Biology subjects

Navarro, L.

Publications and source records attributed to Navarro, L..

At least 19 recordsLinked to original sources

bioRxiv2026

A reproducible buccal transcriptomic response to music exposure in autism spectrum disorder: insights into the oral-brain axis

Music-based interventions (MIs) have shown promise in autism spectrum disorder (ASD), yet the molecular mechanisms underlying their effects remain poorly understood. The transcriptomic response to music exposure in individuals with ASD and healthy controls (HCs) was analyzed using buccal swab samples and a targeted NanoString gene expression panel. The discovery cohort included baseline and post-intervention samples, whereas the validation cohort added a 25-minute intermediate sample to assess transcriptional dynamics. Thirty-three candidate genes were identified in the discovery cohort, of which 20 (61%) remained significantly differentially expressed in the independent validation cohort, including 13 that withstood multiple-testing correction. Replicated genes included several key regulators of innate immunity and inflammatory signaling, such as CXCL8, MYD88, RELA, PTGS2, PTPRC, SELL, LYN, and LTBR. Functional enrichment analyses revealed robust innate immune and inflammatory pathways, characterized by TLR/IL-1-MYD88 signaling, cytokine activity, leukocyte activation, and antimicrobial responses. Co-expression network analysis identified coordinated remodeling of immune transcriptional programs in ASD. Consensus feature selection identified a two-gene signature that accurately discriminated pre- and post-musical stimulation samples in ASD but not in HCs. The same signature detected transcriptomic responses after only 25 minutes of music exposure by discriminating baseline and intermediate samples, with intermediate expression levels between baseline and post-intervention values, suggesting a progressive duration-dependent response. These findings demonstrate a reproducible transcriptional response to music in ASD across independent cohorts implicating neuroimmune pathways. The resulting transcriptional signature supports the development of minimally invasive biomarkers for monitoring MIs in neurodevelopmental disorders.

genomics↗

bioRxiv2026

Benchmarking long-read RNA sequencing for de novo transcriptome assembly in non-model plant species: insights from Moricandia arvensis

De novo transcriptome assembly is the standard approach for constructing a reference transcriptome in non-model plants that lack a high-quality genome, yet short-read assemblies struggle to resolve full-length isoforms. Long-read Iso-Seq (PacBio) captures full-length transcripts directly, but its use as a primary reference and the choice of downstream assembly pipeline remains poorly benchmarked. Here, we construct genome-free Iso-Seq reference transcriptomes for two organs, flower and leaf, of the non-model species Moricandia arvensis (L.) DC. (Brassicaceae), and systematically compare pipeline strategies combining Iso-Seq clustering, CD-HIT redundancy reduction, and Cogent graph-based reconstruction, benchmarked by BUSCO completeness, RSEM short-read mapping, and TransDecoder ORF completeness. We find that the optimal pipeline is organ specific. For flower, CD-HIT pre-filtering followed by Cogent reconstruction produced a high-quality reference (95.3% BUSCO complete). For the leaf, the same Cogent step was detrimental, reducing BUSCO completeness from 90.1% to 78.0% by incorrectly merging distinct genes; therefore, CD-HIT at 95% identity without reconstruction was retained. We trace this divergence to organ-specific input-data characteristics: leaf transcripts show extreme full-length-read expression skew and predominantly single-isoform gene support, depriving Cogent's graph algorithm of the multi-isoform evidence it requires. We find that the concentration of full-length reads among the most highly expressed transcripts predicts pipeline suitability before reconstruction, with per-transcript read depth acting as a necessary but non-discriminating floor. Because the leaf reference lacked gene-level structure, we further recovered gene-isoform grouping using expression-aware read-clustering (Corset), which preserved completeness while restoring the paralog structure expected of a paleopolyploid genome and outperformed sequence-only clustering. Our results provide a robust, genome-free framework for constructing full-length reference transcriptomes in non-model plant species and demonstrate that pipeline choice must be evaluated per organ rather than assuming one size fits all.

bioinformatics↗

bioRxiv2026

Plant-parasitic nematode microRNAs hijack plant AGO1 to induce host-cell reprogramming

