Biology subjects

Liu, H.

Publications and source records attributed to Liu, H..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Loss of NKX2-1 predisposes thyroid to neoplasm development through regulation of oxidative stress

Many factors including ionizing radiation and iodine deficiency are known to increase thyroid carcinogenesis risk. Our dataset analysis of The Cancer Genome Atlas (TCGA) showed that lower mRNA expression of NK2 homeobox 1 (NKX2-1) transcription factor, a master regulator of genesis, homeostasis, and function of thyroid, is linked to poor prognosis of papillary thyroid cancer patients. Here we provide the findings that thyroid-specific Nkx2-1 conditional knockout (Nkx2-1{Delta}T) mice develop thyroid adenoma and carcinoma in higher frequency with combined exposure to radiation and iodine deficiency than control Nkx2-1fl/fl mice. Iodine deficiency caused oxidative stress, which subsequently resulted in DNA damage, leading to transformation of thyroid follicular cells. RNA-seq gene set enrichment analysis indicated higher production of reactive oxygen species (ROS) in the thyroids of Nkx2-1{Delta}T as compared to Nkx2-1fl/fl mice with combined exposure to radiation and iodine deficiency. This was accompanied by a feedback induction of SOD3 (superoxide dismutase 3) and GPX2 (glutathione peroxidase 2). These antioxidants were naturally expressed at higher levels in the thyroids of Nkx2-1{Delta}T than Nkx2-1fl/fl mice without iodine deficiency or radiation. Nkx2-1{Delta}T thyroids exhibited abnormal follicle architecture and up-regulation of Acox2 (encoding acyl-CoA oxidase 2), which produces hydrogen peroxide. These results suggest that loss of NKX2-1 may contribute to excess ROS production, which elevates basal oxidative stress resulting in the promotion of ROS-induced carcinogenesis. We propose a role for NKX2-1 as a regulator of ROS production homeostasis in the thyroid. Its disturbance would dispose thyroid follicular cells more vulnerable to the ROS-producing carcinogens.

cancer biology↗

bioRxiv2026

Programmable De Novo Design of Mesoporous Protein Crystal Frameworks

Three-dimensional protein crystals are ordered, porous macroscopic materials with potential applications in catalysis, biosensing, and biomedicine. However, most protein crystals are obtained by empirical screening, providing limited control over the lattice architecture, pore geometry or component composition that determine material function. Here, we present a modular strategy for the programmable design of highly porous, framework-like protein crystals using predefined protein-protein interactions. This strategy yielded over 30 distinct protein crystals, including single-component and multicomponent P213 and I213 lattices that grow to over 100 micrometers in size. Small-angle X-ray scattering and electron microscopy showed close agreement between experimental lattices and computational models. RFdiffusion-guided design generated isomorphous variants with matched lattice parameters, enabling coherent protein crystal alloys, epitaxial core-shell growth and reversible shell assembly. The designed crystals exhibit tunable mesoporous architectures, with limiting apertures of 2-18 nm, and support genetically encoded incorporation of fluorescent protein guests. These results establish a general route to programmable lattice engineering of protein crystals and position them as genetically encoded, compositionally tunable mesoporous materials.

synthetic biology↗

bioRxiv2026

Small intestinal microbiota of undernourished women perturbs placental development in mice

Children of undernourished women have impaired pre- and postnatal growth. Undernourished women and children have a high incidence of environmental enteric dysfunction (EED), an enteropathy characterized by gut barrier dysfunction and systemic inflammation. Here, we employ gnotobiotic mice to compare the effects of bacterial consortia cultured from the duodenal microbiota of Bangladeshi women with EED and their healthy counterparts. Female mice harboring the EED-derived consortium exhibited fetal and placental growth restriction. Transcriptomic and proteomic analyses disclosed pronounced effects of the EED-derived consortium on the decidual component of the maternal-fetal interface involving tissue-resident uterine natural killer (uNK) cells and disruption of TGF-{beta} signaling between uNK and decidual stromal cells. Co-housing mice with EED and healthy consortia ameliorated these effects, disclosing bacterial targets to improve prenatal development.

