Biology subjects

Navarrete, C.

Publications and source records attributed to Navarrete, C..

9 recordsLinked to original sources

bioRxiv2025

Diversity and evolution of chromatin regulatory states across eukaryotes

Histone post-translational modifications (hPTMs) are key regulators of chromatin states1,2, influencing gene expression, epigenetic memory, and transposable element repression across eukaryotic genomes. While many hPTMs are evolutionarily conserved3, the extent to which the chromatin states they define are similarly preserved remains unclear. Here, we developed a combinatorial indexing ChIP-seq method to simultaneously profile specific hPTMs across diverse eukaryotic lineages4, including amoebozoans, rhizarians, discobans, and cryptomonads. Our analyses revealed highly conserved euchromatin states at active gene promoters and gene bodies. In contrast, we observed diverse configurations of repressive heterochromatin states associated with silenced genes and transposable elements, characterized by various combinations of hPTMs such as H3K9me3, H3K27me3 and/or different H3K79 methylations. These findings suggest that while core hPTMs are ancient and broadly conserved, their functional readout has diversified throughout eukaryotic evolution, shaping lineage-specific chromatin landscapes.

evolutionary biology↗

bioRxiv2024

Adenine DNA methylation associated to transcription is widespread across eukaryotes

DNA methylation in the form of 5-methylcytosine (5mC) is widespread in eukaryotes, while the presence of N6-methyladenine (6mA) has sparked considerable debate. Methodological disparities in quantifying and mapping 6mA in genomic DNA have fueled this controversy. Yet, the distantly related early branching fungi, ciliates and the algae Chlamydomonas reinhardtii exhibit robust 6mA methylation patterns, but the origin and evolution of 6mA remain unknown. Here we use Oxford Nanopore modified base calling to profile 6mA at base pair resolution in 18 unicellular eukaryotes spanning all major eukaryotic supergroups. Our results reveal that only species encoding the adenine methyltransferase AMT1 display robust genomic 6mA patterns. Notably, 6mA consistently accumulates downstream of transcriptional start sites, aligning with H3K4me3-enriched nucleosomes, suggesting a conserved role in placing transcriptionally permissive nucleosomes. Intriguingly, the recurrent loss of the 6mA pathway across eukaryotes, particularly in major multicellular lineages, implies a convergent alteration in the dual methylation system of the Last Eukaryotic Common Ancestor, which featured transcription-associated 6mA and repression-associated 5mC.

genomics↗

bioRxiv2024

Etrinabdione (VCE-004.8), a B55a activator, promotes angiogenesis and arteriogenesis in critical limb ischemia.

