Biology subjects

Xu, L.

Publications and source records attributed to Xu, L..

At least 163 records · Page 9Linked to original sources

bioRxiv2024

Global Stability and Tipping Point Prediction of the Coral Reef Ecosystem

Coral reef ecosystems are remarkable for their biodiversity and ecological significance, exhibiting the capacity to exist in different stable configurations with possible abrupt shifts between these alternative stable states. This study applies landscape-flux theory to analyze how these complex systems behave when subjected to random environmental disturbances. We use this theory to formulate and investigate several early warning indicators of ecosystem transitions in a well-known coral-reef model. We studied a number of specific indicators, including the average flux (the driving force when the system is out of equilibrium), the entropy production rate, the nonequilibrium free energy and the time irreversibility of the cross-correlation functions. These indicators demonstrate a distinctive advantage when compared to classical indicators based on the phenomenon of critical slowing down; they exhibit turning points midway between two bifurcations, enabling them to forecast transitions in both directions substantially earlier than conventional methods. In contrast, early warning indicators based on the critical slowing down phenomenon typically only become apparent when the system approaches the actual bifurcation or tipping point(s). Our findings offer improved tools for anticipating critical transitions in coral reef and other at-risk ecosystems, with the potential to enhance conservation and management strategies.

ecology↗

bioRxiv2024

Global Stability and Tipping Point Prediction of the cell fate decision making model

This study investigates global stability and tipping point prediction in cell fate decision-making systems through non-equilibrium landscape flux theory. We demonstrate that cell fate dynamics are governed by the interplay between potential landscape and curl flux, where the landscape guides systems toward stable states while curl flux mediates transitions between them. Our analysis reveals that non-zero curl flux generates irreversible dominant pathways between multi-stable states. We identify several quantitative measures for transition prediction, including barrier heights, kinetic switching times, entropy production rates, and average flux. We introduce novel non-equilibrium early warning indicators based on time irreversibility of cross-correlations ({Delta}C), average flux, and entropy production rate. These indicators exhibit significant changes near bifurcations, enabling transition prediction before state stability loss, with superior predictive capability compared to traditional critical slowing down theory. The rotational nature of curl flux is shown to destabilize attractor states, providing a dynamical foundation for phase transitions in cell differentiation, reprogramming, and transdifferentiation processes. These findings advance our understanding of non-equilibrium dynamics in cell fate decisions and offer practical implications for stem cell research and regenerative medicine, potentially enabling more precise therapeutic strategies in stem cell applications.

biophysics↗

bioRxiv2024

Mapping Global Causal Responses to Noninvasive Modulation of Genetically and Spatially Targeted Neural Populations with Sonogenetic-fPET

Despite significant progress in brain circuit mapping over recent decades, a major challenge remains: no method currently allows for the noninvasive modulation of genetically and spatially defined neural populations while simultaneously monitoring their global effects throughout the brain and body. Here, we present sonogenetic-fPET, a technique that integrates sonogenetics with [18F]-2-fluoro-2-deoxy-D-glucose functional positron emission tomography (FDG-fPET) to overcome this challenge. Sonogenetics enables noninvasive, spatially targeted modulation of neurons genetically engineered to express the ultrasound-sensitive ion channel TRPV1, while FDG-fPET captures glucose metabolic changes triggered by this stimulation across the brain and body. We demonstrate the effectiveness of this technique by targeting neurons in the dorsal striatum, showcasing its capability to map global network responses to specific neuronal activation. Incorporating an acoustic hologram for sonogenetics further enables flexible modulation of different brain regions within a single mouse while concurrently mapping the resulting network activity. In summary, sonogenetic-fPET offers a tool for dissecting the global responses of the brain and body to the noninvasive modulation of genetically and spatially defined neuronal populations.

neuroscience↗

bioRxiv2024

Accurate nucleic acid-binding residue identification based on domain-adaptive protein language model and explainable geometric deep learning

Protein-nucleic acid interactions play a fundamental and critical role in a wide range of life activities. Accurate identification of nucleic acid-binding residues helps to understand the intrinsic mechanisms of the interactions. However, the accuracy and interpretability of existing computational methods for recognizing nucleic acid-binding residues need to be further improved. Here, we propose a novel method called GeSite based the domain adaptive protein language model and explainable E(3)-equivariant graph convolution neural network. Prediction results across multiple benchmark test sets demonstrate that GeSite is superior or comparable to state-of-the-art prediction methods. The performance comparison on low structure similarity and newly released test proteins demonstrates the robustness and generalization of the method. Detailed experimental results suggest that the advanced performance of GeSite lies in the well-designed nucleic acid-binding protein adaptive language model. Meanwhile, interpretability analysis exposes the perception of the prediction model on various remote and close functional domains, which is the source of its discernment. The data and source code of GeSite are freely accessible at https://github.com/pengsl-lab/GeSite.

bioinformatics↗

bioRxiv2024

Shroom3-Rock interaction and profibrotic function: Resolving mechanism of an intronic CKD risk allele.