Cross-kingdom RNA interference (ckRNAi) is emerging as a mode of inter-organismal gene regulation, yet mechanistic examples in plant-metazoan interactions remain limited. Here, we demonstrate miRNA-driven ckRNAi in the nematode-plant pathosystem. Root-knot nematodes are among the most destructive plant pathogens, reprogramming root tissues to develop into galls containing multinucleated, hypermetabolic giant feeding cells essential for parasitism. AGO1-associated small-RNA immunoprecipitation (AGO1-RIP) from tomato galls revealed the selective in planta loading of 10 M. incognita miRNAs into host AGO1. Integrating degradome profiling, target prediction, and dual-luciferase reporter assays, we validated miRNA-directed silencing of nine tomato transcripts by four secreted nematode miRNAs. These targets map to major pathway classes involved in immune signaling, metabolic regulation, and cellular reprogramming linked to feeding-site establishment. Functional analyses further show that the nematode-secreted miR-2b is enhances giant feeding cell development. Comparative AGO1-RIP in Arabidopsis thaliana identified a conserved subset of AGO1-loaded nematode miRNAs, including miR-2b and miR-100, consistent with shared small-RNA effectors across hosts. Finally, the overlap between AGO1-loaded miRNA families and helminth secreted small-RNA repertoires supports evolutionary convergence on RNA-based virulence strategies. Collectively, our findings establish miRNA-mediated ckRNAi as a mechanistic component of plant-root-knot nematode interactions and provide a framework for leveraging RNA-based vulnerabilities for nematode control.

plant biology↗

bioRxiv2025

Decoding the peripheral transcriptomic and meta-genomic response to music in Autism Spectrum Disorder via saliva-based RNA sequencing

Saliva-based RNA sequencing (RNA-seq) poses technical challenges due to high bacterial content, RNA degradation, and sample heterogeneity. This study investigates the transcriptional effects of music exposure in individuals with autism spectrum disorder (ASD) using this non-invasive approach. To address saliva-specific limitations, we employed two complementary library preparation methods, Poly-A selection and Human-Enriched protocols, allowing us to maximize human transcript detection and ensure reproducibility. By merging them, we ensured reproducibility and captured both host and microbial signals. While each dataset individually revealed a limited number of differentially expressed genes (DEGs), their integration enhanced biological resolution. Among the consistently modulated genes were HERC6, TSPAN5, and REM2, pointing to music-induced transcriptional changes relevant to neurodevelopmental and immune processes. Functional enrichment analyses highlighted pathways involved in immune regulation, oxidative phosphorylation, and epithelial differentiation. These findings align with evidence of immune dysregulation, mitochondrial dysfunction, and altered cellular communication in ASD. Importantly, co-expression network analysis identified modules significantly correlated with music exposure. Notably, the AKNA module, previously associated with ASD risk, was downregulated and enriched for Ras-related GTPase signaling and immune pathways, suggesting that music may modulate intracellular signaling and inflammation. Conversely, upregulation of the UBE2D3 module pointed to activation of endoplasmic reticulum stress response mechanisms, a known contributor to ASD neurodevelopmental deficits. These results suggest that music engages specific stress-adaptive and immunomodulatory networks in buccal cells, potentially reflecting systemic effects. Our exploratory metagenomic analysis highlights 15 microbial species with consistent abundance shifts across both methods. Notably, Acidipropionibacterium acidipropionici and Propionibacterium freudenreichii, associated with propionic acid production, emerged as music-responsive taxa. Elevated propionic acid has been implicated in ASD-like behaviors and neuroinflammation, suggesting a microbiota-mediated pathway. Music may influence both host gene expression and oral microbiota, potentially affecting neuroimmune processes via the microbiota-brain axis. Although exploratory, the results support the feasibility of using saliva for integrated molecular profiling in ASD.

genomics↗

bioRxiv2025

Can music modulate gene expression involved in traumatic brain injury? An integrative transcriptomic and epigenomic proof of concept

Music-based interventions have shown promise in aiding recovery in individuals with brain damage (BD), including acquired and traumatic brain injury (ABI and TBI). To investigate the underlying molecular mechanisms, we conducted a proof-of-concept study integrating transcriptomic and epigenomic data. We compared gene expression changes driven by musical stimuli in healthy individuals exposed to music with transcriptomic data from TBI patients, identifying 154 common differentially expressed genes (DEGs) affected in TBI and impacted by music, including STK35, HNRNPA0, MT-CYB, and MT-ND2. These genes are notably involved in mitochondrial function, synaptic plasticity, and neurodegenerative processes. Epigenomic analysis revealed that 92 of these DEGs also exhibited significant differential methylation in TBI samples, particularly in genes associated with neurodevelopment, neuroinflammation, and mood regulation. Pathway enrichment and cross-validation in independent datasets of TBI patients highlighted the cGMP- PKG signaling pathway, a key regulator of memory and plasticity. Co-expression network analysis further revealed six gene modules significantly associated with TBI, including modules centered on TXNIP and ALG13, genes previously implicated in neuroinflammation and epilepsy, two conditions commonly associated with TBI. Interestingly, several hub genes from these modules also showed sensitivity to musical stimuli, suggesting that music may target biologically relevant networks involved in TBI pathology. These findings provide preliminary evidence that music exposure may modulate gene expression and methylation in ways that support neural repair and functional recovery. This molecular insight reinforces the potential of music as a biologically grounded component of neurorehabilitation. Future studies should directly assess transcriptomic and epigenomic responses to music-based interventions in BD patients.

