Biology subjects

Lu, J.

Publications and source records attributed to Lu, J..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Effect Of Perinatal Perfluorinated Compounds (PFASs) Exposure On Behavior Of SD Rats

Perfluorinated compounds (PFASs) are persistent environmental pollutants recognized for their bioaccumulation and potential neurotoxic effects, particularly in relation to attention deficit hyperactivity disorder (ADHD). This study investigated the effects of perinatal PFAS exposure on Sprague-Dawley (SD) rats, with a focus on behavioral outcomes and dopamine metabolism in the prefrontal cortex (PFC). Pregnant rats were administered PFASs at concentrations of 1 mg/L, 3 mg/L, and 10 mg/L through drinking water during gestation and lactation, with a control group included for comparison. The offspring were subjected to behavioral assessments, including open field, marble burying, and jump tests, to evaluate locomotor activity, attention, and impulsivity. Neurochemical analyses were conducted to measure the expression of tyrosine hydroxylase (TH), aromatic L-amino acid decarboxylase (DDC), and dopamine receptor D1 (Drd1) in the PFC using Western blotting and quantitative PCR (qPCR). The results indicated that high-dose PFAS exposure (10 mg/L) resulted in hyperactivity, attention deficits, and impulsive behavior (p < 0.05), along with decreased TH and DDC expression and altered Drd1 levels, suggesting disrupted dopamine metabolism. These findings imply that perinatal PFAS exposure leads to behavioral abnormalities and disruptions in dopamine-related processes.

animal behavior and cognition↗

bioRxiv2025

Hydroxychloroquine-functionalized Ionizable Lipids Mitigate Inflammatory Responses in mRNA Therapeutics

Lipid nanoparticle (LNP)-based mRNA therapeutics, highlighted by the success of SARS-CoV-2 vaccines, face challenges due to inflammation caused by ionizable lipids. These ionizable lipids can activate the immune system, particularly when co-delivered with nucleic acids, leading to undesirable inflammatory responses. We introduce a novel class of anti-inflammatory ionizable lipids functionalized with hydroxychloroquine (HCQ), which suppresses both lipid-induced and nucleic acid-induced immune activation. These HCQ-functionalized LNPs (HL LNPs) exhibit reduced proinflammatory responses while maintaining efficient mRNA delivery. Structural and physicochemical analyses revealed that HCQ-functionalization results in a distinct particle structure with significantly improved stability. The efficacy of HL LNPs was demonstrated across various therapeutic contexts, including a prophylactic vaccination model against varicella-zoster virus (VZV) and CRISPR-Cas9 gene editing targeting PCSK9. Notably, HL LNPs showed robust mRNA expression after repeated administration, addressing concerns of inflammation and ensuring sustained therapeutic effects. These findings highlight the potential of HCQ-functionalized LNPs in expanding the safe use of mRNA therapeutics, particularly for applications requiring repeated dosing and in scenarios where inflammation-induced side effects must be minimized.

bioengineering↗

bioRxiv2025

TXA11114: Discovery of an in vivo efficacious efflux pump inhibitor in Pseudomonas aeruginosa

Multi-drug resistance in Pseudomonas aeruginosa is often associated with overexpression of drug efflux pumps which limit antibiotics exposure. So far, successful development of efflux pump inhibitors (EPIs) has been plagued by undesirable toxicities and inconsequential in vivo efficacy. TAXIS Pharmaceuticals Inc. has discovered an effective anti-pseudomonal therapy involving a novel indole carboxamide class of EPI, TXA11114, with a fluorine substituted diamine sidechain, as an adjunctive to levofloxacin. TXA11114 has demonstrated excellent potentiation of levofloxacin MIC by [≥] 8-fold in 90% of Walter-Reed and CDC multi-drug resistant (MDR) isolates. Biophysical and genetic studies with TXA11114 support efflux inhibition while ruling out membrane disruption as a mechanism of action. TXA11114 enhanced the levofloxacin killing and diminished the frequency of resistance emergence to levofloxacin to undetectable levels. Moreover, in murine thigh and lung P. aeruginosa infection models, the TXA11114-levofloxacin combination showed pronounced killing compared to levofloxacin alone, achieving a validated in vivo efficacy milestone that previous EPIs could not. Most importantly, TXA11114 exhibits a safe toxicology profile when screened for cytotoxicity, hERG channel inhibition, in vitro nephrotoxicity, and acute toxicity. Further, pharmacokinetic (PK) parameters of TXA11114 have a complementary profile with that of levofloxacin in plasma and bronchoalveolar lavage fluid (BALF) samples of infected mice, maximizing pharmacodynamic (PD) benefits. Overall, studies on the TXA11114-levofloxacin combination highlight its potential as an anti-pseudomonal agent for combating multidrug-resistant infections.