BackgroundVasculogenic therapies explored for the treatment of peripheral artery disease (PAD) have encountered minimal success in clinical trials. Addressing this, B55, an isoform of protein phosphatase 2A (PP2A), emerges as pivotal in vessel remodeling through activation of hypoxia-inducible factor 1 (HIF-1). This study delves into the pharmacological profile of VCE-004.8 (Etrinabdione) and evaluates its efficacy in a preclinical model of critical limb ischemia, with a focus on its potential as a PP2A/B55 activator to induce angiogenesis and arteriogenesis. MethodsVascular endothelial cells were used for in vitro experiments. Aorta ring assay was performed to explore sprouting activity. Matrigel plug-in assay was used to assess the angiogenic potential. Critical limb ischemia (CLI) in mice was induced by double ligation in the femoral arteria. Endothelial vascular and fibrotic biomarkers were studied by immunohistochemistry and qPCR. Arteriogenesis was investigated by microvascular casting and micro-CT. Proteomic analysis in vascular tissues was analyzed by LC-MS/MS. Ex-vivo expression of B55 and biomarkers were investigated in artery samples from PAD patients. ResultsVCE-004.8 exhibited the ability to induce B55 expression and activate the intersecting pathways B55/AMPK/Sirtuin 1/eNOS and B55/PHD2/HIF-1. VCE-004.8 prevented OxLDL and H2O2-induced cytotoxicity, senescence, and inflammation in endothelial cells. Oral VCE-004.8 increased aorta sprouting in vitro and angiogenesis in vivo. In CLI mice VCE-004.8 improved collateral vessel formation and induced endothelial cells proliferation, angiogenic gene expression and prevented fibrosis. The expression of B55, Caveolin 1 and Sirtuin-1 is reduced in arteries from CLI mice and PAD patient, and the expression of these markers was restored in mice treated with VCE-004.8. ConclusionsThe findings presented in this study indicate that Etrinabdione holds promise in mitigating endothelial cell damage and senescence, while concurrently fostering arteriogenesis and angiogenesis. These observations position Etrinabdione as a compelling candidate for the treatment of PAD, and potentially other cardiovascular disorders. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSO_LIThe phosphatase PPA2/B55 stabilizes endothelial cells (ECs) in response to cell stress conditions, thereby protecting ECs from apoptosis and promoting angiogenesis. C_LIO_LIEtrinabdione (VCE-004.8) functions as a potent activator of PPA2/B55 inducing PHD2 dephosphorylation at ser125 and fostering HIF activation. C_LIO_LIVCE-004.8 prevents vascular damage in preclinical models of systemic and cardiac fibrosis and alleviates blood-brain barrier disruption in neuroinflammatory conditions. C_LIO_LIVCE-004.8 is also a dual agonist of PPAR{psi} and CB2 receptors and shows antiinflammatory activity. C_LIO_LIOral VCE-004.8 has meet the primary endpoints of safety and tolerability in a Phase IIa clinical trial with systemic sclerosis patients (clinicaltrial.gov: NCT03745001). C_LI What New Information Does This Article Contribute?O_LIEtrinabdione induces HIF-1 expression in endothelial cells through a novel pathway that potentially involves two axes: B55/PHD2 and B55/AMPK/Sirt1 signaling that may converge on HIF stabilization. C_LIO_LIEtrinabdione prevented endothelial cell damage and senescence, while inducing arteriogenesis and angiogenesis in CLI mice. C_LIO_LIIn arteries of patients with PAD and in CLI mouse models, the expression levels of B55, Caveolin 1, and Sirtuin 1 are diminished. However, treatment with Etrinabdione specifically in CLI mice prompts an increase in the levels of these proteins. C_LIO_LIEtrinabdione triggers neovascularization and angiogenesis specifically within hypoxic tissue in a critical ischemia model, with no impact on healthy tissue. C_LI

pharmacology and toxicology↗

bioRxiv2022

High-throughput screening of a Debaryomyces hansenii library for potential candidates with improved stress tolerance and wider carbon utilisation capabilities

Industrial biotechnology comprises the manufacturing of bulk chemicals and high-value end-products from renewable feedstocks, thus it presents a valuable aspect in the present transition from traditional-resource demanding manufacturing to sustainable solutions. The non-conventional yeast Debaryomyces hansenii encompasses halotolerant characteristics that ensures its use in industrial applications, and hence, its industrial importance. For this purpose, a comprehensive and holistic understanding of its behaviour and response to abiotic stresses is essential. Through high-throughput screening methods, using advanced robotics and automation devices, the present study enlightens intraspecies behavioural characteristics of novel D. hansenii strains in response to sodium, as well as their ability to tolerate abiotic stress in semi-controlled micro-fermentations and spot-test studies. A significantly improved performance under those abiotic stresses was observed under the presence of 1M NaCl. Moreover, a positive and summative effect on growth was also found in pH 4 and high salt content. Our results align with previous findings suggesting the halophilic (and not just halotolerant) behaviour of D. hansenii, which is now extensive to all the D. hansenii strains included in this study. Strain-specific differential responses to the presence of sodium were also observed, with some strains exerting a more notable induction by the presence of salt than the standard strain (CBS767). Furthermore, our study provides indications of the use of D. hansenii in industrial bioprocesses based on lignocellulosic biomass and non-lignocellulosic feedstocks.

microbiology↗

bioRxiv2021

Comparative proteogenomics deciphers the origin and evolution of eukaryotic chromatin

Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically-comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in Archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (e.g., methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.

evolutionary biology↗

bioRxiv2021

Adar-mediated A-to-I editing is required for establishment of embryonic body axes in zebrafish

