Biology subjects

Medrano, M.

Publications and source records attributed to Medrano, M..

12 recordsLinked to original sources

bioRxiv2026

Transgenerational imprint of subindividual variation: somatic epigenetic divergence within trees cascades into epigenetic and phenotypic pollen divergence

The evolutionary significance of somatic mosaicism created within plants by random epigenetic drift or localized responses to the environment will rest on its transgenerational implications. This paper tests whether the epigenetic mosaicism exhibited by individuals of a long-lived tree leaves some discernible "imprint" in the next gametophytic generation. Paired samples of leaves and pollen from five distinct branches within each of five wild-growing Pistacia terebinthus (Anacardiaceae) trees were characterized epigenetically using genome-wide DNA cytosine methylation level and multivariate epigenetic fingerprinting. Pollen grains were also characterized phenotypically by size and shape. Individual trees were somatically heterogeneous with regard to both cytosine methylation level and multilocus epigenetic fingerprints of leaf tissue, and within-tree variance in leaf epigenetic features exceeded among-tree variance. Phenotypic and epigenetic features of pollen differed significantly among branches of individual trees, and intraplant variation in phenotype and epigenetic fingerprints of pollen was predicted by intraplant variation in epigenetic features of leaves. Results provide evidence that intraindividual epigenetic heterogeneity arising in long-lived plants can leave its imprint into subsequent sporophyte generations via the production of epigenetically and phenotypically heterogeneous haploid gametophytes. Testable hypotheses for future epigenetic research on wild populations of non-model plants are suggested.

Plant Biology↗

bioRxiv2025

Understanding epigenetic regulation in non-model plants: Transcriptomic responses to seed demethylation in leaves and roots of the annual herb Erodium cicutarium (Geraniaceae)

Epigenetic regulation has emerged as a significant element in adaptation to heterogeneous and stressful environments, with modifications in DNA methylation being particularly relevant in plants. DNA methylation inhibitors have been used to investigate the relationship between DNA methylation and plastic plant phenotypes. However, their effect in gene expression regulation along lifetime remains understudied in non-model plants. Here, we analyze the effects of seed exposure to 5-azacytidine (5-azaC) in plant gene regulation. Scarified seeds from a single inbred line of Erodium cicutarium were soaked for 48 h in either water or a low concentration solution of 5-azaC before sowing. Subsequently, RNA was extracted from juvenile roots, juvenile leaves and adult leaves, and their transcriptomes were sequenced. Differential gene expression analysis was performed between treatments (control vs. treated) for all tissues together and separately. Beforehand, a draft genome of E. cicutarium was assembled to use it as reference for the transcriptome analysis, and its DNA methyltransferase genes were characterized. We found that 5-azaC up-regulated chromomethylase CMT1 across all treated samples, and the domain rearranged DNA methyltransferase DRM2 in juvenile roots. Furthermore, adult leaves showed more differentially expressed genes between control and 5-azaC treated samples compared to juvenile leaves, supporting long term transcriptomic effects of a short exposure to 5-azaC at seed germination. At adult stage, leaves of individuals treated with 5-azaC exhibited up-regulation of genes involved in seed dormancy release, photoinhibition, and osmotic stress. Finally, gene co-expression network analysis revealed a module of co-expressed genes with differential gene expression linked to 5-azaC treatment in juvenile roots, that was enriched with genes involved in retrotransposon activity and in anthocyanin metabolism. Altogether, this study illustrates how the experimental treatment with 5-azaC at seed stage generates tissue- and age-specific transcriptional shifts, directly affecting gene regulation and potentially broadening phenotype variation in this fast-growing annual plant.

genomics↗

bioRxiv2025

Somatic epigenetic mosaicism within Pistacia terebinthus (Anacardiaceae) trees leaves signature in reproductive cells

