cancer is an age-related disease, many cancer studies utilize younger animal models. Here, we uncover how a cancer, B-cell lymphoma, develops as a consequence of a naturally aged system. We show that this malignancy is associated with increased cell size, splenomegaly, and a newly discovered age-associated clonal B-cell (ACBC) population. Driven by exogenous c-Myc activation, hypermethylated promoters and somatic mutations, ACBC cells clonally expand independent of germinal centers (IgM+) and show increased biological age and hypomethylation in partially methylated domains related to mitotic solo-CpGs. Epigenetic changes in transformed mouse B cells are enriched for changes observed in human B-cell lymphomas. Mechanistically, the data suggest that cancerous ACBC cells originate from age-associated B cells, in part involving CD22 protein signaling fostered by the aging microenvironment. Transplantation assays demonstrate that ACBC evolve to become self-sufficient and support malignancy when transferred into young recipients. Inhibition of mTOR or c-Myc in old mice attenuates premalignant changes in B cells during aging and emerges as a therapeutic strategy to delay the onset of age-related lymphoma. Together, we show how aging contributes to B-cell lymphoma through a previously unrecognized mechanism involving cell-intrinsic changes and the aged microenvironment, characterize a model that captures the origin and progression of spontaneous cancer during aging and identify candidate interventions against age-associated lymphoma.

cancer biology↗

bioRxiv2019

The tuatara genome: insights into vertebrate evolutionfrom the sole survivor of an ancient reptilian order

The tuatara (Sphenodon punctatus), the only living member of the archaic reptilian order Rhynchocephalia (Sphenodontia) once widespread across Gondwana, is an iconic and enigmatic terrestrial vertebrate endemic to New Zealand. A key link to the now extinct stem reptiles from which dinosaurs, modern reptiles, birds and mammals evolved, the tuatara provides exclusive insights into the ancestral amniotes. The tuatara genome, at [~]5 Gbp, is among the largest vertebrate genomes assembled. Analysis of this genome and comparisons to other vertebrates reinforces the uniqueness of the tuatara. Phylogenetic analyses indicate tuatara diverged from the snakes and lizards [~]250 MYA. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Genome sequence analysis identifies expansions of protein, non-protein-coding RNA families, and repeat elements, the latter of which show an extraordinary amalgam of reptilian and mammalian features. Sequencing of this genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. It also provides important insights into both the technical challenges and the cultural obligations associated with genome sequencing.

genomics↗

bioRxiv2019

The hematopoietic landscape at single-cell resolution reveals unexpected stem cell features in naked mole-rats

Naked mole-rats are the longest-lived rodents endowed with resistance to cancer and age-related diseases, yet their stem cell characteristics remain enigmatic. We profiled the naked mole-rat hematopoietic system down to single-cell resolution, and identified several unique features likely contributing to longevity. In adult naked mole-rats red blood cells are formed in spleen and marrow, a neotenic feature beneficial for hypoxic environments and to prevent anemia. Platelet numbers are lower compared to short-lived mice, which may preclude age-related platelet increase and thrombosis. T cells mature in thymus and lymph nodes, providing a supply of T cells after age-related thymus involution. The pool of quiescent stem cells is higher than in mice, and HSCs overexpress an oxidative phosphorylation signature, revealing a new paradigm of stem cell metabolism to benefit longevity and oppose oncogenesis. Our work provides a platform to study immunology and stem cell biology in an animal model of healthy aging. HIGHLIGHTSO_LIFlow cytometry labelling panel to purify viable naked mole-rat HSPCs C_LIO_LIThe spleen as the major site of erythropoiesis in the naked mole-rat C_LIO_LINaked mole-rats show extrathymic T-cell development under homeostatic conditions C_LIO_LINaked mole-rat hematopoietic stem cells (HSCs) have high OXPHOS activity C_LI

immunology↗

bioRxiv2018

Use of selenocysteine, the 21st amino acid, in the fungal kingdom

Selenoproteins are a diverse class of proteins containing selenocysteine (Sec), the 21st amino acid, incorporated into proteins during translation through a unique recoding mechanism. Selenoproteins fulfil essential roles in several lineages, including vertebrates; yet, they are not ubiquitous across the tree of life. In particular, the fungal kingdom was thought to lack selenoproteins, a paradigm that we defy here. We show that the genetic machinery for Sec utilization is present in the genomes of five species belonging to diverse early-branching fungal phyla (Chytridiomycota, Zoopagomycota, and Mucoromycota). We identified several selenoprotein genes in each of these genomes, and we detected canonical Sec insertion RNA structures (SECIS elements) for some of them. The identified selenoproteins are known or predicted oxidoreductases, some of which are conserved in mammals. Phylogenetic analyses support a scenario of vertical inheritance of the Sec trait within eukaryotes and fungi. Sec was then lost in numerous independent events in various fungal lineages, even within Sec-containing phyla. Notably, Sec was lost at the base of Dikarya, resulting in the absence of this trait in Saccharomyces cerevisiae and other well studied fungi. Our results indicate that, despite scattered occurrence, selenoproteins are found in all kingdoms of life.

genomics↗

bioRxiv2017

The Spectral Features Of EEG Responses To Transcranial Magnetic Stimulation Of The Primary Motor Cortex Depend On The Amplitude Of The Motor Evoked Potentials

Transcranial magnetic stimulation (TMS) of the primary motor cortex (M1) can excite both cortico-cortical and cortico-spinal axons resulting in TMS-evoked potentials (TEPs) and motor-evoked potentials (MEPs), respectively. Despite this remarkable difference with other cortical areas, the influence of motor output and its amplitude on TEPs is largely unknown. Here we studied TEPs resulting from M1 stimulation and assessed whether their waveform and spectral features depend on the MEP amplitude. To this aim, we performed two separate experiments. In experiment 1, single-pulse TMS was applied at the same supra-threshold intensity on primary motor, prefrontal, premotor and parietal cortices and the corresponding TEPs were compared by means of local mean field power and time-frequency spectral analysis. In experiment 2 we stimulated M1 at resting motor threshold in order to elicit MEPs characterized by a wide range of amplitudes. TEPs computed from high-MEP and low-MEP trials were then compared using the same methods applied in experiment 1. In line with previous studies, TMS of M1 produced larger TEPs compared to other cortical stimulations. Notably, we found that only TEPs produced by M1 stimulation were accompanied by a late ([~]300 ms after TMS) event-related desynchronization (ERD), whose magnitude was strongly dependent on the amplitude of MEPs. Overall, these results suggest that M1 produces peculiar responses to TMS possibly reflecting specific anatomo-functional properties, such as the re-entry of proprioceptive feedback associated with target muscle activation.

neuroscience↗