Biology subjects

Fernandez, N.

Publications and source records attributed to Fernandez, N..

17 recordsLinked to original sources

bioRxiv2026

Celldega: Integrated Toolkit for Visualization and Analysis of Spatial Data

Spatial-transcriptomics integrates high-dimensional single-cell data with microscopy to reveal cellular states, communication, and tissue organization. Analyzing this data requires a combination of multi-modal data processing, high-dimensional data analysis, spatial analysis, and integrated visualization. However, computational analysis is increasingly becoming a bottleneck as approaches mature and dataset sizes increase. Additionally, visualization can be challenging as open-source visualization tools struggle to scale to large datasets (exceeding 1 billion transcripts), and commercial visualization tools are costly, closed source, and inflexible. We present Celldega, an open-source Python and JavaScript library for scalable, interactive visualization and analysis of spatial-omics data. Celldega integrates custom analyses, performs neighborhood analysis, implements an efficient visualization-specific file format, and enables interactive exploration in notebooks and web galleries. We demonstrate Celldega across multiple technologies, tissues, and datasets, including 3D reconstructions of the developing whole mouse head comprising over four million cells. Finally, we demonstrate how Celldega can be utilized throughout the entire lifecycle of spatial data analysis, from quality control to building a public shareable gallery.

bioinformatics↗

bioRxiv2026

The Hidden Costs of Climate Change Tracking: Climate Velocity, Movement Energetics, and Connectivity in European Protected Areas

Rapid climate change is reducing the capacity of protected areas (PAs) to conserve biodiversity, but exposure metrics alone do not show whether species can reach areas where suitable climates persist. We developed a climate-informed connectivity framework integrating climate velocity, PA climatic residence time, PA size, and functional connectivity based on energetics-informed resistance surfaces from species distribution models. Using high-resolution climate projections and omnidirectional connectivity modelling across Europe, we show that climate-tracking opportunities are more limited and spatially uneven than structural connectivity alone suggests. Small, climate-exposed PAs are especially vulnerable because they provide little internal climatic buffering and are often embedded in landscapes with low movement feasibility, whereas larger and more climatically stable PAs are more often situated in landscapes that can support redistribution. These findings provide a spatially explicit basis for restoration and conservation planning to maintain the functionality of PA networks under future climate change. TeaserMany European protected areas are too isolated, climate-exposed, and energy-constrained to support climate-tracking connectivity.

ecology↗

bioRxiv2025

Glycolysis and hexosamine biosynthesis pathways are key for inflammatory protein maturation and leukocyte adhesion to human aortic valve cells

Inflammation and metabolism reprogramming are hallmarks of calcific aortic valve disease (CAVD). Recent studies link inflammation to hyperglycolysis and calcification in valve interstitial cells (VICs). The metabolism of valve endothelial cells (VECs) has received less attention despite both resident valve cells are exposed to alike inflammatory clues involved in the biosynthesis of pathologically relevant glycoproteins during the early stages of CAVD. On this basis, we investigated the outcomes of glucose metabolism rewiring on glycoprotein maturation and immune cell adhesion in human resident valve cells. Real-time metabolic analysis revealed that basal VECs are more glycolytic than VICs. Also, VECs and VICs exposed to inflammatory stimuli exhibited a distinct rewiring, with VECs shifting to a more energetic metabolism, despite a similar upregulation of glycolytic genes. Blunting glucose metabolism in VICs and VECs inhibited inflammatory routes canonically associated with glycolysis, and the expression of proteins associated to the inflammatory response like interleukin-6 and cyclooxigenase-2. Moreover, Western blot and adhesion assays revealed that glycolysis is necessary for the expression and post-translational modifications of intercellular adhesion molecule-1 and vascular cell adhesion molecule-1, and the ensuing process of monocyte-VECs adhesion. Notably, inhibition of the hexosamine biosynthetic pathway using DON and of N-glycosylation by tunicamycin, further disrupted adhesion molecule maturation and monocyte-VECs adhesion. In conclusion, glycolysis and its side-branch route the hexosamine biosynthesis pathway are necessary for nutrient-driven post-translational modifications of inflammatory proteins in inflamed valve cells and the subsequent process of monocyte-VECs adhesion that plays a key role in the initial stages of CAVD pathogenesis. NEW & NOTEWORTHYThe study uncovers a relevant role of glycolysis and its side-branch route the hexosamine biosynthesis pathway in sugar-driven post-translational modifications that are critical for the proper function of leukocyte adhesion molecules and other relevant proinflammatory molecules in aortic valve cells. These events are essential for the recruitment of cells of the monocytic lineage to aortic valve leaflets in the initial stages of calcific aortic valve disease. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/693904v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1211b22org.highwire.dtl.DTLVardef@7c5df7org.highwire.dtl.DTLVardef@fd0da2org.highwire.dtl.DTLVardef@18a40a1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