genomics↗

bioRxiv2025

A pre-loaded and assembled human Ago2-miRISC orchestrates Shigella-induced vacuolar rupture through the targeting of RhoGDIα

The enteroinvasive bacterium Shigella flexneri causes bacillary dysentery. It invades intestinal epithelial cells and forms a bacterium-containing vacuole, which it rapidly ruptures to reach the cytosol. Here, we found that human Argonaute 2 (Ago2), the central component of miRNA-induced silencing complex (miRISC), positively regulates early steps of Shigella infection, including vacuolar rupture. This is consistent with the rapid recruitment of Ago2 at Shigella entry foci. The ability of Ago2 to form an assembled miRISC was found required for vacuolar maturation, while its slicer activity is dispensable for this process. Furthermore, we found that the RhoGTPase inhibitor RhoGDI is targeted by specific miRNAs, pre-loaded in Ago2, which, collectively, accelerate vacuolar rupture. Therefore, a pre-loaded and assembled Ago2-miRISC orchestrates vacuolar maturation by targeting RhoGDI. These findings may have wider implications in the understanding of how stored Ago2-loaded miRNAs control immediate steps of infection, prior to the differential expression of microbe-responsive miRNAs.

molecular biology↗

bioRxiv2024

Monocytes Mobilized by Gut Neurons Remodel the Enteric Nervous System

The proper organization of the enteric nervous system (ENS) is critical for normal gastrointestinal (GI) physiology. Inflammatory bowel disease (IBD) dysregulates GI physiology, including bowel movements (motility), but in many IBD patients, GI motility disorders persist in remission through a poorly understood pathological process. Here we uncover that post-inflammatory GI dysmotility (PI-GID) stems from structural ENS remodeling driven by a combination of neuronal loss and neurogenesis. Enteric neurons respond to mucosal inflammation by upregulating CCL2 expression and facilitating the recruitment of CCR2+ monocytes into the neural myenteric plexus within the intestinal muscle. This is followed by the expansion of monocyte-derived macrophages and their migration into the myenteric ganglia and phagocytosis of neurons. However, excessive recruitment of monocytes results in disproportionate ENS remodeling and PI-GID. The expansion of inflammatory cells is known to promote tissue hypoxia. We find that enteric neurons become hypoxic upon colitis, but hypoxia-induced signaling via HIF1 initiates an adaptation program in enteric neurons to attenuate CCL2 expression and limit monocyte recruitment. We demonstrate that reinforcing HIF1 signaling in enteric neurons prevents PI-GID by reducing colitis-associated monocyte recruitment in the myenteric plexus and protecting against ENS remodeling. In summary, our findings unveil PI-GID pathogenesis and identify a regulatory axis for its prevention. One Sentence SummaryIntestinal mucosal inflammation engages enteric neurons in the inflammatory response leading to neurogenic recruitment of monocytes into the extra-mucosal myenteric plexus followed by pathological structural remodeling of the enteric nervous system by monocyte-derived macrophages.

immunology↗

bioRxiv2024

Music elicits different gene expression responses in the buccal cavity of age-related cognitive disorders patients and healthy controls