Propagation of epimutations over the branching topology of individuals often produces epigenetic mosaicism in long-lived plants, but whether such epigenetic mosaics can bear some evolutionary relevance remains largely unknown. We test here whether epigenetic reprogramming during gametogenesis completely erases intraplant epigenetic variation or, alternatively, some "signature" of the somatic mosaicism persists into reproductive cells. Intraplant variation in global cytosine methylation of leaf and pollen DNA samples was studied in five adult males of the dioecious tree Pistacia terebinthus (Anacardiaceae). Paired samples of fresh expanding leaves and pollen grains were taken from five different twigs in each tree, and percent cytosine methylation estimated using HPLC. Trees were internally heterogeneous in global cytosine methylation of both leaf and pollen. Within-tree variance accounted for 49.7% and 30.5% of population-wide variance in methylation for leaves and pollen, respectively. Tree means and within-tree variances in pollen methylation were directly correlated, respectively, with tree means and within-tree variances in leaf methylation. As a consequence of the epigenetic variability accumulated in somatic tissues over the individual plants lifetimes being only weakly eroded by gametogenesis, intraplant epigenetic heterogeneity became a natural source of epigenetic gametic diversity in the wild-growing population of P. terebinthus trees studied.

evolutionary biology↗

bioRxiv2025

Prenatal alcohol exposure dysregulates the expression of clock genes and alters rhythmic behaviour in mice

Foetal Alcohol Spectrum Disorders (FASD) refer to a range of adverse physical, behavioural, and cognitive effects caused by perinatal alcohol exposure. While cognitive impairments are well-documented, FASD has also been associated with sleep disturbances and circadian rhythm disruptions. This study aimed to examine the effects of perinatal alcohol exposure on circadian rhythms at behavioural and gene expression levels across two developmental stages (adolescence and adulthood) in both, male and female mice. Using a validated prenatal and lactation alcohol exposure (PLAE) protocol, we assessed circadian patterns of locomotor activity under free-running conditions and spatial memory performance during adolescence and adulthood. Additionally, we evaluated the impact of PLAE on circadian expression of clock and non-circadian genes involved in neurotransmission across key brain regions, including the medial prefrontal cortex and hippocampus. PLAE altered circadian rhythmicity and impaired spatial memory. Gene expression analyses revealed disrupted oscillatory patterns in clock genes and in genes related to plasticity and cognition, including those from the expanded endocannabinoid system (e.g. Cnr1, Dagla, Faah) and other neurotransmitter systems (e.g. Oprm1, Slc17a8, Drd1, Gabra1). These findings underscore the impact of early alcohol exposure on biological rhythms and neurobehavioral function, highlighting circadian dysregulation as a contributing factor to FASD.

neuroscience↗

bioRxiv2024

Decoupled genetic and epigenetic variation at local scale in an endemic and a widespread Erodium (Geraniaceae) species

Epigenetic states offer an additional layer of variation besides genetic polymorphism that contribute to phenotypic variation and may arise either randomly or in response to environmental factors. We hypothesize that closely related species with different life-histories and habitat requirements could show distinct patterns of intraspecific epigenetic variation. We used Restriction-site Associated DNA sequencing (RADseq) and its bisulfite-converted variant (bsRADseq) to investigate in Sierra de Cazorla (SE Spain) the genetic and epigenetic population structure of two congeneric species, the endemic woody perennial Erodium cazorlanum and the widely distributed annual herb E. cicutarium. Population genomics analyses revealed no structure in either E. cazorlanum and E. cicutarium, suggesting substantial gene flow between the study populations. In contrast, we found that the mean proportion of global DNA methylation was different between populations and species, with E. cazorlanum DNA showing higher methylation average and across-individuals variation. For each species, we searched for the loci with the strongest epigenetic differentiation between populations (differentially methylated cytosines, DMCs), and summarized them across regions (differentially methylated regions, DMRs). Multivariate analysis and hierarchical clustering of single cytosines methylation percentages did not group individuals by population, pointing to high epigenetic variation within populations. DMRs were enriched in Copia transposable elements, putatively associated with stress response in plants. Our results suggest that variation at both genetic and epigenetic levels in our study area occur mainly within natural populations of E. cazorlanum and E. cicutarium, with stronger population structure in E. cicutarium, and highlight the relevance of analyzing short distance spatial patterns.