TREM2 macrophages are associated with enhanced response to PD-1 blockade in human hepatocellular carcinoma

Macrophages are known to dampen tumor immunity. However, identifying druggable targets that modulate these cells to improve existing immunotherapies has been limited by a dearth of studies identifying macrophages that associate with pathological response to immune checkpoint blockade. To fulfill this unmet clinical need, we leveraged transcriptional and spatial profiling of specimens collected from a Phase II clinical trial studying neoadjuvant PD-1 blockade in patients with hepatocellular carcinoma (HCC). We determined that the intratumoral abundance of TREM2-expressing macrophages and serological levels of soluble TREM2 are elevated in patients who responded to PD-1 blockade, compared to non-responders. We validated these findings in a second HCC cohort and in the IMbrave150 trial. These highlight the robust potential for TREM2 macrophages to predict therapeutic responses of HCC to immunotherapy. Therefore, our study provides a novel basis for the use of TREM2 macrophages to strategize treatment for patients with HCC to maximize therapeutic benefit.

immunology↗

bioRxiv2025

TOWARDS CLIMATE-SMART REWILDING: AN INTEGRATED FRAMEWORK FOR BIODIVERSITY, CLIMATE CHANGE, AND SOCIETY

The UN Decade on Ecosystem Restoration and the Kunming-Montreal Global Biodiversity Framework aim to restore 30% of degraded ecosystems. Both the IPCC and IPBES highlight the crucial role of ecosystem restoration in addressing the interconnected crises of climate change and biodiversity loss. One key restoration strategy is rewilding, which enhances ecosystem complexity with minimal human intervention. While traditional rewilding strategies often focus on benefits for biodiversity, we propose a climate-smart rewilding framework as a new approach designed to deliver climate benefits alongside biodiversity restoration. This framework seeks to integrate biodiversity, climate change adaptation and mitigation, as well as socio-economic benefits and trade-offs. We illustrate how this framework can be utilized to identify areas across Europe where rewilding could increase carbon sequestration, enhance species abilities to adapt to the velocity of climate change, and maximize wildlife-watching benefits while minimizing the costs associated with livestock-wildlife conflict. Finally, we acknowledge some limitations of climate-smart rewilding, but we argue that its adaptability and low cost render it a promising solution to the challenges facing Europe and beyond.

ecology↗

bioRxiv2025

Finding space for rewilding: participatory scenarios reveal ecological opportunities based on plural values of nature

O_LIRewilding aims to restore degraded ecosystems in human-dominated areas by promoting self-sustained ecosystems and reducing human control over ecological processes. However, co-benefits and trade-offs between rewilding actions and the interests of local societies must be thoroughly considered. IPBES proposed the Nature Futures framework, a scenario tool to engage society in conservation planning. However, its potential for co-designing ecological restoration remains to be explored. C_LIO_LIThis paper presents a novel methodology that utilises the Nature Futures Framework to address opportunities, co-benefits and trade-offs using rewilding. The study aims to investigate the Nature futures Framework effectiveness in rewilding by involving stakeholders in participatory scenario development. To accomplish this, we conducted stakeholder interviews to co-design three distinct scenarios that reflect diverse values of nature and rewilding strategies for the German Oder Delta. C_LIO_LIThe scenario development process identified spatial priorities for three scenarios: Nature for Nature, Nature for Society (NfS) and Nature as Culture. (NaC). The first, focused on rewilding and increasing forest and river connectivity across 65.8% of the study area. NfS narratives covering 14.4% of the area emphasised de-intensification of forestry and reflooding of peatlands, while NaC prioritised transformation towards extensive agriculture and reflooding for paludiculture across 8.6%. C_LIO_LIThe study identified regions with single and multiple values of nature. Further, there were regions of overlap between scenarios, highlighting the interconnectedness of different rewilding actions and priorities. By pinpointing corresponding values, the research highlighted actions that could result in co-benefits. The findings emphasise the importance of considering pluralistic values when designing rewilding actions, which encourages stakeholders to highlight areas of less resistance to rewilding and co-adapt to the changes in the landscape. C_LIO_LIThis study presents a methodological framework for participatory scenario development for rewilding initiatives. By combining participatory processes with the Nature Futures Framework, our structured approach helps identify priority areas and navigate socio-ecological challenges in landscape restoration. It employs participatory mapping to aid the visualization of land-use changes and aligning rewilding actions with ecological and societal needs. This approach enhances governance frameworks and promotes inclusive rewilding efforts, creating a replicable model for landscape restoration that connects rewilding with sustainability and societal well-being goals. C_LI