Common intronic enhancer SNPs in Shroom3 associate with CKD in GWAS, although there is paucity of detailed mechanism. Previously, we reported a role for Shroom3 in mediating crosstalk between TGF{beta}1- & Wnt/Ctnnb1 pathways promoting renal fibrosis (TIF). However, beneficial roles for Shroom3 in proteinuria have also been reported suggesting pleiotropic effects. Here we focused on identifying the specific profibrotic Shroom3 motif. Given known therapeutic roles for Rho-kinase inhibitors in experimental CKD, and the established interaction between Shroom3 and Rock via its ASD2 domain, we hypothesized that Shroom3-mediated ROCK activation played a crucial role in its profibrotic function in high expressors. To test this hypothesis, we developed transgenic mice and cell lines that inducibly overexpressed wild-type- (WT-Sh3) or ASD2-domain deletion- Shroom3 (ASD2{Delta}-Sh3). Prior scRNAseq data showed that during TIF, Shroom3 and Rock co-expression occurred in injured tubular cells and fibroblasts, highlighting cell-types where this mechanism could be involved. Using HEK293T cells, we first confirmed absent ROCK binding and inhibited TGF{beta}1-signaling with ASD2{Delta}-Sh3-overexpression vs WT-Sh3. In mIMCD cells, ASD2{Delta}-Sh3 overexpression, reduced Rock activation (phospho-MYPT1), pro-fibrotic and pro-inflammatory transcripts vs WT-Sh3. Fibroblast proliferation (3T3) was also reduced with ASD2{Delta}-Sh3. In vivo, we studied ureteric obstruction (UUO) and Aristolochic nephropathy (AAN) as TIF models. In AAN, inducible global-, or Pan-tubular specific-, WTSh3-overexpression showed increased azotemia, and TIF vs ASD2{Delta}-Sh3 mice. WT-Sh3 mice consistently showed significant enrichment of Rho-GTPase, TGF{beta}1- and Wnt/CtnnB1- signaling in kidney transcriptome, paralleling Shroom3-coexpressed genes in tubulo-interstitial transcriptomes from human CKD. In UUO, again WT-Sh3 mice recapitulated increased fibrosis vs ASD2{Delta}-Sh3. Importantly, ASD2{Delta}-Sh3 did not develop albuminuria vs WT-Sh3, while mutating a disparate Fyn-binding Shroom3 motif induced albuminuria in mice, suggesting motif-specific roles for Shroom3 in the kidney. Hence, our data show a critical role for the Rock-binding, ASD2-domain in mediating TIF in milieu of Shroom3 excess, with relevance to human CKD.

systems biology↗

bioRxiv2024

A unified central thalamus mechanism underlying diverse recoveries in disorders of consciousness

Disorders of consciousness (DoC) encompass a range of states characterized by prolonged altered awareness due to heterogeneous brain damage and are associated with highly diverse prognoses. However, the neural mechanisms underlying such diverse recoveries in DoC remain unclear. To address this issue, we analysed neuronal spiking activities recorded from the central thalamus (CT), a key hub in arousal regulation, in a cohort of 23 DoC patients receiving deep brain stimulation treatment. Using machine learning techniques, we identified a core set of electrophysiological features of the CT, particularly the theta rhythm, that could account for individual recovery outcomes across highly varied etiologies (trauma, brainstem hemorrhage, and anoxia), clinical baselines and patient ages. These features also correctly identified one subgroup of patients who exhibited poor initial clinical manifestations but recovered unexpectedly. Simulating a conductance-based model further revealed the neurodynamics of the theta rhythm in the CT during different stages of consciousness recovery. Taken together, these findings uncover a previously unknown, unified CT mechanism that governs the recoveries in DoC.