microbiology↗

bioRxiv2025

Basic-Leucine-Zipper Transcription Factors Regulate Selective Molecular Phenotypes in Regulatory T Cells During IL-2-Induced Activation

Regulatory T (Treg) cells have long been recognized as modulators of immunological tolerance and homeostasis. Previously, we used scRNA-seq to reveal significant Treg heterogeneity in response to IL-2-induced activation. Herein, we leveraged enrichment analyses, as well as bulk and single-nucleus multi-omics in splenic and lung Tregs, to uncover and confirm the importance of transcription factors (TFs) and chromatin remodeling in Treg activation. Multiple bZIP TF motifs showed increased chromatin accessibility post IL-2 treatment, with correlated transcriptional changes resembling Th1 and Th2 molecular phenotypes, further confirmed by spatial ATAC-seq. By combining gene perturbation and CUT&RUN assays before and after Treg stimulation, we show that bZIP TFs, such as BATF and BACH1, are critical to IL-2-induced Treg activation, coordinating epigenetic and transcriptional changes that selectively drive T-helper phenotypes and metabolic pathways.

genomics↗

bioRxiv2025

Human milk-derived extracellular vesicle treatment promotes the heat shock response in neonates with perinatal high fat diet exposure.

Maternal consumption of a high-fat diet (mHFD) during perinatal life (the collective prenatal and postnatal periods) influences neonatal development, initiates hypothalamic-pituitary-adrenal (HPA) axis activation, and impacts the long-term physiological and metabolic health of offspring. Milk-derived extracellular vesicles (MEVs) are lipid-coated nanovesicles found in mammalian milk that survive intestinal degradation and cross complex biological barriers, including the blood-brain barrier. MEVs have known cytoprotective activity in peripheral organs; however, their pro-survival functions in response to chronic pro-inflammation stemming from early life nutrient stress remain unknown in the neonatal brain. Further, sex differences resulting from MEV treatment require investigation, as male and female neonates illicit variable responses to early life nutrient stress. We investigated whether MEVs promote the heat shock response (HSR), a principal pro-survival mechanism responsible for refolding or degrading misfolded protein aggregates through the action of heat shock protein (HSP) chaperones. We investigated the interaction between MEVs and the HSR in the liver, hypothalamus, and prefrontal cortex in male and female neonatal rats exposed to perinatal mHFD within the stress hyporesponsive period at postnatal day 11. MEV treatment robustly modulated the HSR in female neonates with the largest response recorded in the prefrontal cortex. Specifically, in the prefrontal cortex, MEV treatment led to an upregulation of the main transcription factor (HSF1), while downregulating the negative regulators of HSF1 (Hsp70 and Hsp90). These results suggest that MEVs may influence pro-survival outcomes in the prefrontal cortex by activating HSF1-mediated pro-survival in a sex specific manner in response to mHFD.

molecular biology↗

bioRxiv2025

A Generalized Platform for Artificial Intelligence-powered Autonomous Protein Engineering

Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent1-3. Here we report a generally applicable platform for autonomous protein engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this autonomous platform can be applied to engineer virtually any protein. As a proof of concept, we engineered Arabidopsis thaliana halide methyltransferase (AtHMT)4 for a 90-fold improvement in substrate preference and 16-fold improvement in ethyltransferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase)5,6 variant with 26-fold improvement in activity at neutral pH. This was accomplished in four rounds over four weeks, while requiring construction and characterization of fewer than a total of 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.

synthetic biology↗

bioRxiv2025

The lower jaw of Devonian ray-finned fishes (Actinopterygii): anatomy, relationships, and functional morphology