genomics↗

bioRxiv2024

A dynamic epigenetic perspective on above and below-ground phenotypic responses to drought: insights from global DNA methylation in Erodium cicutarium

O_LIPremise of the study. Mounting evidence supports the view that the responses of plants to environmental stress are mediated by epigenetic factors, including DNA methylation. Understanding the relationships between DNA methylation, plant development and individual fitness under contrasting environments is key to uncover the potential impact of epigenetic regulation on plant adaptation. Experimental approaches that combine a controlled alteration of epigenetic features with exposure to some relevant stress factor can contribute to this end. C_LIO_LIMethods. We combined the experimental application of a demethylating agent (5-azacytidine) with recurrent drought, and recorded their effects on above- and below-ground phenotypic traits related to early development, phenology and fitness in Erodium cicutarium from two provenances. C_LIO_LIKey results. We found that 5-azacytidine significantly reduced DNA methylation in leaf and root tissues. Moreover, it slowed plant development, delayed flowering, and reduced the number of inflorescences produced, and such detrimental effects occurred independently of water regime. Recurrent drought reduced final above- and below-ground biomass and total inflorescence production, and such negative effects were unaffected by artificial changes in DNA methylation. Increased fruit and seed-set were the only adaptive responses to drought observed in E. cicutarium, together with an increased number of flowers per inflorescence recorded in water stressed plants previously treated with 5-azacytidine. C_LIO_LIConclusion. Epigenetic effects can desynchronize plant growth, flowering and senescence among individual plants in both favourable and adverse environments. Future studies should focus on understanding intraspecific variation in the ability to change plant methylome in response to stress. C_LI

ecology↗

bioRxiv2023

Assessing the links between pollinators and the genetic and epigenetic features of plant species with contrasting distribution ranges

In flowering plants, pollinators contribute to gene flow while they also respond to variation in plant traits together determined by genetic, epigenetic and environmental sources of variation. Consequently, a correlation between abundance and diversity of pollinators and the genetic and epigenetic characteristics of plant populations such as diversity or distinctiveness is to be expected, yet no study has explored such long-term dimensions of plant-pollinator interactions. Mediterranean narrow endemics often exhibit unexpectedly high levels of population (epi)genetic diversity. We hypothesize that pollinators may contribute to explain this pattern. Specifically, we expect a stronger association of pollinators with population (epi)genetic variability in narrow endemics than in widely distributed congeners. We studied five pairs of congeneric plant species, consisting of one narrow endemic with a restricted distribution and one widespread congener, found in the Sierra de Cazorla mountains (SE Spain). In up to three populations per species, a comprehensive characterisation of pollinators was carried out to estimate pollinator diversity and visitation rate. Genetic and epigenetic diversity and distinctiveness of each population was calculated using AFLP markers and methylation-sensitive AFLP markers (MSAP) respectively. The relationships with pollinator diversity and visitation rate were assessed. The diversity of pollinators did not vary according to the plant distribution range, whereas visitation rate was higher in widespread species. As predicted, only narrow endemics showed a significant association between pollinators and their population genetic and epigenetic characteristics. Specifically, higher pollinator diversity and visitation rates entailed higher population genetic diversity and lower epigenetic distinctiveness. This work shows the value of exploring the relationships between pollinator abundance and diversity and population (epi)genetics for understanding the evolution of plant rarity.

ecology↗

bioRxiv2023

Comparative epigenetic and genetic spatial structure in Mediterranean mountain plants: a multispecific comparison