ecology↗

bioRxiv2024

Narratives for positive nature futures in Europe

O_LIThe Nature Futures Framework (NFF) is a novel tool for the development of positive scenarios centred on the relationship of nature and people, emphasising biodiversity as part of the solution to environmental challenges across various spatial and temporal scales, explicitly addressing a plurality of values for nature. C_LIO_LIIn this work, we describe the process that has led to the formulation of continental-scale positive narratives for conservation in Europe based on the NFF and its value perspectives (Nature for Nature; Nature for Society; Nature as Culture), through a stakeholder group elicitation. We focused on 6 topics in the narratives: Nature Protection and Restoration; Forestry; Freshwater Ecosystems; Urban Systems; Agriculture, and Energy. We analyse differences and similarities among the narratives across these topics. C_LIO_LIWe develop three novel Nature Futures narratives for Europe with contrasting perspectives and priorities for the six topics. Within the EU socioeconomic trends and policy framework, common solutions that simultaneously tackle biodiversity conservation and instrumental and cultural Natures Contributions to People (NCP) provision emerged. C_LIO_LIThis set of narratives may integrate preferences concerning EU-level conservation targets and plausible socio-ecological development pathways, supporting the modelling of positive scenarios for nature that can be crucial in guiding policy decisions towards recovery of nature. C_LI

ecology↗

bioRxiv2023

Biodiversity monitoring in Europe: user and policy needs

To implement the goals of the 2030 Global Biodiversity Framework, the European Biodiversity Strategy and the EU Green Deal, biodiversity monitoring is a pivotal instrument to achieve accountability and progress in conservation. Monitoring efforts in Europe, however, suffer from gaps and biases in taxonomy, spatial coverage, and temporal resolution, resulting in fragmented and disconnected data which does not provide sufficient evidence for policy making. To assess user and policy needs in biodiversity monitoring, we employed with EuropaBON a four-step user-centred stakeholder engagement process, including an international public stakeholder workshop, a standardised online survey, semi-structured interviews, and an expert meeting with representatives of EU member states, the European Commission and the European Environment Agency. The resulting insights into national and European biodiversity monitoring schemes identify policy needs, current challenges and potential solutions. Based on this in-depth policy and science stakeholder assessment, we recommend the establishment of a European Biodiversity Observation Network through a permanent Biodiversity Monitoring and Coordinating Centre to optimise existing observation efforts, harmonise data, and enhance our ability to predict and respond to key challenges related to biodiversity loss in a changing climate in Europe.

ecology↗

bioRxiv2023

Predicting the timing of ecological phenomena across regions using citizen science data