Actinopterygii is a major extant vertebrate group, but limited data are available for its earliest members. Here we investigate the morphology of Devonian actinopterygians, focusing on the lower jaw. We use X-Ray Computed Tomography (XCT) to provide comprehensive descriptions of the mandibles of 19 species, which span the whole of the Devonian and represent roughly two thirds of all taxa known from more than isolated or fragmentary material. Our findings corroborate previous reports in part but reveal considerable new anatomical data and represent the first detailed description for roughly half of these taxa. The mandibles display substantial variation in size, spanning more than an order of magnitude. Although most conform to a generalized pattern of a large dentary and one or two smaller infradentaries, XCT data reveal significant differences in the structure of the jaw and arrangement of teeth that may be of functional relevance. We report the presence of a rudimentary coronoid process in several taxa, contributed to by the dentary and/or infradentaries, as well a raised articular region, resulting in a mandible with an offset bite and that functions as a bent level arm. Among the most striking variation is that of tooth morphology: several taxa have heterodont dentary teeth that vary in size and orientation, and multiple variations on enlarged, whorl-like and posteriorly-oriented anterior coronoid dentition are observed. We use these new data to revise morphological characters that may be of phylogenetic significance and consider the possible functional implications of these traits. The observed variation in mandible form and structure suggests previously unappreciated functional diversity among otherwise morphologically homogenous Devonian ray-finned fishes.

paleontology↗

bioRxiv2025

ASTRO: Automated Spatial Whole-Transcriptome RNA-Expression Workflow

MotivationDespite significant advances in spatial transcriptomics, the analysis of formalin-fixed paraffin-embedded (FFPE) tissues, which constitute most clinically available samples, remains challenging. Additionally, capturing both coding and noncoding RNAs in a spatial context poses significant challenges. We recently introduced Patho-DBiT, a technology designed to address these unmet needs. However, the marked differences between Patho-DBiT and existing spatial transcriptomics protocols necessitate specialized computational tools for comprehensive whole-transcriptome analysis in FFPE samples. ResultsHere, we present ASTRO, an automated pipeline developed to process spatial transcriptomics data. In addition to supporting standard datasets, ASTRO is optimized for whole-transcriptome analyses of FFPE samples, enabling the detection of various RNA species, including non-coding RNAs such as miRNAs. To compensate for the reduced RNA quality in FFPE tissues, ASTRO incorporates a specialized filtering step and optimizes spatial barcode calling, increasing the mapping rate. These optimizations allow ASTRO to spatially quantify coding and non-coding RNA species in the entire transcriptome and achieve robust performance in FFPE samples. AvailabilityCodes are available at GitHub (https://github.com/gersteinlab/ASTRO).

bioinformatics↗

bioRxiv2025

Epigenetic priming promotes acquisition of tyrosine kinase inhibitor resistance and oncogene amplification in human lung cancer

In mammalian cells, gene copy number is tightly controlled to maintain gene expression and genome stability. However, a common molecular feature across cancer types is oncogene amplification, which promotes cancer progression by drastically increasing the copy number and expression of tumor-promoting genes. For example, in tyrosine kinase inhibitor (TKI)-resistant lung adenocarcinoma (LUAD), oncogene amplification occurs in over 40% of patients tumors. Despite the prevalence of oncogene amplification in TKI-resistant tumors, the mechanisms facilitating oncogene amplification are not fully understood. Here, we find that LUADs exhibit a unique chromatin signature demarcated by strong CTCF and cohesin deposition in drug-naive tumors, which correlates with the boundaries of oncogene amplicons in TKI-resistant LUAD cells. We identified a global chromatin priming effect during the acquisition of TKI resistance, marked by a dynamic increase of H3K27Ac, cohesin loading, and inter-TAD interactions, which occurs before the onset of oncogene amplification. Furthermore, we have found that the METTL7A protein, which was previously reported to localize to the endoplasmic reticulum and inner nuclear membrane, has a novel chromatin regulatory function by binding to amplified loci and regulating cohesin recruitment and inter-TAD interactions. Surprisingly, we discovered that METTL7A remodels the chromatin landscape prior to large-scale copy number gains. Furthermore, while METTL7A depletion has little effect on the chromatin structure and proliferation of drug-naive cells, METTL7A depletion prevents the formation and maintenance of TKI resistant-clones, highlighting the specific role of METTL7A as cells are becoming resistant. In summary, we discovered an unexpected mechanism required for the acquisition of TKI resistance regulated by a largely uncharacterized factor, METTL7A. This discovery sheds light into the maintenance of oncogene copy number and paves the way to the development of new therapeutics for preventing TKI resistance in LUAD.