AO_SCPLOWBSTRACTC_SCPLOWEpigenetic information can be heritable, but also respond to key environmental variables in situ, endowing individuals with an additional capacity to adapt to environmental changes. Thus, it is likely that in sesile organisms such as plants, part of the spatial epigenetic variation found across individuals will reflect the environmental heterogeneity of populations. Analysing the departure of the spatial epigenetic structure from the baseline genetic variation can help in understanding the value of epigenetic regulation in species with different breath of optimal environmental conditions. We performed a multispecies study that considered seven pairs of congeneric plant species, each encompassing a narrow endemic with habitat specialization and a widespread species. In three populations per species we used AFLP and methylation-sensitive AFLP markers to characterise the spatial genetic and epigenetic structures. In contrast to widespread species, narrow endemics showed a significant and generalised lower epigenetic than genetic differentiation across species. Within most populations of narrow species, epigenetic variation was less spatially structured than the genetic variation. This pattern resulted from a lack of correlation between epigenetic and genetic information in populations of narrow endemics. We argue that the differences found between narrow endemics and widespread congeners reflect contrasting breaths of environmental requirements. We pose the hypothesis that in species with a narrow niche breath, epigenetic variation may be more similar across populations and among individuals within a population given the expected higher similarity in environmental requirements.

genetics↗

bioRxiv2023

The FAAH inhibitor URB597 reduces cocaine seeking during conditioned punishment and withdrawal

The endocannabinoid system is prominently implicated in the control of cocaine reinforcement due to its relevant role in synaptic plasticity and neurotransmitter modulation in the mesocorticolimbic system. The inhibition of fatty acid amide hydrolase (FAAH), and the resulting increase in anandamide and other N-acylethanolamines, represents a promising strategy for reducing drug seeking. In the present study, we aimed to assess the effects of the FAAH inhibitor URB597 (1 mg/kg) on crucial features of cocaine addictive-like behaviour in mice. Therefore, we tested the effects of URB597 on acquisition of cocaine (0.6 mg/kg/inf) self-administration, compulsive-like cocaine intake and cue-induced drug-seeking behaviour during withdrawal. URB597 reduced cocaine intake under conditioned punishment while having no impact on acquisition. This result was associated to increased cannabinoid receptor 1 gene expression in the ventral striatum and medium spiny neurons activation in the nucleus accumbens shell. Moreover, URB597 reduced cue-induced drug-seeking behaviour during prolonged abstinence and prevented the withdrawal-induced increase in FAAH gene expression in the ventral striatum. In this case, URB597 decreased activation of medium spiny neurons in the nucleus accumbens core. Our findings evidence the prominent role of endocannabinoids in the development of cocaine addictive-like behaviours and support the potential of FAAH inhibition as a therapeutical target for the treatment of cocaine addiction.

neuroscience↗

bioRxiv2023

Long-term methylome changes after experimental seed demethylation and their interaction with recurrent water stress in Erodium cicutarium (Geraniaceae)

O_LIThe frequency and length of drought periods are increasing in subtropical and temperate regions worldwide. Epigenetic responses to water stress could be key for plant resilience to this largely unpredictable challenge. Experimental DNA demethylation together with application of a stress factor stands as a suitable strategy to uncover the contribution of epigenetics to plant responses to stress. C_LIO_LIWe analysed leaf cytosine methylation changes in adult plants of the Mediterranean weed, Erodium cicutarium, after seed demethylation with 5-Azacytidine and/or recurrent water stress in a greenhouse. We used bisulfite RADseq (BsRADseq) and a newly reported reference genome for E. cicutarium to characterize methylation changes in a 2x2 factorial design, controlling for plant relatedness. C_LIO_LIIn the long-term, 5-Azacytidine treatment alone caused both hypo and hyper-methylation at individual cytosines, with substantial hypomethylation in CG contexts. In control conditions, drought resulted in a decrease in methylation level in all but CHH contexts. In contrast, the genome of plants that experienced recurrent water stress and had been treated with 5-Azacytidine increased DNA methylation level by ca. 5%. C_LIO_LISeed demethylation and recurrent drought exhibited a highly significant interaction in terms of global and context-specific cytosine methylation supporting an epigenetic contribution in response to stress at molecular level. C_LI

ecology↗

bioRxiv2023

Neuroanatomical characterization of the Nmu-Cre knock-in mice reveals an interconnected network of unique neuropeptidergic cells