Spatial predictions of intra-annual ecological variation enhance ecological understanding and inform decision-making. Unfortunately, it is often challenging to use statistical or machine learning techniques to make such predictions, due to the scarcity of systematic, long-term observational data. Conversely, opportunistic time-stamped observation records, supported by highly informative data such as photographs, are increasingly available for diverse ecological phenomena in many regions. However, a general framework for predicting such phenomena using opportunistic data remains elusive. Here, we introduce a novel framework that leverages the concept of relative phenological niche to model observation records as a sample of temporal environmental conditions in which the represented ecological phenomenon occurs. We demonstrate its application using two distinct, management-relevant, ecological events: the emergence of the adult stage of the invasive Japanese beetle (Popillia japonica), and of fruiting bodies of the winter chanterelle mushroom (Craterellus tubaeformis). The framework accounts for spatial and temporal biases in observation data, and it contrasts the temporal environmental conditions (e.g., in temperature, precipitation, wind speed, etc.) associated with the observation of these events to those available in their occurrence locations. To discriminate between the two sets of conditions, we employ machine-learning algorithms (boosted regression trees and random forests). The proposed approach can accurately predict the temporal dynamics of ecological events across large geographical scales. Specifically, it successfully predicted the intra-annual timing of occurrence of adult Japanese beetles and of winter chanterelle mushrooms across Europe and North America. We further validate the approach by successfully predicting the timing of occurrence of adult Japanese beetles in Northern Italy, a recent hotspot of invasion in continental Europe, and the winter chanterelle mushroom in Denmark, a country with a high number of records of this mushroom. These results were also largely insensitive to temporal bias in recording effort. Our results highlight the potential of opportunistic observation data to predict the temporal variation of a wide range of ecological phenomena in near real-time. Furthermore, the conceptual and methodological framework is intuitive and easily applicable for the large number of ecologists already using machine-learning and statistical-based predictive approaches.

ecology↗

bioRxiv2022

RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding

Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology optimized for samples of fresh cells. Complexes of one cell paired with one barcoded bead are stabilized by a chemical linker and dispersed in a hydrogel in the liquid state. Upon gelation on ice the complexes are immobilized and physically separated without requiring nanowells or droplets. Cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcoded beads for further processing with reverse transcription and preparation for cDNA sequencing. As a proof of concept, analysis of PBMC using RevGel-seq achieves results similar to microfluidic-based technologies when using the same original sample and the same data analysis software. In addition, a clinically relevant application of RevGel-seq is presented for pancreatic islet cells. Furthermore, characterizations carried out on cardiomyocytes demonstrate that the hydrogel technology readily accommodates very large cells. Standard analyses are in the 10,000-input cell range with the current gelation device, in order to satisfy common requirements for single-cell research. A convenient stopping point after two hours has been established by freezing at the cell lysis step, with full preservation of gene expression profiles. Overall, our results show that RevGel-seq represents an accessible and efficient instrument-free alternative, enabling flexibility in terms of experimental design and timing of sample processing, while providing broad coverage of cell types.

cell biology↗

bioRxiv2022

Intratumoral mregDC and CXCL13 T helper niches enable local differentiation of CD8 T cells following PD-1 blockade

Here, we leveraged a large neoadjuvant PD-1 blockade trial in patients with hepatocellular carcinoma (HCC) to search for correlates of response to immune checkpoint blockade (ICB) within T cell-rich tumors. We show that ICB response correlated with the clonal expansion of intratumoral CXCL13+ CH25H+ IL-21+ PD-1+ CD4 T helper cells (CXCL13+ Th) and Granzyme K+ PD-1+ effector-like CD8 T cells, whereas terminally exhausted CD39hi TOXhi PD-1hi CD8 T cells dominated in non-responders. Strikingly, most T cell receptor (TCR) clones that expanded post-treatment were found in pre-treatment biopsies. Notably, PD-1+ TCF-1+ progenitor-like CD8 T cells were present in tumors of responders and non-responders and shared clones mainly with effector-like cells in responders or terminally differentiated cells in non-responders, suggesting that local CD8 T cell differentiation occurs upon ICB. We found that these progenitor CD8 T cells interact with CXCL13+ Th cells within cellular triads around dendritic cells enriched in maturation and regulatory molecules, or "mregDC". Receptor-ligand analysis revealed unique interactions within these triads that may promote the differentiation of progenitor CD8 T cells into effector-like cells upon ICB. These results suggest that discrete intratumoral niches that include mregDC and CXCL13+ Th cells control the differentiation of tumor-specific progenitor CD8 T cell clones in patients treated with ICB.

immunology↗

bioRxiv2022

Inhibition of Tgfβ signaling enables durable ventricular pacing by TBX18 gene transfer