Recent evidence suggests that external stimuli can shape transcriptomes (sensogenomics). Specifically, the analysis of capillary blood samples has shown that musical stimuli can modulate gene expression patterns, in healthy individuals but also in those with age-related cognitive disorders (ACD), based on. Here, we present groundbreaking evidence indicating that brief exposure to music can also impact the salivary transcriptome in both healthy donors and ACD patients. Our findings reveal that music has a more pronounced effect on patients compared to controls, inducing global gene expression changes towards upregulation in ACD patients but downregulation in controls. The most significantly dysregulated genes in ACD patients include LGALS3 (downregulated) and CXCL8 (upregulated), whereas in controls, THOP1 was the top significant gene (downregulated). These genes play important roles in normal brain functions and are also altered in neurodegenerative conditions. Weighted Gene Co-expression Network Analysis reveals relevant and significant modules, both positive and negative correlated with music, implicated in neurodegenerative (e.g. autophagy) and immunological processes (e.g. IL-1, MHC). This sheds light on the complex interplay between music and molecular responses in the human body. This study underscores the potential of musical stimuli to influence gene expression patterns outside of systemic circulation, paving the way for further exploration of musics therapeutic effects. Sensogenomics Working GroupAntonio Salas Ellacuriaga - PI; Federico Martinon-Torres - PI; Laura Navarro Ramon - Coordinator GenPoB/GenVip - Instituto de Investigacion Sanitaria (IDIS) (alphabetic order)Alba Camino Mera, Albert Padin Villar, Alberto Gomez Carballa, Alejandro Perez Lopez, Alicia Carballal Fernandez, Ana Cotovad Bellas, Ana Isabel Dacosta Urbieta, Narmeen Mallah, Ana Maria Pastoriza Mourelle, Ana Maria Senin Ferreiro, Andres Muy Perez, Antia Rivas Oural, Antonio Justicia Grande, Antonio Pineiro Garcia, Anxela Cristina Delgado Garcia, Belen Mosquera Perez, Blanca Diaz Esteban, Carlos Duran Suarez, Carmen Curros Novo, Carmen Gomez Vieites, Carmen Rodriguez-Tenreiro Sanchez, Celia Varela Pajaro, Claudia Navarro Gonzalo, Cristina Seren Trasorras, Cristina Talavero Gonzalez, Eines Monteagudo Vilavedra, Estefania Rey Campos, Esther Montero Campos, Fernando Alvez Gonzalez, Fernando Caamano Vinas, Francisco Garcia Iglesias, Gloria Viz Rodriguez, Hugo Alberto Tovar Velasco, Irene Alvarez Rodriguez, Irene Garcia Zuazola, Irene Rivero Calle, Iria Afonso Carrasco, Isabel Ferreiros Vidal, Isabel Lista Garcia, Isabel Rego Lijo, Ivan Prieto Gomez, Ivan Quintana Cepedal, Jacobo Pardo Seco, Jesus Eiris Punal, Jose Gomez Rial, Jose Manuel Fernandez Garcia, Jose Maria Martinon Martinez, Julia Cela Mosquera, Julia Garcia Curras, Julian Montoto Louzao, Lara Martinez Martinez, Laura Navarro Marron, Lidia Pineiro Rodriguez, Lorenzo Redondo Collazo, Lua Castelo Martinez, Lucia Company Arciniegas, Luis Crego Rodriguez, Luisa Garcia Vicente, Manuel Vazquez Donsion, Maria Dolores Martinez Garcia, Maria Elena Gamborino Carames, Maria Elena Sobrino Fernandez, Maria Jose Curras Tuala, Maria Martinez Leis, Maria Soledad Vilas Iglesias, Maria Sol Rodriguez Calvo, Maria Teresa Autran Garcia, Marina Casas Perez, Marta Aldonza Torres, Marta Bouzon Alejandro, Marta Lendoiro Fuentes, Miriam Ben Garcia, Miriam Cebey Lopez, Montserrat Lopez Franco, Nour El Zahraa Mallah, Narmeen Mallah, Natalia Garcia Sanchez, Natalia Vieito Perez, Patricia Regueiro Casuso, Ricardo Suarez Camacho, Rita Garcia Fernandez, Rita Varela Estevez, Rosaura Picans Leis, Ruth Barral Arca, Sandra Carnota Antonio, Sandra Viz Lasheras, Sara Pischedda, Sara Rey Vazquez, Sonia Marcos Alonso, Sonia Seren Fernandez, Susana Rey Garcia, Vanesa Alvarez Iglesias, Victoria Redondo Cervantes, Vanesa Alvarez Iglesias, Wiktor Dominik Nowak, Xabier Bello Paderne, Xabier Mazaira Lopez Nursing volunteers (alphabetic order)Alejandra Fernandez Mendez, Ana Isabel Abadin Campana, Ana Maria Leon Caamano, Ana Maria Buide Illobre, Angeles Mera Cores, Carmen Nieves Vastro, Carolina Suarez Crego, Concepcion Rey Iglesias, Cristina Candal Regueira, Dolores Barreiro Puente, Elvira Rodriguez Rodriguez, Eugenia Gonzalez Budino, Eva Rey Alvarez, Fernando Rodriguez Gerpe, Gemma Albela Silva, Isabel Castro Perez, Isabel Dominguez Rios, Jose Angel Fernandez de la Iglesia, Jose Cruces Vazquez, Jose Luis Cambeiro Quintela, Jose Ramon Magarinos Iglesias, Julia Rey Brandariz, Julio Abel Fernandez Lopez, Luisa Garcia Vicente, Manuel Gonzalez Lito, Manuel Gonzalez Lijo, Manuela Perez Rivas, Margarita Turnes Paredes, Maria Aurora Mendez Lopez, Maria Begona Tome Arufe, Maria Campos Torres, Maria del Carmen Baloira Nogueira, Maria del Carmen Garcia juan, Maria Esther Moricosa Garcia, Maria Luz Chao Jarel, Maria Martinez Leis, Maria Mercedes Jimenez Santos, Maria Salome Buide Illobre, Maria Victoria Lopez Pereira, Mercedes Jorge Gonzalez, Mercedes Isolina Rodriguez Rodriguez, Miren Payo Puente, Natalia Carter Dominguez, Olga Maria Reyes Gonzalez, Pilar Mera Rodriguez, Purificacion Sebio Brandariz, Salome Quintans lago, Yolanda Rodriguez Taboada, Maria Pereira Grau. Other volunteers (alphabetic order)Alba Arias Gomez, Alejandro Moreno Diaz, Ana Arca Maran, Astro Gonzalez Guirado, Brais Garcia Iglesias, Carlos Sanchez Rubin, Carmen Otero de Andres, Clara Perez Errazquin Barrera, Claudia Rey Posse, Cristina Rojas Garcia, Eduardo Xavier Gimenez Bargiela, Elena Gloria Morales Garcia, Fabio Izquierdo Garcia Escribano, Gabriel Guisande Garcia, Jaime Lopez Martin, Lara Pais Ramiro, Lucia Rico Montero, Luis Estevez Martinez, Manuel Estevez Casal, Maria Aranzazu Palomino Cano, Maria Rubio Valdes, Marisol Nogales Benitez, Miryam Tilve Perez, Nuria Villar Muinos, Pablo Del Cerro Rodriguez, Pablo Pozuelo Martinez Cardenoso, Salma Ouahabi El Ouahabi, Santiago Vazquez Calvache