systems biology↗

bioRxiv2026

mV2G: a multiomic atlas for tissue-specific variant-to-gene prioritization

The multiomic Variant-to-Gene (mV2G, https://mv2g.hbliulab.org) is a comprehensive atlas that integrates diverse functional genomic evidence to prioritize tissue-specific variant-to-gene (V2G) associations. While genome-wide association studies (GWAS) have identified millions of associations between genetic variants and diseases, translating these findings into biological mechanisms remains challenging because >90% of variants reside in noncoding regions. Existing V2G resources provide complementary regulatory evidence but are fragmented and often lack tissue-specific interpretation. To address this challenge, we constructed the mV2G atlas by integrating 24 types of functional genomic evidence across 50 human tissues, including molecular quantitative trait loci, enhancer-gene predictions, three-dimensional chromatin interactions, and experimental validation. The atlas contains 188,634,118 evidence-supported V2G pairs involving 13,618,039 variants and 69,521 genes. We further developed a unified tissue-specific V2G prioritization framework and prioritized 1,530,420 high-confidence functional V2G pairs involving 1,131,316 unique variants, with 87% exhibiting tissue-specificity. The mV2G atlas provides searchable variant- and gene-centered interfaces, an interactive browser for visualizing variants, target genes, cis-regulatory elements, and chromatin states, as well as downloadable datasets. By integrating complementary regulatory evidence into a unified framework, mV2G provides an accessible resource for interpreting the functional and phenotypic impact of genomic variation in relevant tissues for human diseases. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/743997v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@ac8319org.highwire.dtl.DTLVardef@1d31920org.highwire.dtl.DTLVardef@169225org.highwire.dtl.DTLVardef@1d4dc02_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2026

Cell line resources for the study of neurofibromin: functions, phenotypes, and drug discovery/development

Our labs have been studying neurofibromin function and phenotype for over a decade with the intent of generating targeted therapeutics for Neurofibromatosis type 1 (NF1). In the process, we have generated numerous human cell lines containing variants within the NF1 gene. Herein, we present data characterizing these cell lines and make them publicly available for use by researchers both within and outside the NF1 community. We describe lines that contain both well-characterized patient-specific variants either at their endogenous locus or as exogenous cDNAs, as well as variants of uncertain significance (VUS), engineered as heterozygous, homozygous, and compound heterozygous variants. Methods to generate each line and subsequent validation steps are detailed including targeted sequencing, Western blot analysis for neurofibromin expression and ERK activation. The utility of each line is dependent on the variant of interest, the parental cell line, and the mechanism of action relevant to possible therapeutic targeting.

genetics↗

bioRxiv2026

Cross-Species Comparison of Topologically Associating Domains (TADs) in Cereals Reveals Their Role in Genome Stability During Evolution

Topologically associating domains (TADs) are essential structural and functional modules of the genome that play a crucial role in regulating gene expression. In this study, we systematically investigated the conservation and evolution of TADs in five closely related crops, including maize, sorghum, coix, foxtail millet and broomcorn millet. Our results show that 74% of TAD boundaries are conserved between two inbred maize lines, B73 and Mo17, and that approximately 50% or more of TAD boundaries are conserved across different crop species. TAD number remains relatively stable in the face of changes in genome size. However, the length of TADs varies depending on genome size. Furthermore, we found that large-scale transposable element expansion leads to TAD expansion, while chromosomal inversions lead to TAD fusion and the formation of new TAD boundaries. Frequent chromatin interactions between subgenome chromosomes occur after whole-genome duplication. Moreover, we also found that crossovers are enriched at TAD boundaries in maize, indicating the importance of TADs as a fundamental unit during species evolution. Overall, our study provides insights into the conservation and evolution of TADs in crop genomes and their roles in genome organization and function.

plant biology↗

bioRxiv2026

The cellular and genetic basis of inflorescence divergence between maize and teosinte