neuroscience↗

bioRxiv2024

A cereblon (CRBN) molecular glue degrader of NIMA-related kinase 7 (NEK7) reveals a context-dependent role in NLRP3 inflammasome activation

The NLRP3 (NACHT-, leucine-rich repeat [LRR]- and pyrin domain [PYD]- containing protein 3) inflammasome is a cytoplasmic signaling complex that promotes inflammation in response to signals from infection and cellular damage. Increased activation of the NLRP3 inflammasome is linked to numerous diseases including gout, osteoarthritis, cardiovascular disease, neuroinflammatory diseases and cancer, which has prompted the search for therapeutics that can inhibit the NLRP3 pathway. Recent work suggested that NIMA-related kinase 7 (NEK7) may be required for proper assembly and activation of the NLRP3 inflammasome independent of its kinase activity, and that hence reduction of NEK7 protein levels may block NLRP3 activation. Since NEK7 contains a glycine beta hairpin loop structural degron found in many targets of cereblon (CRBN) molecular glue degraders, we used this strategy to degrade NEK7 and inhibit the NLRP3 inflammasome. We identified NK7-902, a CRBN glue degrader of NEK7. NK7-902 potently and selectively degraded NEK7 in human primary monocytes, peripheral blood mononuclear cells (PBMCs) and whole blood. Unexpectedly, full NEK7 degradation led to only partial blockade of NLRP3-dependent interleukin-1{beta} (IL-1{beta}) release in these cells under different stimulation conditions, with the extent of IL-1{beta} inhibition varying greatly across donors. Unlike most CRBN glue degraders, NK7-902 degraded NEK7 in mouse cells and efficiently inhibited NLRP3-dependent IL-1{beta} release in a mouse cryopyrin-associated syndrome (CAPS) model. By contrast, oral administration of NK7-902 in non-human primates led to profound and long lasting NEK7 degradation but only transiently blocked IL-1{beta} production in blood. Collectively, our data suggest that NEK7 is involved but may not be strictly required for NLRP3 activation in primates and humans. HighlightsO_LIIdentification of NK7-902, a CRBN molecular glue degrader of NEK7 C_LIO_LINK7-902 fully degrades NEK7 in human primary monocytes and whole blood but only partially inhibits NLRP3-dependent IL-1{beta} production C_LIO_LIUnlike most CRBN glue degraders, NK7-902 shows activity in murine systems C_LIO_LIIn vivo oral administration of NK7-902 in non-human primates leads to profound and long-lasting NEK7 degradation but only transiently blocks NLRP3 inflammasome activation C_LI

immunology↗

bioRxiv2024

Machine learning engineered PoLixNano nanoparticles overcome delivery barriers for nebulized mRNA therapeutics

There continues to be a dearth of competent inhalable mRNA delivery although it holds great potential for addressing a wide variety of refractory diseases. The huge advances seen with parenteral-administered lipid nanoparticle (LNP) have not been translated into nebulized mRNA delivery due to the aggressive nebulization process and insurmountable barriers inherent to respiratory mucosa. Here, we show amphiphilic block copolymers revealed by machine learning (ML) can spontaneously form stabilized nanoparticles (PoLixNano) with the lipids components of LNP and simultaneously impart the PoLixNano with "shield" (shear force-resistant) and "spear" (pulmonary barriers-penetrating abilities) capabilities. We present a ML approach that leverages physicochemical properties and inhaled mRNA transfection profiles of a chemically diverse library of polymeric components to validate the integration of "shield" and "spear" properties as highly predictive indicators of transfection efficiency. This quantitative structure-mRNA transfection prediction (QSMTP) model identifies top-performing amphiphilic-copolymers from more than 10000 candidates and suggests their mucus-penetrating ability outweights the shear force-resistant property in contributing to efficient mRNA transfection. The optimized PoLixNano substantially outperforms the LNP counterpart and mediates up to 1114-times higher levels of mRNA transfection in animal models with negligible toxicities. The PoLixNano promotes overwhelming SARS-CoV-2 antigen-specific sIgA antibody secretion and expansion of TRM cells which collectively confers 100% protection in mice against lethal SARS-CoV-2 challenges and blocks the transmission of Omicron variant between hamsters. PoLixNano also displays versatile therapeutic potential in lung carcinoma and cystic fibrosis models. Our study provides new insights for designing delivery platforms of aerosol-inhaled mRNA therapeutics with clinical translation potential.