genomics↗

bioRxiv2023

Tuning gene expression to music: the compensatory effect of music on age-related cognitive disorders

Extensive literature has explored the beneficial effects of music in age-related cognitive disorders (ACD), but limited knowledge exists regarding its impact on gene expression. We analyzed transcriptomes of ACD patients and healthy controls, pre-post a music session (n=60), and main genes/pathways were compared to those dysregulated in mild cognitive impairment (MCI) and Alzheimers disease (AD) as revealed by a multi-cohort study (n=1269 MCI/AD and controls). Music was associated with 2.3 times more whole-genome gene expression, particularly on neurodegeneration-related genes, in ACD than controls. Co-expressed gene-modules and pathways analysis demonstrated that music impacted autophagy, vesicle and endosome organization, biological processes commonly dysregulated in MCI/AD. Notably, the data indicated a strong negative correlation between musically-modified genes/pathways in ACD and those dysregulated in MCI/AD. These findings highlight the compensatory effect of music on genes/biological processes affected in MCI/AD, providing insights into the molecular mechanisms underlying the benefits of music on these disorders.

genomics↗

bioRxiv2022

Arabidopsis hydathodes are sites of intense auxin metabolism and nutrient scavenging

Hydathodes are small organs located on the leaf margins of all vascular plants. They release excess xylem sap through guttation when stomata are closed or when the humidity level is high. Many promoter analyses have suggested other hydathode functions in metabolite transport and auxin metabolism, but experimental demonstration is still lacking. Here, we compared the transcriptomic and metabolomic features of mature Arabidopsis hydathodes to the leaf blade. 1460 differentially-expressed genes were identified revealing that genes related to auxin metabolism, transport, stress, DNA, plant cell wall, RNA or wax were on average more expressed in hydathodes. On the other hand, genes involved in glucosinolate metabolism, sulfation pathway, metal handling or photosynthesis were downregulated in hydathodes. In hydathodes, there are an increased expression of auxin transcriptional regulators and biosynthetic genes, a lower expression of auxin transport genes and a differential expression of genes related to its vacuolar storage that is consistent with increased contents of free and conjugated auxin. We also found that ca. 78% of the total content of 52 xylem sap metabolites were removed from guttation fluid at the hydathode level. Using reverse genetics, we showed that the capture of nitrate and phosphate in the guttation fluid relies on the NRT2.1 and PHT1;4 transporters, respectively. Thus, hydathodes absorb a significant part of xylem sap nutrients, limiting the loss of valuable chemicals during guttation. Our transcriptomic and metabolomic analyses reveal an organ with its own transcriptomic and physiological identity and highlight hydathode biological processes that may impact the whole plant. One sentence summaryTranscriptome and physiological analysis of mature and healthy hydathodes of Arabidopsis demonstrates that those organs are sites of intense auxin metabolism and nutrient scavenging

plant biology↗

bioRxiv2022

A Legionella pneumophila effector impedes host gene silencing to promote virulence