Adenosine deaminases (ADARs) catalyze the deamination of adenosine to inosine, also known as A-to-I editing, in RNA. Although A-to-I editing occurs widely across animals, and is well studied, new biological roles are still being discovered. Here, we study the role of A-to-I editing in early zebrafish development. We demonstrate that Adar, the zebrafish orthologue of mammalian ADAR1, is essential for establishing the antero-posterior and dorso-ventral axes and patterning. Genome-wide editing discovery revealed pervasive editing in maternal and the earliest zygotic transcripts, the majority of which occurred in the 3-UTR. Interestingly, transcripts implicated in gastrulation as well as dorso-ventral and antero-posterior patterning were found to contain multiple editing sites. Adar knockdown or overexpression affected gene expression and global editing patterns at 12 hpf, but not earlier. Our study established that RNA editing by Adar is necessary for the earliest steps of embryonic patterning along the zebrafish antero-posterior and dorso-ventral axes.

developmental biology↗

bioRxiv2020

A Physiological Characterization in Controlled Bioreactors Reveals a Novel Survival Strategy for Debaryomyces hansenii at High Salinity and Confirms its Halophilic Behavior

Debaryomyces hansenii is traditionally described as a halotolerant non-conventional yeast, being the model organism for the study of osmo- and salt tolerance mechanisms in eukaryotic systems for the past 30 years. However, unravelling of D. hanseniis biotechnological potential has always been difficult due to the persistent limitations in the availability of efficient molecular tools described for this yeast. Additionally, there is a lack of consensus and contradictory information along the recent years that limits a comprehensive understanding of its central carbon metabolism, mainly due to a lack of physiological studies in controlled and monitored environments. Moreover, there is controversy about the diversity in the culture conditions (media composition, temperature and pH among others) used by different groups, which makes it complicated when trying to get significant conclusions and behavioural patterns. In this work, we present for the first time a physiological characterization of D. hansenii in batch cultivations using highly instrumented and controlled lab-scale bioreactors. Our findings contribute to a more complete picture of the central carbon metabolism and the external pH influence on the yeast ability to tolerate high Na+ and K+ concentrations. Finally, the controversial halophilic/halotolerant character of this yeast is further clarified.

microbiology↗

bioRxiv2019

Age-dependent loss of mitochondrial DNA integrity in mammalian muscle

Ribonucleotides (rNMPs) incorporated in the nuclear genome are a well-established threat to genome stability and can result in DNA strand breaks when not removed in a timely manner. However, the presence of a certain level of rNMPs is tolerated in mitochondrial DNA (mtDNA), although aberrant mtDNA rNMP content has been identified in disease models. We investigated the effect of incorporated rNMPs on mtDNA stability over the mouse lifespan and found that the mtDNA rNMP content increased during early life. The rNMP content of mtDNA varied greatly across different tissues and was defined by the rNTP/dNTP ratio of the tissue. Accordingly, mtDNA rNMPs were nearly absent in SAMHD1-/- mice that have increased dNTP pools. The near absence of rNMPs did not, however, appreciably affect mtDNA copy number or the levels of mtDNA molecules with deletions or strand breaks in aged animals near the end of their lifespan. The physiological rNMP load therefore does not contribute to the progressive loss of mtDNA quality that occurs as mice age.

molecular biology↗

bioRxiv2019

Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci

Understanding how genetic regulatory variation affects gene expression in different T cell states is essential to deciphering autoimmunity. We conducted a high-resolution RNA-seq time course analysis of stimulated memory CD4+ T cells from 24 healthy individuals. We identified 186 genes with dynamic allele-specific expression, where the balance of alleles changes over time. These genes were four fold enriched in autoimmune loci. We found pervasive dynamic regulatory effects within six HLA genes, particularly for a major autoimmune risk gene, HLA-DQB1. Each HLA-DQB1 allele had one of three distinct transcriptional regulatory programs. Using CRISPR/Cas9 genomic editing we demonstrated that a single nucleotide variant at the promoter is causal for T cell-specific control of HLA-DQB1 expression. Our study in CD4+ T cells shows that genetic variation in cis regulatory elements may affect gene expression in a lymphocyte activation status-dependent manner contributing to the inter-individual complexity of immune responses.

genomics↗