synthetic biology↗

bioRxiv2024

Microbial lysates as low-cost serum replacements in cellular agriculture media formulation

Cultivated meat, the process of generating meat in vitro without sacrificing animals, is a promising alternative to the traditional practice of livestock agriculture. However, the success of this field depends on finding sustainable and economical replacements for animal-derived and expensive fetal bovine serum (FBS) that is typically used in cell culture processes. Here, we outline an effective screening process to vet the suitability of microbial lysates to support the growth of immortalized bovine satellite cells (iBSCs) and mackerel (Mack1) cells. We show that easily producible, low-cost whole-cell lysates from Vibrio natriegens can be used to create serum-free media for the long-term growth of iBSCs. The optimized medium, named "VN40" (basal B8 media containing Vibrio natriegens lysate proteins at 40 {micro}g/mL), outperforms previously established serum-free media while maintaining cell phenotype and myogenicity. Overall, this study shows a novel approach to producing serum-free media for cultivated meat production using microbially-derived lysates.

bioengineering↗

bioRxiv2024

Retinoid X Receptor Signaling Mediates Cancer Cell Lipid Metabolism in the Leptomeninges

Cancer cells metastatic to the leptomeninges encounter a metabolically-challenging extreme microenvironment. To understand adaptations to this space, we subjected leptomeningeal-metastatic (LeptoM) mouse breast and lung cancers isolated from either the leptomeninges or orthotopic primary sites to ATAC-and RNA-sequencing. When inhabiting the leptomeninges, the LeptoM cells demonstrated transcription downstream of retinoid-X-receptors (RXRs). We found evidence of local retinoic acid (RA) generation in both human leptomeningeal metastasis and mouse models in the form of elevated spinal fluid retinol and expression of RA-generating dehydrogenases within the leptomeningeal microenvironment. Stimulating LeptoM cells with RA induced expression of transcripts encoding de novo fatty acid synthesis pathway enzymes in vitro. In vivo, while deletion of Stra6 did not alter cancer cell leptomeningeal growth, knockout of Rxra/b/g interrupted cancer cell lipid biosynthesis and arrested cancer growth. These observations illustrate a mechanism whereby metastatic cancer cells awake locally-generated developmental cues for metabolically reprograming, suggesting novel therapeutic approaches.

cancer biology↗

bioRxiv2024

Synthesis and Evaluation of Carmofur Analogs as Antiproliferative Agents, Inhibitors to the Main Protease (Mpro) of SARS-CoV-2, and Membrane Rupture-Inducing Agents

Initially developed as a derivatized analog of 5-fluorouracil for the treatment of colorectal cancer, carmofur has more recently demonstrated potent covalent inhibition of the main protease (Mpro) of SARS-CoV-2. Harnessing our previously described workflow for the optimized preparation of carmofur using benchtop 19F NMR spectroscopy, here, we prepared and evaluated a synthetic library of nine carmofur analogs with a selection of side chain motifs or single-atom substitution to explore the diversifiability of these compounds as Mpro inhibitors, where we discovered that a hexyl carbamate analog outperformed carmofur, and as antiproliferative agents in model human cell lines to identify differences in potency when the carbonyl electrophilicity and/or alkyl side chains are modified. Finally, we describe a novel workflow for the evaluation of membrane-rupturing small molecules through imaging of fluorescently labeled giant unilamellar vesicles (GUVs), and through this, we identified two lipophilic urethane analogs of carmofur bearing dodecyl urethane and octadecyl urethane side chains that have potent membrane-rupturing capability in the nanomolar range, providing insight into a potential mechanism for the in vitro activities of lipidated 5-fluorouracil analogs.

biochemistry↗

bioRxiv2024

Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information

Microbial maximum growth rates vary widely across species and are key parameters for ecosystem modeling. Measuring these rates is challenging, but genomic features like codon usage statistics provide useful signals for predicting growth rates for as-yet uncultivated organisms, though current predictors often show high variance. To improve accuracy, we integrate phylogenetic signals, leveraging the evolutionary relationships among species to refine trait predictions. We present Phydon, which combines codon statistics and phylogenetic information to enhance the precision of maximum growth rate estimates, especially when a close relative with a known growth rate is available. We construct the largest and most taxonomically broad database of temperature-corrected growth rate estimates for 111,349 microbial species. The results reveal a bimodal distribution of maximum growth rates, resolving distinct groups of fast and slow growers. Our hybrid approach advances the accuracy of genome-based growth rate predictions and presents a new framework for accurate genome-based trait prediction.