RNA silencing is a gene silencing mechanism directed by small RNAs. Human miRNAs act as central regulators of host-bacteria interactions. However, it is unknown whether human pathogenic bacteria could impede RNA silencing to promote virulence. Here, we show that the Legionella pneumophila type IV-secreted effector LegK1 efficiently suppresses siRNA and miRNA activities in human cells. This effect depends on its known kinase activity, but also on its novel capacity, found here, to bind Argonaute (Ago) proteins. We further demonstrate that the ability of LegK1 to activate NF-{kappa}B signaling is required for RNA silencing suppression, establishing a link between effector-mediated NF-{kappa}B signaling and RNA silencing suppression. LegK1 also promotes L. pneumophila growth in both amoeba and human macrophages, supporting a role for this effector in virulence. Finally, we show that, in infected-macrophages, the latter activity relies, in part, on the genetic targeting of human Ago4. These findings indicate that a L. pneumophila effector has evolved to suppress RNA silencing to promote virulence. Significance StatementIt is now well established that mammalian viruses suppress RNAi to promote their replication in host cells. However, whether mammalian pathogenic bacteria use a similar virulence strategy remains unknown. Here, we show that the LegK1 effector from Legionella pneumophia, the causal agent of Legionnaires disease, efficiently suppresses RNAi in human cells. This effect depends on its ability to interact with Argonaute (Ago) proteins and to activate NF-{kappa}B signaling. In addition, LegK1 promotes virulence in infected-macrophages through the genetic targeting of human Ago4. Based on the lack of NF-{kappa}B-related factors in amoebae, and on the presence of canonical Ago proteins in these natural L. pneumophila hosts, we propose that the RNAi suppression activity of LegK1 represents its primary virulence function.

molecular biology↗

bioRxiv2022

DNA methylation at a single cytosine embedded in the W-box cis-element repels binding of WRKY transcription factors through steric hindrance

Previously, we showed that the Arabidopsis active demethylase ROS1 prunes DNA methylation at the promoters of a subset of immune-responsive genes to facilitate their transcriptional activation during antibacterial defence (Halter et al., 2021). In particular, ROS1 was shown to demethylate the RLP43 promoter in a region carrying a functional W-box cis-element, thereby ensuring a tight binding of WRKY transcriptional factors (TFs) onto DNA. Here, we first extend these findings by showing that DNA methylation at W-box elements decreases the binding of several Arabidopsis WRKY TFs in vitro. Furthermore, we provide evidence that DNA methylation at a single cytosine located in the W-box of the RLP43 promoter strongly repels DNA binding of an Arabidopsis WRKY TF in vitro. Using structural modelling, we demonstrate that this cytosine interacts through van der Waals contacts with the conserved tyrosine of WRKY DNA binding domains. Significantly, our model predicts steric hindrance when a 5-methyl group is present on this specific cytosine, thereby likely preventing tight binding of WRKY DNA binding domains. Finally, because the WRKY motif and the residues involved in DNA contacts are conserved, we propose that this methylation-dependent WRKY-DNA binding inhibitory mechanism must be widespread across plant species.

plant biology↗

bioRxiv2021

Phenotypic plasticity triggers rapid morphological convergence

Phenotypic convergence, the independent evolution of similar traits, is ubiquitous in nature, happening at all levels of biological organizations and in most kinds of living beings. Uncovering its mechanisms remains a fundamental goal in biology. Evolutionary theory considers that convergence emerges through independent genetic changes selected over long periods of time. We show in this study that convergence can also arise through phenotypic plasticity. We illustrate this idea by investigating how plasticity drives Moricandia arvensis, a mustard species displaying within-individual polyphenism in flowers, across the morphological space of the entire Brassicaceae family. By compiling the multidimensional floral phenotype, the phylogenetic relationships, and the pollination niche of over 3000 Brassicaceae species, we demonstrated that Moricandia arvensis exhibits a plastic-mediated within-individual floral disparity greater than that found not only between species but also between higher taxonomical levels such as genera and tribes. As a consequence of this divergence, M. arvensis moves outside the morphospace region occupied by its ancestors and close relatives, crosses into a new region where it encounters a different pollination niche and converges phenotypically with distant Brassicaceae lineages. Our study suggests that, by inducing phenotypes that explore simultaneously different regions of the morphological space, plasticity triggers rapid phenotypic convergence.