The domestication of maize from teosinte involved dramatic remodeling of the ear, yet the cellular and genetic bases of this transformation remain unclear. Here, we generate a single-nucleus and spatial transcriptome atlas of developing maize and teosinte ears. Comparative analysis reveals divergence in cob-associated cell types, with enhanced cytokinin signaling and reduced growth-inhibitory signals collectively driving cob thickening and enlargement in maize. We further demonstrate that domestication expanded the spatial expression domain of key transcription factors in maize meristem cells, enhancing the potential for increasing kernel number. Additionally, we verified a major domestication gene, ZmSPD1, in which two nonsynonymous SNPs differentiate maize from teosinte and alter jasmonic acid (JA) levels in the ear, thereby suppressing spikelet abortion to effectively double kernel production. These findings provide a cell-resolved mechanistic framework for how cob architecture and kernel number were shaped during maize domestication, offering new insights into the formation of key agronomic traits.

plant biology↗

bioRxiv2026

Evolution-inspired multi-objective Bayesian optimization for protein engineering

Protein engineering requires efficient navigation of vast sequence spaces under limited evaluation budgets, especially when multiple properties must be optimized simultaneously. We developed Evolution-inspired Multi-Objective Bayesian Optimization (EvoMOBO), an active-learning framework that integrates path-dependent sequence generation, global competition among generated variants, and explicit multi-objective optimization. Benchmarking against state-of-the-art methods on complete steroid receptor DNA-binding domain and ParD3 antitoxin landscapes demonstrated robust target-region enrichment, Pareto-front advancement, and sequence diversity across two- and three-objective tasks. In the DBD landscape, simulation-derived geometric descriptors served as labels for both initialization and iterative updating, enriching variants with favorable measured activities without experimental labels. Building on this validation, we applied EvoMOBO to two enzyme-engineering tasks using simulation-derived mechanistic descriptors, with experiments reserved for final validation. For an old yellow enzyme (GkOYE), 16 of 26 tested variants outperformed the wild type, and the best increased non-native oxidative dehydrogenation conversion from 17.5% to 95%. For a formate oxidase (AoFOx), EvoMOBO identified aggregation-resistant variants, two of which nearly doubled diethyl phthalate degradation in a photoenzymatic cascade. Together, these results establish EvoMOBO as a modular framework for multi-objective protein engineering using experimental or mechanism-derived labels.

bioengineering↗

bioRxiv2026

Multiomic Integration Reveals Transposable Element-Embedded Regulatory Variants Underlying Brain Aging

Genome-wide association studies (GWAS) have identified thousands of variants associated with brain aging, most in noncoding regions whose regulatory effects remain poorly understood. Transposable elements (TEs) constitute a major, understudied component of brain regulatory DNA. To interpret noncoding brain-aging variants through TE-derived regulatory architecture, we integrated brain-aging GWAS variants with TE annotations, ENCODE candidate cis-regulatory elements (cCREs), single-nucleus ATAC-seq accessibility maps, HOMER motif analysis, experimental enhancer-promoter interaction maps, and multiomic variant-to-gene resources. Of 6,323 genome-wide-significant variants, 633 (10.0%) localized within 367 TE-derived cCREs. These elements were predominantly enhancer-like and frequently carried transcription factor-associated annotation. Alu-derived elements formed the largest family component, followed by L1, L2, MIR and ERVL-MaLR elements. Single-nucleus accessibility maps resolved these variants across brain cell types, including a TcMar-Tigger-associated signal in oligodendrocytes, and motif analysis of SINE-associated cCREs identified reproducible nuclear-receptor, immune (PU.1:IRF8) and chromatin-regulatory (RFX-family) signatures. Because this localization reflects correlated variants within a limited number of independent loci rather than independent enrichment signals, we prioritized candidate regulatory variants and their target genes using the Brain Aging Genetic ScoreCard, which integrates 27 orthogonal evidence layers across independent, LD-defined loci and identified 25 loci with TE-derived regulatory support. The chromosome 17q21.31 MAPT locus emerged as the top candidate genome-wide, where a MIR-derived enhancer shows convergent evidence linking it to MAPT, a prioritization robust to locus-size effects. Overall, our study provides an integrative framework for interpreting noncoding GWAS variation through TE-derived regulatory architecture.