microbiology↗

bioRxiv2024

Generation of a PARPi-sensitive homozygous BRCA1-methylated OVCAR8 cell line using targeted CRISPR gene editing

Up to 17% of high grade serous ovarian carcinomas (HGSOC) harbour BRCA1 promoter methylation (meBRCA1), making them susceptible to treatment with targeted PARP inhibitor (PARPi) therapy. Unfortunately, meBRCA1 loss can be acquired following PARPi or platinum chemotherapy, resulting in BRCA1 re-expression and PARPi resistance. Our understanding of meBRCA1 stability in HGSOC is currently limited, in part due to a paucity of pre-clinical models with homozygous meBRCA1. Herein, we describe the generation of a several OVCAR8 cell line derivatives containing landing pad constructs, for future functional studies, and representing various BRCA1 states, including a homozygous meBRCA1 variant. Our PARPi resistant OVCAR8 has two methylated BRCA1 copies and one unmethylated copy, enabling BRCA1 expression. CRISPR-Cas9 gene editing was used to delete copies of the BRCA1 gene in landing pad-containing clones of this cell line (A6 and H4). We produced one variant with deletion of all BRCA1 copies (H4-53), and another with two copies deleted and only a single methylated gene copy remaining (A6-30 - validated further using nanopore long-read sequencing). These both lacked BRCA1 gene expression and were sensitive to PARPi treatment. The A6-30 line was transplanted into immunocompromised mice to generate a xenograft model that retained homozygous meBRCA1 and demonstrated some response to PARPi in vivo. Thus, using CRISPR gene editing we have created several novel isogenic HGSOC cell line models, including one with homozygous meBRCA1, that will support future studies of meBRCA1 stability and PARPi resistance.

cancer biology↗

bioRxiv2024

Airway applied IVT mRNA vaccine needs specific sequence design and high standard purification that removes devastating dsRNA contaminant

The development of next-generation mucosal mRNA vaccines is promising but extremely challenging. Major efforts have been focused on optimizing delivery systems, whereas it is still unknown whether the intrinsic quality of IVT mRNA significantly impacts the potency of airway inoculated mRNA vaccines. Here, we systematically demonstrate the mucosal mRNA vaccine requires a higher standard of purification and tailor-designed sequence to fulfil its potency compared to the parenteral route inoculated counterpart. We found double strand RNA (dsRNA) contaminants are prone to trigger innate immunoreaction in the airway that activates the mRNA degradation mechanism, thereby diminishing the mRNA expression and subsequent antigen-specific immune responses. To address these challenges, we developed a strategy that combines optimized untranslated regions (UTRs) screened from endogenous genes of pulmonary cells with affinity chromatography-based purification which removes almost all the dsRNA contaminants. The optimized mRNA administered via the airway route not only demonstrates superior protein expression (30-fold increase) and reduces inflammation in the lung, but also promotes robust immunity comprising significantly elevated systemic, cellular, and mucosal immune responses, which is in stark contrast to intramuscular injected counterpart that displays less pronounced benefits. Our findings offer new insight into the development of mucosal mRNA therapeutics from an overlooked but crucial perspective of optimizing mRNA components.

synthetic biology↗

bioRxiv2024

BrainSTEM: A multi-resolution fetal brain atlas to assess the fidelity of human midbrain cultures

Many midbrain dopaminergic neuron (mDA) differentiation protocols aimed at Parkinsons disease (PD) modeling and cell replacement therapy have been developed. However, comprehensive evaluations of the transcriptomic fidelity of these protocols at the single-cell level against a common in vivo reference have been lacking. To this end, we constructed an integrated human fetal whole-brain atlas and a midbrain subatlas to use as a standard of comparison. From the whole-brain atlas, we observed distinct brain-region-specific gene expression in most neural cell types, emphasizing the need to first evaluate in vitro protocols at the whole-brain level to identify midbrain-associated cells. These cells are then mapped to the midbrain subatlas for more refined neuronal subtype specification and trajectory analysis specific to the midbrain. We surveyed all publicly available single-cell datasets of human midbrain culture models and performed the two-tier mapping. Using this biologically-driven multi-resolution mapping strategy which we termed BrainSTEM (brain Single-cell Two tiEr Mapping), we confirmed the presence of multiple midbrain cell types ( on-target), but also a substantial proportion of cells associated with non-midbrain regions and subtypes ( off-target). This leads to an overall inflation of mDA presence, stemming from non-midbrain-associated cells, across all published protocols. BrainSTEM thus offers an unbiased framework for understanding the current state of midbrain models and aids the improvement of midbrain differentiation protocols for PD studies.