evolutionary biology↗

bioRxiv2020

The Arabidopsis demethylase ROS1 cis-regulates defense genes by erasing DNA methylation at promoter-regulatory regions

Active DNA demethylation has emerged as an important regulatory process of plant and mammalian immunity. However, very little is known about the mechanisms by which active demethylation controls transcriptional immune reprogramming and disease resistance. Here, we first show that the Arabidopsis active demethylase ROS1 promotes basal resistance towards Pseudomonas syringae by antagonizing RNA-directed DNA methylation (RdDM). Furthermore, we found that ROS1 facilitates the flagellin-triggered induction of the disease resistance gene RMG1 by limiting RdDM at the 3 boundary of a remnant RC/Helitron transposable element (TE) embedded in its promoter. We further identify flagellin-responsive ROS1 putative primary targets, and show that at a subset of promoters, ROS1 erases methylation at discrete regions exhibiting WRKY transcription factors (TFs) binding. In particular, we demonstrate that ROS1 removes methylation at the orphan immune receptor RLP43 promoter, to ensure DNA binding of WRKY TFs. Finally, we show that ROS1-directed demethylation of the RMG1 and RLP43 promoters is causal for both flagellin responsiveness of these genes and for basal resistance. Overall, these findings significantly advance our understanding of how active demethylases shape transcriptional immune reprogramming to enable antibacterial resistance. HIGHLIGHTSO_LIThe TNL RMG1 that is regulated by ROS1 positively regulates basal resistance towards Pto DC3000 C_LIO_LIROS1 regulates the flg22-triggered differential expression of more than 2000 thousands genes, among which 10% are demethylated by ROS1 C_LIO_LIROS1 facilitates the transcriptional activation of a subset of flg22-induced genes by antagonizing RdDM at discrete promoter regions C_LIO_LIWRKY transcription factors (TFs) bind to the demethylated promoter regions of a subset of flg22-induced ROS1 targets C_LIO_LIThe hypermethylation at the RLP43 promoter, caused by the lack of ROS1, repels DNA binding of two PAMP-responsive WRKY TFs C_LIO_LISpecific hypermethylation at the ROS1-targeted promoter regions of RMG1 and RLP43 is causal for their silencing as well as for disease susceptibility against Pto DC3000 C_LI

genomics↗

bioRxiv2020

Low ribosomal RNA genes copy number provoke genomic instability and chromosomal segment duplication events that modify global gene expression and plant-pathogen response

Among the hundreds of ribosomal RNA (rRNA) gene copies organized as tandem repeats in the nucleolus organizer regions (NORs), only a portion is usually actively expressed in the nucleolus and participate in the ribosome biogenesis process. The role of these extra-copies remains elusive, but previous studies suggested their importance in genome stability and global gene expression. Because the nucleolus is also a platform for nuclear organization, we tested the impact of a decreased amount of rRNA gene copies on the Arabidopsis thaliana 3D genome organization and stability, using an A. thaliana line only containing 20% of rRNA gene copies (20rDNA line). Compared to the wild-type Col-0, the 20rDNA line shows several signs of genomic instability, such as variations in 3D genome organization, spontaneous double-strand breaks accumulation, transcriptomic changes, and higher DNA methylation level. Strikingly, using genomic and microscopic approaches, we identified seven large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. As a consequence, more than 600 genes were duplicated, often associated with an increase in their expression level. Among them, we found several upregulated genes involved in plant-pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and we discuss their potential implications on plant genome evolution.

plant biology↗

bioRxiv2019

Polycomb Repressive Complex 2 antagonizes linker DNA methylation and chromatin compaction in Arabidopsis thaliana