genomics↗

bioRxiv2026

Molecular principles for graded activation of dopamine D1 receptor

G protein-coupled receptors (GPCRs) signal across a continuum of activation states, yet how ligands encode distinct signaling efficacies remains poorly understood. Here, we define the molecular mechanism underlying graded activation of the dopamine D1 receptor (D1R), a major therapeutic target for neuropsychiatric disorders. Functional analyses reveal that two widely used pharmacological tools, LE300 and SCH23390, possess intrinsic efficacy as an inverse agonist and a weak partial agonist, respectively, rather than the efficacy-silent neutral antagonists. Structural, molecular dynamics and mutagenesis analyses capture previously unrecognized inactive and intermediate receptor activation states that bridge known active conformations, and reveal that ligand efficacy is encoded through the progressive engagement of a conserved activation pathway centered on the W6.48 toggle switch. Guided by this mechanism, a single chemical modification markedly increases the agonist efficacy of SCH23390. Comparison with dopamine D2 receptor structures further reveals a conserved mechanism of inverse agonism despite distinct subtype-specific recognition. Together, these findings establish a structural framework for graded agonism at D1R and provide general principles for the rational design of efficacy-tuned therapeutics at dopamine receptors and related GPCRs.

biochemistry↗

bioRxiv2026

The Proposed Bone Post-Arterial Type R Capillaries Resolve into Venous and Fatty Acid-Handling Endothelial Cells

Endothelial specialization is increasingly recognized as a fundamental regulator of tissue homeostasis, yet the cellular diversity of the skeletal vasculature remains incompletely resolved. Here, we integrate large-scale single-cell transcriptomics, cross-tissue comparisons, and imaging to comprehensively define endothelial heterogeneity across the skeleton. Our analyses demonstrate that the proposed post- arterial "type R" endothelial population is not a distinct endothelial subtype but instead comprises canonical venous endothelial cells and fatty acid-handling endothelial state. RNA velocity supports a venous continuum, while the proposed type R markers FMO2, and AQP7 lack both endothelial and skeletal specificity. The fatty acid-handling endothelial state, characterized by Lpl and Cd36 is conserved across multiple skeletal sites and non-skeletal tissues, indicating a general endothelial metabolic programme. Within bone, this endothelial state expands following high-fat diet and is suppressed during injury. Together, these findings redefine skeletal endothelial heterogeneity and establish the proposed type R population as part of a venous continuum.

cell biology↗

bioRxiv2026

Pan-Peroxisome Proliferator-Activated Receptor Agonist IVA337 Alleviates Secondary Lymphedema via Inhibiting TGFβ/SMAD2/3 Signaling Pathway

Lymphedema is a chronic disease characterized by impaired lymph drainage and accumulation of protein-rich interstitial fluid, which progresses to develop irreversible fibrosis. Importantly, effective therapies and treatments are lacking to alleviate and mitigate the disease. The pathological inflammation and fibrogenesis underlying lymphedema prompted us to evaluate a preclinical medicine IVA337, a pan-peroxisome proliferator-activated receptor (PPAR) agonist that improves liver fibrosis in patients with metabolic dysfunction-associated steatohepatitis (MASH) by activating three PPAR isoforms (, {beta}/{delta}, {lambda}), which play critical roles in lipid metabolism, anti-inflammation responses, and anti-fibrogenesis. Here, we investigate the therapeutic effects of IVA337 during the early stage of surgery-induced secondary lymphedema in mice and explored the underlying mechanisms. IVA337 administration alleviated lymphedema progression, improved lymphatic drainage, reduced dermal thickness, and resolved lymphatic vessel dilation. Mechanistically, IVA337 suppressed the TGF{beta}/SMAD2/3 signaling pathway, reduced immune cells infiltration, and improves lymphatic vessels integrity. In human dermal lymphatic endothelial cells (HDLECs), IVA337 attenuated TGF{beta} induced SMAD2/3 phosphorylation and preserved the expression of cell junction Claudin5, reduced VE-Cadherin-stained cell-cell gaps. Collectively, our findings demonstrate that IVA337 protects against early stage lymphedema by inhibiting TGF{beta}/SMAD2/3-mediated inflammatory and fibrotic responses. This study provides a potential therapeutic strategy to improve lymphatic function during the early phase of lymphedema and prevent progressive fibrosis in patients with lymphedema and related disorders.

