Biology subjects

Jiao, R.

Publications and source records attributed to Jiao, R..

8 recordsLinked to original sources

bioRxiv2026

Design of synthetic activators for programmable gene expression

Transcription factors control gene expression by recruiting transcriptional coactivators through intrinsically disordered transcriptional activation domains (TADs), whose weak and promiscuous interactions make it difficult to establish quantitative relationships between coactivator recruitment and transcriptional output, and to precisely modulate gene expression. To overcome this limitation, we set out to design coactivator-recruiting proteins using AlphaFold3-predicted TAD-coactivator interactions as a guide. We developed a high-throughput functional screening platform in mammalian cells and identified over 300 well folded nanomolar affinity binders to the transcription coactivators Mediator (multiple subunits), BRD4, NCOA, and p300; targeted interface mutations enabled systematic tuning of their binding affinities. Using a panel of p300 binders spanning nanomolar to micromolar affinities, we found an ultrasensitive relationship between coactivator-binding affinity and transcriptional output, with a sharp transcriptional activation threshold at ~500 nM. Incorporating p300 binder designs into CRISPRa yielded compact synthetic effectors that drove stronger activation than VPR across multiple genomic loci with minimal detectable cytotoxicity. Combining p300- and Mediator-specific binders further enhanced transcription, revealing functional synergy between these coactivators. Together, our work establishes a quantitative framework linking coactivator-binding affinity to transcriptional output and provides compact synthetic effectors for programmable gene activation.

synthetic biology↗

bioRxiv2026

Sequence-Independent In Situ Imaging of GlycoRNA in Living Cells and Tissues based on COMPASS

Current methods for the imaging of glycosylated RNAs (glycoRNAs) focus on limited types with identified RNA sequences, making the distribution of global glycoRNAs at single-cell and tissue levels largely unexplored. To address this gap, we developed a co-metabolic proximity labeling assay (COMPASS) for sequence-independent imaging of glycoRNAs. COMPASS employs metabolic chemical reporters (MCRs) to label glycans and RNAs, followed by click-chemistry-based dye conjugation to generate Forster resonance energy transfer (FRET) signals. The MCR-enabled RNA labeling allows for sequence-independent imaging, and FRET ensures accurate localization of glycoRNA distributions. COMPASS facilitates glycoRNA imaging across multiple cell lines, cerebral organoids, and mouse tissues. We observed the downregulation of glycoRNAs in metastatic lung nodules and upregulation in original regions of brain development in cerebral organoids, suggesting their potential association with carcinogenesis and neurogenesis. COMPASS illuminates previously invisible glycoRNAs and offers a comprehensive profile of glycoRNA distribution for studying their functions.

bioengineering↗

bioRxiv2026

Programming Biomolecular Interactions with All-Atom Generative Model

Biomolecular interactions lie at the core of cellular life, spanning diverse molecular modalities from small molecules to nucleic acids and proteins. Nevertheless, design strategies remain separated despite shared physicochemical principles of molecular recognition. Here we present AnewOmni, a unified generative framework trained on more than 5 million biomolecular complexes, that enables transferable molecular design across molecular scales by assembling chemically meaningful building blocks at atomic resolution. We further introduce programmable graph prompts to support user-defined chemical, topological, and geometric steering during generation, exploring hybrid and unconventional chemistries beyond canonical structures. We demonstrate that transferable learning of interaction patterns and physical constraints across molecular modalities is possible, via an atom-to-block latent space capturing both atomic details and structural priors. The framework successfully designed small molecules, peptides, and nanobodies targeting the challenging KRAS G12D switch II pocket, as well as orthosteric peptides and allosteric small-molecule inhibitors for PCSK9 in the absence of known binding site, achieving 23%-75% success with only low-throughput validation, bypassing modality-specific high-throughput screening. AnewOmni is the first to succeed in functional molecular design across all scales, from small chemical entities to large biologics, and represents a stepstone towards general molecular reasoning engines, advocating a generative foundation model for biomolecular interactions to enter regimes where data and human intuition remain limited.

bioengineering↗

bioRxiv2025

Separately prestored proteasome components to prevent polyspermy

To ensure genome stability across generations, an egg must be fertilized by only a single sperm. However, how sperm actively contribute to preventing polyspermy has remained unknown. Here, we demonstrate that testis-specific 20S proteasome core particles (CPs) are pre-stored within the sperm heads of both mice and humans. Upon fertilization, these testis-specific 20S CPs assemble with oocyte-derived 19S regulatory particles (RPs), forming chimeric proteasomes that efficiently degrade Fetuin B, which is ubiquitinated by the E3 ligase MARCH3. The clearance of Fetuin B triggers ZP2 cleavage and subsequent zona pellucida hardening, thereby blocking additional sperm entry. The newly assembled chimeric proteasome in the zygote represents a novel strategy to prevent polyspermy during fertilization in mammals.

developmental biology↗

bioRxiv2025

Functional Characterization of Paillotin: An Immune Peptide Regulated by the Imd Pathway with Pathogen-Specific Roles in Drosophila Immunity