Neuromedin U (NMU) is an evolutionary conserved neuropeptide that has been implicated in multiple processes, such as circadian regulation, energy homeostasis, reward processing and stress coping. Although central expression of NMU has been addressed previously, the lack of specific and sensitive tools has prevented a comprehensive characterization of NMU-expressing neurons in the brain. We have generated a knock-in mouse model constitutively expressing Cre recombinase under the Nmu promoter. We have validated the model using a multi-level approach based on quantitative reverse-transcription polymerase chain reactions, in situ hybridization, a reporter mouse line and an adenoviral vector driving Cre-dependent expression of a fluorescent protein. Using the Nmu-Cre mouse, we performed a complete mapping of NMU expression in adult mouse brain, unveiling a potential midline NMU modulatory circuit with the ventromedial hypothalamic nucleus (VMH) as a key node. Moreover, immunohistochemical analysis suggested that NMU neurons in the VMH mainly constitute a unique population of hypothalamic cells. Taken together, our results suggest that Cre expression in the Nmu-Cre mouse model largely reflects NMU expression in the adult mouse brain, without altering endogenous NMU expression. Thus, the Nmu-Cre mouse model is a powerful and sensitive tool to explore the role of NMU neurons in mice.

neuroscience↗

bioRxiv2018

Rare variants imputation in admixed populations: Comparison across reference panels and bioinformatics tools.

BackgroundImputation has become a standard approach in genome-wide association studies (GWAS) to infer in silico untyped markers. Although feasibility for common variants imputation is well established, we aimed to assess rare and ultra-rare variants imputation in an admixed Caribbean Hispanic population (CH). MethodsWe evaluated imputation accuracy in CH (N = 1,000), focusing on rare (0.1% [≤]minor allele frequency (MAF) [≤] 1%) and ultra-rare (MAF < 0.1%) variants. We used two reference panels, the Haplotype Reference Consortium (HRC; N = 27,165) and 1000 Genome Project (1000G phase 3; N = 2,504) and multiple phasing (SHAPEIT, Eagle2) and imputation algorithms (IMPUTE2, MACH-Admix). To assess imputation quality, we reported: a) high-quality variant counts according to imputation tools internal indexes (e.g. IMPUTE2 "Info"[≥]80%). b) Wilcoxon Signed-Rank Test comparing imputation quality for genotyped variants that were masked and imputed; c) Cohens kappa coefficient to test agreement between imputed and whole-exome sequencing (WES) variants; d) imputation of G206A mutation in the PSEN1 (ultra-rare in the general population an more frequent in CH) followed by confirmation genotyping. We also tested ancestry proportion (European, African and Native American) against WES-imputation mismatches in a Poisson regression fashion. ResultsSHAPEIT2 retrieved higher percentage of imputed high-quality variants than Eagle2 (rare: 51.02% vs. 48.60%; ultra-rare 0.66% vs 0.65%, Wilcoxon p-value < 0.001). SHAPEIT-IMPUTE2 employing HRC outperformed 1000G (64.50% vs. 59.17%; 1.69% vs 0.75% for high-quality rare and ultra-rare variants, respectively; Wilcoxon p-value < 0.001). SHAPEIT-IMPUTE2 outperformed MaCH-Admix. Compared to 1000G, HRC-imputation retrieved a higher number of high-quality rare and ultra-rare variants, despite showing lower agreement between imputed and WES variants (e.g. rare: 98.86% for HRC vs. 99.02% for 1000G). High Kappa (K = 0.99) was observed for both reference panels. Twelve G206A mutation carriers were imputed and all validated by confirmation genotyping. African ancestry was associated with higher imputation errors for uncommon and rare variants (p-value < 1e-05). ConclusionReference panels with larger numbers of haplotypes can improve imputation quality for rare and ultra-rare variants in admixed populations such as CH. Ethnic composition is an important predictor of imputation accuracy, with higher African ancestry associated with poorer imputation accuracy.

bioinformatics↗