bioinformatics↗

bioRxiv2024

A T6SS DNase effector induces nuclear DNA Damage to trigger apoptosis via activation of the cGAS-STING-TNF axis

In the relentless battle for survival, bacteria have evolved sophisticated weaponry like the Type VI secretion system (T6SS) to not only outcompete rivals but also manipulate host cell processes to their advantage. Apoptosis, a controlled form of programmed cell death without triggering inflammatory responses, is often exploited by pathogens. While many bacterial pathogens are known to induce apoptosis, the role of T6SS effectors in this process remains unexplored. In this study, we discovered that Yersinia pseudotuberculosis (Yptb) utilizes its T6SS to secrete a DNase effector, TkeA, which induces apoptosis in host cells. Mechanistically, the translocation of TkeA into host cells causes nuclear DNA damage, leading to the release of fragmented DNA into the cytoplasm. This, in turn, activates the DNA-sensing cyclic GMP-AMP synthase (cGAS)/stimulator of interferon genes (STING) pathway. The activation of the cGAS-STING pathway by TkeA subsequently triggers apoptosis in host cells via extrinsic pathways, with tumor necrosis factor (TNF) signaling playing a critical role. Additionally, TkeA also mediates interbacterial competition, promoting the colonization of Yptb in mices gut. Our findings reveal that the T6SS-secreted DNase effector TkeA acts as a trans-kingdom effector, enhancing interbacterial competition and inducing apoptosis in host cells by activating the cGAS-STING-TNF axis. This discovery adds a new dimension to the mechanisms employed by bacterial pathogens to manipulate host cell death pathways by using their secretion systems. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/613802v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@1bfd70org.highwire.dtl.DTLVardef@19bfc89org.highwire.dtl.DTLVardef@1e0bf9dorg.highwire.dtl.DTLVardef@4412b9_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTS* Yptb T6SS secretes a trans-kingdom DNase effector TkeA * TkeA degrades bacterial DNA to mediate interbacterial competition * TkeA causes nuclear DNA damage in host cells to induce apoptosis * TkeA induces apoptosis via the cGAS-STING-TNF axis

microbiology↗

bioRxiv2024

The H3K4me3 binding ALFIN-LIKE proteins recruit SWR1 for gene-body deposition of H2A.Z

The H2A.Z histone variant is highly enriched over gene bodies, playing an essential role in several genome-templated processes, including transcriptional regulation and epigenetic patterning across eukaryotes. The SWR1 chromatin remodeling complex deposits H2A.Z. How SWR1 is directed to gene bodies is largely unknown. Here, we show that ALFIN-LIKE (AL) proteins are responsible for H2A.Z gene body patterning in Arabidopsis. AL proteins encode H3K4me3-binding PHD domains, and by ChIP-seq, we confirm preferential binding of AL5 to H3K4me3 over H3K4me1/2 in planta. We observe a global reduction in H2A.Z in al septuple mutants (al7m), especially of over H3K4me3-enriched genic regions. While MBD9 recruits SWR1 to nucleosome-free regions, ALs act non-redundantly with MBD9 for deposition of H2A.Z. Notably, al7m mutants show severe developmental abnormalities and upregulation of H2A.Z gene body-enriched responsive genes. Therefore, we propose a model whereby AL proteins direct gene body enrichment of H2A.Z by recruiting SWR1 to H3K4me3-containing responsive genes.

plant biology↗

bioRxiv2024

Development of a DNA-encoded library screening method DEL Zipper to empower the study of RNA-targeted chemical matter

To date, RNA-targeted chemical matter is under explored due to a lack of robust screening assays. In this study, we present a novel RNA-targeted small molecule screening approach using a specialized DNA-encoded library (DEL). Our findings reveal that the specialized DEL library, called "DEL Zipper", can significantly reduce single-stranded DNA-RNA region interaction signals during various kinds of RNA selection. By performing the selection against both G-quadruplex, we have identified novel hits that interact with RNA targets and the results are validated through binding. This study demonstrates that the "DEL Zipper" method is a robust screening assay that has potential for discovering small molecule ligands for diverse RNA targets.

molecular biology↗