genetics↗

bioRxiv2025

Built-environment professionals welcome prescriptive ecology evidence to enhance communication with stakeholders for biodiversity-inclusive cities: Insights from professionals in both the Global North and South

Cities play a crucial role in addressing the biodiversity crisis. Despite advancements in urban ecology, effectively integrating biodiversity into urban planning remains limited. Built-environment professionals (BEPs), who are responsible for local actions, often face criticism for their unwillingness to prioritize biodiversity and are seldom studied from their perspectives, especially those from the Global South. Therefore, understanding the viewpoints of diverse BEPs from both the Global South and North on biodiversity-inclusive urban planning and design (BIPD) is crucial. This study employs Q-Methodology to analyze BEPs perspectives in Ethiopia, China, Spain, and the United States, revealing four viewpoints: Pluralist, Enthusiast, Pragmatist, and Contextualist. Challenges in realizing BIPD include widespread unawareness among BEPs of existing biodiversity data and methodologies, structural-physical barriers such as land use conflicts and competing resources, and misaligned values with stakeholders. Our research challenges the notion that BEPs resist incorporating biodiversity into their practices by broadly exploring their viewpoints. BEPs exhibit readiness to transcend legislative structural barriers and leverage professional norms to advocate for urban biodiversity, particularly when equipped with evidence-based tools. Pluralists and Enthusiasts demonstrate heightened interest in multidisciplinary collaboration and prescriptive, visual tools to communicate biodiversitys value to stakeholders. Critically, BEPs capacity to act hinges on the availability of contextually sensitive methods, necessitating empowerment through transdisciplinary collaborations to foster transformative changes in cities, especially in the Global South, where complex socioeconomic-ecological trade-offs demand co-produced solutions.

ecology↗

bioRxiv2025

Human milk-derived extracellular vesicles promote the heat shock response in polarized microglia.

Proteotoxic stress induces microglia polarization and attenuates cytoprotective, pro-survival cellular cascades. Milk-derived extracellular vesicles (MEVs) are lipid-coated nanovesicles that combat pro-inflammation in peripheral cells and tissues; however, the cytoprotective potential of MEVs remains unknown in brain macrophages. We investigated whether MEVs reduce neuroinflammation in human microglia by activating the heat shock response (HSR). The HSR triggers the upregulation of molecular chaperones (heat shock proteins; HSPs) to restore proteostasis by refolding or degrading misfolded aggregates. MEVs were isolated from unpasteurized human donor milk. Human microglia clone 3 (HMC3) cells were primed with 10 ng/mL IFN-{gamma} to induce polarization, and a subset of cells were supplemented with 200 {micro}g of MEVs. The abundance of HSF1 and candidate HSPs (Hsp70, Hsp90, Hsp40, Hsp27) were analyzed via RT-qPCR and western immunoblotting at 6h, 12h, and 24h post-MEV supplementation. We found that MEV supplementation promoted the HSR in polarized microglia, compared to homeostatic cells. Furthermore, MEVs increased the duration of the HSR in response to pro-inflammatory stress, exerting robust and continued pro-survival benefits.

molecular biology↗

bioRxiv2024

Osteoporosis with different causation exhibits different changes in bone tissue mineral and organic matrix

Osteoporosis (OP) which is a common skeletal disease with different causation is prevalent in aging population. Postmenopause women generally suffer from OP with bone loss due to estrogen deficiency. Diabetes are also associated with OP by complex metabolic mechanisms. Bone qualities of OP caused by aging were compared with the ovariectomy (OVX) model and the Type 2 diabetic model using Sprague-Dawley (SD) rats in our study. Combining with micro-computed tomography (-CT) and solid-state NMR (SSNMR) methods, this research studied bone changes in SD rats from tissue level to the molecular level. The studies revealed bone loss was most significant for cancellous bones, but not for cortical bones in OP rats. However, at the molecular level, the content of HAP in cortical bone increased with aging, contributing to the brittleness of the bone. Triglyceride, as a senescence maker of osteocyte in cortical bone, was also identified to be closely associated with OP in aging and OVX rats, but not in diabetic rats. This research suggests differing bone qualities in molecular level of OP with various causes more objectively reflect the bone tissue reconstruction rather than bone loss in -CT analysis.

biochemistry↗

bioRxiv2024

Development of a novel peripherally acting alpha2A-adrenergic receptor antagonist for anti-diabetic