Implantable cardiac pacemaker devices are generally effective for patients with symptomatic bradyarrhythmia. However, device-dependent cardiac pacing is far from ideal and often inadequate, particularly for pediatric patients who need to go through invasive revision of the indwelling hardware. Biological pacemakers have been proposed as device-free alternatives to the current treatment, but sustained, unwavering biological pacing beyond days after the biologic delivery has not been demonstrated. We have previously demonstrated that re-expression of an embryonic transcription factor, TBX18, could reprogram ventricular cardiomyocytes into induced pacemaker myocytes (iPMs). Here, we report that exogenous expression of TBX18 per se leads to severe fibrosis in situ, impairing the iPMs ability to pace together. Acute fibrosis is accompanied with proliferation and activation of cardiac fibroblasts via Tgf{beta}-Smad2/3 pathway. Small molecule inhibition of Tgf{beta} signaling mitigated the interstitial remodeling, independent from TBX18-induced iPM reprogramming at the single-cell level. Direct and focal gene transfer of TBX18 into the left ventricular myocardium created ventricular pacing in a rat model of chronic atrioventricular block, but such activity began to wane in a week. In contrast, a combination therapy consisting of TBX18 gene transfer and Tgf{beta} inhibition enabled sustained biological pacing beyond the four-week study period. Our data demonstrate that inhibition of Tgf{beta} signaling suffices to achieve durable cardiac pacing by TBX18-induced biological pacemakers.

cell biology↗

bioRxiv2020

Time-dependent dual effect of NLRP3 inflammasome in brain ischemia

Background and purposePost-ischemic inflammation contributes to worsening of ischemic brain injury and in this process, the inflammasomes play a key role. Inflammasomes are cytosolic multiprotein complexes which upon assembly activate the maturation and secretion of the inflammatory cytokines IL-1{beta} and IL-18. However, participation of the NLRP3 inflammasome in ischemic stroke remains controversial. Our aims were to determine the role of NLRP3 in ischemia and to explore the mechanism involved in the potential protective effect of the neurovascular unit. MethodsWT and NLRP3 knock-out mice were subjected to ischemia by middle cerebral artery occlusion (60 minutes) with or without treatment with MCC950 at different time points post-stroke. Brain injury was measured histologically with 2,3,5-triphenyltetrazolium chloride (TTC) staining. ResultsWe identified a time-dependent dual effect of NLRP3. While neither the pre-treatment with MCC950 nor the genetic approach (NLRP3 KO) proved to be neuroprotective, post-reperfusion treatment with MCC950 significantly reduced the infarct volume in a dose-dependent manner. Importantly, MCC950 improved the neuro-motor function and reduced the expression of different pro-inflammatory cytokines (IL-1{beta}, TNF-), NLRP3 inflammasome components (NLRP3, pro-caspase-1), protease expression (MMP9) and endothelial adhesion molecules (ICAM, VCAM). We observed a marked protection of the blood-brain barrier (BBB), which was also reflected in the recovery of the tight junctions proteins (ZO-1, Claudin-5). Additionally, MCC950 produced a reduction of the CCL2 chemokine in blood serum and in brain tissue, which lead to a reduction in the immune cell infiltration. ConclusionsThese findings suggest that post-reperfusion NLRP3 inhibition may be an effective acute therapy for protecting the blood-brain barrier in cerebral ischemia with potential clinical translation.

neuroscience↗

bioRxiv2019

Immune Profiling of Atherosclerotic Plaques Identifies Innate and Adaptive Dysregulations Associated with Ischemic Cerebrovascular Events

Atherosclerosis is driven by multifaceted contributions of the immune system within the circulation and at vascular focal sites. Yet the specific immune dysregulations within the atherosclerotic lesions that lead to clinical cerebro- and cardiovascular complications (i.e. ischemic stroke and myocardial infarction) are poorly understood. Here, using single-cell mass cytometry with Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) we found that atherosclerotic plaques were enriched in activated, differentiated, and exhausted subsets of T cells vs. blood. Next, using single-cell proteomic, transcriptomic, and cell-to-cell interaction analyses we found unique functional dysregulations of both T cells and macrophages in plaques of patients with clinically symptomatic (SYM; recent stroke of TIA) or asymptomatic (ASYM, no recent stroke) carotid artery disease. SYM plaques were enriched with a distinct CD4+ T cell subset, and T cells were activated, differentiated and presented subset specific exhaustion. SYM macrophages presented alternatively activated phenotypes including subsets associated with plaque vulnerability. In ASYM plaques, T cells and macrophages were activated and displayed a strong IL-1{beta} signaling across cell types, that was absent in SYM plaques. The identification of plaque-specific innate and adaptive immune dysregulations associated with cerebrovascular events provides the basis for the design of precisely tailored cardiovascular immunotherapies.