In plants and mammals, DNA methylation is a hallmark of transposable element (TE) sequences that contributes to their epigenetic silencing. In contrast, histone H3 lysine 27 trimethylation (H3K27me3), which is deposited by the Polycomb Repressive Complex 2 (PRC2), is a hallmark of repressed genes. Nevertheless, there is a growing body of evidence for a functional interplay between these pathways. In particular, many TE sequences acquire H3K27me3 when they lose DNA methylation and it has been proposed that PRC2 can serve as a back-up silencing system for hypomethylated TEs. Here, we describe in the flowering plant Arabidopsis thaliana the gain of H3K27m3 at hundreds of TEs in the mutant ddm1, which is defective in the maintenance of DNA methylation specifically over TE and other repeat sequences. Importantly, we show that this gain essentially depends on CURLY LEAF (CLF), which is one of two otherwise partially redundant H3K27 methyltransferases active in vegetative tissues. Finally, our results challenge the notion that PRC2 can be a compensatory silencing system for hypomethylated TEs, as the complete loss of H3K27me3 in ddm1 clf double mutant plants was not associated with further reactivation of TE expression nor with a burst of transposition. Instead, and surprisingly, ddm1 clf plants exhibited less activated TEs, and a chromatin recompaction as well as hypermethylation of linker DNA compared to ddm1. Thus, we have described an unexpected genetic interaction between DNA methylation and Polycomb silencing pathways, where a mutation in PRC2 does not aggravate the molecular phenotypes linked to TE hypomethylation in ddm1 but instead partially suppresses them. Author summaryEpigenetic marks are covalent modifications of the DNA or its associated proteins (Histones) that impact gene expression in a heritable manner without changing DNA sequence. In plants and mammals, DNA methylation and trimethylation of Lysine 27 of Histone 3 (H3K27me3) are two conserved, major epigenetic systems that mediate the transcriptional silencing of transposons (invasive mobile genetic elements) and of developmental genes respectively. However, in the absence of DNA methylation, H3K27me3 marks can be recruited to transposons, suggesting that the two silencing systems can be compensatory. To test this hypothesis, we analyzed a compound DNA methylation and H3K27me3 mutant of the plant model Arabidopsis thaliana (importantly, mammals harboring equivalent mutations would not be viable). First, this approach allowed us to gain mechanistic insights into the recruitment of H3K27me3 at transposons. Furthermore, we also showed that transposon silencing release in the DNA methylation mutant was not enhanced, contrary to our initial hypothesis, but, surprisingly, partially suppressed by a mutation in H3K27me3 deposition. Thus, our genomic analysis revealed an unexpected and antagonistic genetic interaction between two major silencing pathways whose interplay is at the heart of many biological processes, including cancer.

molecular biology↗

bioRxiv2018

Biodiversity trends are stronger in marine than terrestrial assemblages

Human activities have fundamentally altered biodiversity. Extinction rates are elevated and model projections suggest drastic biodiversity declines. Yet, observed temporal trends in recent decades are highly variable, despite consistent change in species composition. Here, we uncover clear spatial patterns within this variation. We estimated trends in the richness and composition of assemblages in over 50,000 time-series, to provide the most comprehensive assessment of temporal change in biodiversity across the planet to date. The strongest, most consistent pattern shows compositional change dominated by species turnover, with marine taxa experiencing up to fourfold the variation in rates of change of terrestrial taxa. Richness change ranged from no change to richness gains or losses of ~10% per year, with tropical marine biomes experiencing the most extreme changes. Earth is undergoing a process of spatial reorganisation of species and, while few areas are unaffected, biodiversity change is consistently strongest in the oceans.

ecology↗

bioRxiv2018

The geography of the Anthropocene differs between the land and the sea

O_LIClimate change and other anthropogenic drivers of biodiversity change are unequally distributed across the world. The geographic patterns of different drivers, and the spatial overlap among these drivers, have important implications for the direction and pace of biodiversity change, yet are not well documented. Moreover, it is unknown if the geographic patterns of drivers differ between the terrestrial and marine realm, as expected due to marked differences in how humans interact with the land and ocean. C_LIO_LIWe compiled global gridded datasets on climate change, land-use, resource exploitation, pollution, species invasions, and human population density. We used multivariate statistics to examine the spatial relationships among the datasets and to characterize the typical combinations of drivers experienced by different parts of the world. C_LIO_LIWe found stronger positive correlations among drivers in the terrestrial than in the marine realm, leading to areas of high intensities of multiple drivers on land. Climate change tended to be negatively correlated with other drivers in the terrestrial realm (e.g., in the tundra and boreal forest with high climate change but low human use and pollution) whereas the opposite was true in the marine realm (e.g., in the Indo-Pacific with high climate change and high fishing). C_LIO_LIWe show that different regions of the world can be defined by anthropogenic threat complexes (ATCs), distinguished by different sets of drivers with varying intensities. The ATCs can be used to test hypothesis about the pattern of biodiversity change, especially the joint effects of multiple drivers. More generally, our global analysis highlights the broad conservation priorities needed to mitigate the effects of anthropogenic change on biodiversity responses, with different priorities emerging on land and in the ocean, and in different parts of the world. C_LI

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