Yohimbine, a potent alpha2A-adrenergic receptor (2AAR) antagonist, was found therapeutic potential for type 2 diabetes through improving insulin release. However, the adverse side effects mediated by its actions in the brain hampered its use. Here, based on molecular docking analysis and structural modification, we have developed a novel peripherally acting yohimbine derivative (CDS479-2). CryoEM data found that yohimbine and CDS479-2 have similar interactions with the structure of 2AAR. Importantly, CDS479-2 shows similar 2AAR antagonist activity as yohimbine, but with very limited access to the brain, and thus avoiding the unwanted central effects such as hypertension and anxiety. Acute administration of CDS479-2 by injection or gavage lowered blood glucose levels and improved glucose tolerance in the high-fat diet-induced obesity (DIO) mice, an animal model for human type 2 diabetes. Remarkably, DIO mice received 2 weeks of daily administration of CDS479-2, but not yohimbine, exhibited sustained normoglycaemia, and increased density of the insulin-producing beta cells, in which important proliferation genes were found upregulated. Moreover, the overall protein expression levels of their pancreas were more similar to that of the healthy chow-fed mice. Thus, CDS479-2 may indicate a new direction for type 2 diabetes treatment. Importantly, the strategy we employed in this study will inspire the optimization for drugs that with both peripheral and central targets. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=166 HEIGHT=200 SRC="FIGDIR/small/628818v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1d3d7corg.highwire.dtl.DTLVardef@1afbad3org.highwire.dtl.DTLVardef@12a1aborg.highwire.dtl.DTLVardef@1341a02_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2024

Alteration of skin fibroblast steady state contributes to healing outcomes

Fibroblasts display complex functions associated with distinct gene expression profiles that influence matrix production and cell communications and the autonomy of tissue development and repair. Thrombospondin-2 (TSP-2), produced by fibroblasts, is a potent angiogenesis inhibitor and negatively associated with tissue repair. Single-cell (sc) sequencing analysis on WT and TSP2KO skin fibroblasts demonstrate distinct cell heterogeneity. Specifically, we found an enrichment of Sox10+ multipotent progenitor cells, identified as Schwann precursor cells, in TSP2KO fibroblasts, while fibrosis-related subpopulations decreased. Immunostaining of tissue and cells validated the increase of this Sox10+ population in KO fibroblasts. Furthermore, in silico analysis suggested enhanced pro-survival signaling, including WNT, TGF-{beta}, and PDGF-{beta}, alongside a reduced BMP4 response. Additionally, the creation of two TSP2KO NIH3T3 cell lines using the CRISPR/Cas9 technique allowed functional and signaling validation in a less complex system. Moreover, KO 3T3 cells exhibited enhanced migration and proliferation, with elevated levels of pro-regenerative molecules including TGF-{beta}3 and Wnt4, and enrichment of nuclear {beta}-catenin. These functional and molecular alterations likely contribute to improved healing and increased neurogenesis in TSP2-deficient wounds. Overall, our findings describe the heterogeneity of dermal fibroblasts and identify pro-regenerative features of TSP2KO fibroblasts.

pathology↗

bioRxiv2024

Reproducible Brain Entropy (BEN) Alterations During Rumination

Rumination, characterized by recurrent and repetitive thinking, is closely associated with mental disorders such as depression. However, the neural mechanisms underlying this mental state remain poorly understood. In this study, we use a relatively novel neuroimaging analysis method-Brain Entropy (BEN) to quantitatively assess the irregularity, disorder, and complexity of brain activity, providing new insights into the neural mechanisms of rumination. We utilized a publicly available MRI dataset from three different scanners. The dataset included 41 healthy adult participants who completed identical fMRI tasks on IPCASGE, PKUGE, and PKUSIEMENS scanners. The time interval between the two visits was 22.0 {+/-} 14.6 days. The fMRI session included four runs: resting state, sad memory, rumination, and distraction. Whole brain voxel-wise BEN differences of task state and resting state, rumination and sad memory, distraction and sad memory, and rumination and distraction were tested and overlap regions after thresholded (p<0.05) across the three scanners were identified as exhibiting significant differences. The results demonstrate distinct alterations in BEN across mental states. Compared to the sad memory condition, decreased BEN was found in the visual cortex (VC) during rumination and decreased BEN in the posterior cingulate cortex/precuneus (PCC/PCu) during distraction. However, when compared to distraction, rumination showed increased BEN in the PCC/PCu. These findings suggest that rumination involves heightened internal focus and reduced processing of external environmental information. This study highlights BEN as a valuable metric for elucidating the neural mechanisms underlying rumination and its role in depression.