immunology↗

bioRxiv2019

Cyclic di-GMP Increases Catalase Production and Hydrogen Peroxide Tolerance in Vibrio cholerae

Vibrio cholerae is a Gram-negative bacterial pathogen that causes the disease cholera, which affects nearly 1 million people each year. In between outbreaks, V. cholerae resides in fresh and salt water environments where it is able to persist through changes in temperature, oxygen, and salinity. One key characteristic that promotes environmental persistence of V. cholerae is the ability to form multicellular communities, called biofilms, that often adhere to biotic and abiotic sources. Biofilm formation in V. cholerae is positively regulated by the dinucleotide second messenger cyclic dimeric guanosine monophosphate (c-di-GMP). While most research on the c-di-GMP regulon has focused on biofilm formation or motility, we hypothesized the c-di-GMP signaling network encompassed a larger set of effector functions than reported. We found that high intracellular c-di-GMP increased catalase activity approximately 4-fold relative to strains with unaltered c-di-GMP. Genetic studies demonstrated that c-di-GMP mediated catalase activity was due to increased expression of the catalase encoding gene katB. Moreover, c-di-GMP mediated regulation of catalase activity and katB expression required the c-di-GMP dependent transcription factors VpsT and VpsR. Lastly, we found that high c-di-GMP increased survival after H2O2 challenge in a katB, vpsR, and vpsT dependent manner. Our results indicate antioxidant production is regulated by c-di-GMP in V. cholerae uncovering a new node in the growing VpsT and VpsR c-di-GMP signaling network.\n\nImportanceAs a result of infection with V. cholerae, patients become dehydrated leading to death if not properly treated. The marine environment is the natural reservoir for V. cholerae where it can survive alterations in temperature, salinity, and oxygen. The second messenger molecule c-di-GMP is an important signal regulating host and marine environmental persistence because it controls whether V. cholerae will form a biofilm or disperse through flagellar motility. In this work, we demonstrate another function of c-di-GMP in V. cholerae biology: promoting tolerance to the reactive oxygen species H2O2 through differential regulation of catalase expression. Our results suggest a mechanism where c-di-GMP simultaneously controls biofilm formation and antioxidant production, which could promote persistence in human and marine environments.

microbiology↗

bioRxiv2017

Structural basis for terminal loop recognition and processing of pri-miRNA-18a by hnRNP A1

Post-transcriptional mechanisms play a predominant role in the control of microRNA (miRNA) production. Recognition of the terminal loop of precursor miRNAs by RNA-binding proteins (RBPs) influences their processing; however, the mechanistic and structural basis for how levels of individual or subsets of miRNAs are regulated is mostly unexplored. We previously described a role for hnRNP A1, an RBP implicated in many aspects of RNA processing, as an auxiliary factor that promotes the Microprocessor-mediated processing of pri-mir-18a. Here, we reveal the mechanistic basis for this stimulatory role of hnRNP A1 by combining integrative structural biology with biochemical and functional assays. We demonstrate that hnRNP A1 forms a 1:1 complex with pri-mir-18a that involves binding of both RNA recognition motifs (RRMs) to cognate RNA sequence motifs in the conserved terminal loop of pri-mir-18a. Terminal loop binding induces an allosteric destabilization of base-pairing in the pri-mir-18a stem that promotes its down-stream processing. Our results highlight terminal loop RNA recognition by RNA-binding proteins as a general principle of miRNA biogenesis and regulation.

molecular biology↗

bioRxiv2016

Genetic variation and RNA structure regulate microRNA biogenesis

MiRNA biogenesis is highly regulated at the post-transcriptional level; however, the role of sequence and secondary RNA structure in this process has not been extensively studied. A single G to A substitution present in the terminal loop of pri-mir-30c-1 in breast cancer patients had been previously described to result in increased levels of mature miRNA. Here, we report that this genetic variant directly affects Drosha-mediated processing of pri-mir-30c-1 in vitro and in cultured cells. Structural analysis of this variant revealed an altered RNA structure that facilitates the interaction with SRSF3, an SR protein family member that promotes pri-miRNA processing. Our results are compatible with a model whereby a genetic variant in pri-mir-30c-1 leads to a secondary RNA structure rearrangement that facilitates binding of SRSF3 resulting in increased levels of miR-30c. These data highlights that primary sequence determinants and RNA structure are key regulators of miRNA biogenesis.

biochemistry↗