Insects, such as Drosophila melanogaster, rely on innate immune defenses to combat microbial threats. Antimicrobial peptides (AMPs) play an important role in limiting pathogen entry and colonization. Despite intensive research into the regulation and biochemical properties of AMPs, their exact significance in vivo has remained uncertain due to the challenges of mutating small genes. Fortunately, recent technologies have enabled the mutation of individual AMP genes, overcome previous obstacles, and opened new avenues for research. In this study, we characterized one novel host-defense peptide, Paillotin (IM18, CG33706), using loss-of-function mutants. Paillotin is an ancient host defense peptide of Diptera, regulated by the Imd pathway. Loss of Paillotin does not impact the activity of either the Imd or Toll pathways. Importantly, we found that Paillotin mutants are viable but exhibit increased susceptibility to specific infections, particularly Providencia burhodogranariea. Paillotin was further found to contribute synergistically to defense against P. burhodogranariea when combined with other AMPs. However, we did not detect direct microbicidal activity of Paillotin in vitro in our hands. Taken together, our findings identify Paillotin as a novel host defense peptide acting downstream of Imd signaling, advancing our understanding of the Drosophila antimicrobial response.

immunology↗

bioRxiv2025

Peptide Design through Binding Interface Mimicry

Peptides offer distinct advantages for targeted therapy, including oral bioavailability, cellular permeability, and high specificity, which set them apart from conventional small molecules and biologics. In this work, we developed an AI algorithm, named PepMimic, to transform a known protein receptor or an existing antibody of a target into a short peptide drug by mimicking the binding interfaces between targets and known binders. The structural root mean square deviation and interface DockQ with reference binders were 61% and 75% better than the best existing methods on the PepBench datasets. We then applied this novel peptide-design methodology to five drug targets: PD-L1, CD38, BCMA, HER2, and CD4. SPRi results show that 8% of the peptides exhibited dissociation constant (KD) values at the 10-8M level, and 26 peptides achieving KD values as low as 10-9M. This success rate was 20,000 times higher than that observed in a random library screening conducted under identical conditions. PepMimic was applied to target proteins lacking available binders by first utilizing AI algorithms to design protein binders, followed by the generation of peptides through simulation of these artificial interfaces. The top-ranked peptides underwent extensive cellular validation and in vivo testing through tail vein injections in breast, myeloma, and lung tumor mouse models. Experimental results demonstrated effective membrane binding and highlighted the strong potential of these peptides for clinical diagnostic imaging and targeted therapeutic applications.

biochemistry↗

bioRxiv2023

A novel virus-induced cyclic dinucleotide, 2'3'-c-di-GMP, mediates STING-dependent antiviral immunity in Drosophila

In mammals, the enzyme cGAS senses the presence of cytosolic DNA and synthesizes the cyclic dinucleotide (CDN) 2'3'-cGAMP. This CDN binds to and activates the protein STING to trigger immunity. We recently discovered in the model organism Drosophila melanogaster two cGAS-like receptors (cGLRs) that activate STING-dependent antiviral immunity and can produce 3'2'-cGAMP, in addition to 2'3'-cGAMP. Here we explore CDN-mediated immunity in 14 different Drosophila species covering 50 million years of evolution and report that 2'3'-cGAMP and 3'2'-cGAMP fail to control infection by Drosophila C virus in D. serrata, D. sechellia and D. mojavensis. Using an accurate and sensitive mass spectrometry method, we discover an unexpected diversity of CDNs produced in a cGLR-dependent manner in response to viral infection in D. melanogaster, including a novel CDN, 2'3'-c-di-GMP. We show that 2'3'-c-di-GMP is the most potent STING agonist identified so far in D. melanogaster and that this molecule also activates a strong antiviral transcriptional response in D. serrata. Our results shed light on the evolution of cGLRs in flies and provide a basis for the understanding of the function and regulation of this emerging family of PRRs in animal innate immunity.

immunology↗

bioRxiv2020

The BaramicinA gene is required at several steps of the host defense against Enterococcus faecalis and Metarhizium robertsii in a septic wound infection model in Drosophila melanogaster

The Drosophila systemic immune response against many Gram-positive bacteria and fungi is mediated by the Toll pathway. How Toll-regulated effectors actually fulfill this role remains poorly understood as the known antimicrobial peptide (AMP) genes it controls are essentially active only against filamentous fungi and not against Gram-positive bacteria or yeasts. BaramicinA gene expression is transcriptionally regulated by the Toll pathway. BaraA encodes a polyprotein precursor that releases processed proteins into the hemolymph upon immune challenge. Here, we demonstrate that BaraA is required specifically in the host defense against Enterococcus faecalis and against the entomopathogenic fungus Metarhizium robertsii. It does so by protecting the fly from the action of distinct toxins secreted by Gram-positive and fungal pathogens but not by directly attacking them. Thus, in complement to the current paradigm, innate immunity can cope with toxins, effectively, through the secretion of peptides that are not AMPs, independently of xenobiotics detoxification pathways.

immunology↗