neuroscience↗

bioRxiv2024

A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function

Organ function requires coordinated activities of thousands of genes in distinct, spatially organized cell types. Understanding the basis of emergent tissue function requires approaches to dissect the genetic control of diverse cellular and tissue phenotypes in vivo. Here, we develop paired imaging and sequencing methods to construct large-scale, multi-modal genotype-phenotypes maps in tissue with pooled genetic perturbations. Using imaging, we identify genetic perturbations in individual cells while simultaneously measuring their gene expression and subcellular morphology. Using single-cell sequencing, we measure transcriptomic responses to the same genetic perturbations. We apply this approach to study hundreds of genetic perturbations in the mouse liver. Our study reveals regulators of hepatocyte zonation and liver unfolded protein response, as well as distinct pathways that cause hepatocyte steatosis. Our approach enables new ways of interrogating the genetic basis of complex cellular and organismal physiology and provides crucial training data for emerging machine-learning models of cellular function.

genomics↗

bioRxiv2024

Unraveling cfDNA Fragmentation Patterns: Linking Chromatin Architecture to Cancer Diagnostic Sensitivity

Circulating cell-free DNA (cfDNA) liquid biopsies offer a powerful, non-invasive approach for cancer diagnostics, leveraging DNA fragments primarily released during apoptosis. Using droplet digital PCR on cfDNA samples from 88 breast and colorectal cancer patients, we uncovered highly consistent nucleosome breakpoints across individuals. Proximity to these cfDNA breakpoints diminishes the sensitivity of somatic mutation assays, including those targeting IDH1 and NRAS hotspot mutations, underscoring the importance of precise nucleosome positioning data. We introduce a probabilistic nucleosome protection scoring method that enables high-resolution mapping of nucleosome positions and cfDNA breakpoints. These maps reveal distinct nucleosome spacing patterns between heterochromatin and euchromatin, corresponding to different chromatin fiber topologies. Analysis of X-chromosome inactivation further supports the topoisomer model: heterochromatins 187 bp nucleosome repeat length differs from euchromatins 182 bp, generating wave interference patterns in nucleosome signals. Our findings suggest that loop-mediated transitions from T2 to T1 topoisomers shape chromatin accessibility and cfDNA fragmentation, advancing the diagnostic potential of liquid biopsy assays. HighlightsO_LINucleosome breakpoint conservation impacts somatic mutation assay sensitivity C_LIO_LIProbabilistic protection scoring enhances cfDNA nucleosome peak resolution C_LIO_LIChromatin states exhibit unique nucleosome spacing linked to distinct topologies, influencing cfDNA fragmentation C_LIO_LIChromosome X-inactivation phasing analyses reveal waveform interference in nucleosome positioning signals C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/623159v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@65893corg.highwire.dtl.DTLVardef@14c986org.highwire.dtl.DTLVardef@ba9306org.highwire.dtl.DTLVardef@10a7364_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Upstream open reading frames buffer translational variability during Drosophila evolution and development

Protein abundance tends to be more evolutionarily conserved than mRNA levels both within and between species, yet the mechanisms underlying this phenomenon remain largely unknown. Upstream open reading frames (uORFs) are widespread cis-regulatory elements in eukaryotic genomes that regulate translation, but it remains unclear whether and how uORFs contribute to stabilizing protein levels. In this study, we performed ribosome translation simulations on mRNA to quantitatively assess the extent to which uORF translation influences the translational variability of downstream coding sequences (CDSs) across varying contexts. Our simulations revealed that uORF translation dampens CDS translational variability, with buffering capacity increasing in proportion to uORF efficiency, length, and number. We then compared the translatomes at different developmental stages of two Drosophila species, demonstrating that uORFs buffer mRNA translation fluctuations during both evolution and development. Experimentally, deleting a uORF in the bicoid (bcd) gene--a prominent example of translational buffering--resulted in extensive changes in gene expression and phenotypes in Drosophila melanogaster. Additionally, we observed uORF-mediated buffering between primates and within human populations. Together, our results reveal a novel regulatory mechanism by which uORFs stabilize gene translation during development and across evolutionary time.

evolutionary biology↗