pathology↗

bioRxiv2026

Dronedarone hydrochloride reverses obesity-related metabolic syndrome while preserving skeletal muscle mass

Obesity-driven metabolic syndrome poses a critical global threat, yet standard therapies like GLP-1 receptor agonists trigger substantial lean mass wasting, with muscle loss accounting for up to 40% of reduced weight. Here we identify a non-canonical metabolic application for dronedarone hydrochloride, an anti-arrhythmic benzofuran derivative. In diet-induced and ob/ob obese mice, short-term dronedarone hydrochloride administration dose-dependently reduces food intake, clears visceral and subcutaneous adiposity, and reverses steatohepatitis. Head-to-head trials show that dronedarone hydrochloride achieves glycemic control and fat clearance non-inferior to semaglutide, tirzepatide, and empagliflozin, but uniquely and completely preserves skeletal muscle mass. Mechanistically, dronedarone hydrochloride operates independently of central hypothalamic appetite-regulating neuropeptides and the peripheral leptin pathway. By decoupling fat reduction from sarcopenia, our findings establish dronedarone hydrochloride as a muscle-sparing therapeutic candidate for metabolic syndrome.

pharmacology and toxicology↗

bioRxiv2026

A fast 2C-induction method reveals a barrier role of SP2 for totipotency

The acquisition of totipotency in vitro remains a major challenge, limiting our understanding of early embryogenesis and its clinical and translational applications. Here, we reported a robust and rapid chemical reprogramming system that converts mouse embryonic stem cells (mESCs) into totipotent-like cells (TLCs) within 36 hours, with efficiencies exceeding 70%. The induced cells exhibit transcriptomic, epigenomic, and functional features closely resembling 2-cell (2C) stage embryos, as confirmed by scRNA-seq, ATAC-seq, and chimeric embryo analyses. Single-cell trajectory construction revealed a branching reprogramming process that yields both successful totipotent-like and alternative, non-reprogrammed fates. Mechanistically, we identified the transcription factor SP2 as a barrier to totipotency acquisition, promoting lineage-specific gene expression while repressing totipotency networks. Collectively, our study has established a highly efficient in vitro model for totipotency induction and highlighted molecular barriers shaping cell fate decisions, providing a platform to dissect the mechanisms governing the pluripotency-to-totipotency transition.

developmental biology↗

bioRxiv2026

The carbon-nitrogen metabolism gene E1OGDH1 influences maize root system architecture and nitrogen plasticity

Synthetic nitrogen fertilizers have greatly increased crop yields, yet much of the applied nitrogen is lost from agroecosystems and contributes to environmental pollution and higher economic costs. Improving nitrogen uptake efficiency (NUpE) benefits from understanding how root system architecture (RSA) governs soil nitrogen capture. Although root traits have seldom been explicit breeding targets, selection for variation in above-ground nitrogen accumulation has also likely shaped differences in RSA. The Illinois Protein Strain Recombinant Inbred population, derived from more than a century of divergent selection for seed protein concentration, offers a powerful resource for dissecting RSA variation. Using multi-year field phenotyping of excavated root crowns and genome-wide association analysis, we identified a quantitative trait locus on chromosome 10 containing E1OGDH1, which encodes the E1 subunit of the 2-oxoglutarate dehydrogenase (OGDH) complex. OGDH performs a key step in the tricarboxylic acid cycle that also modulates 2-oxoglutarate, an important entry point into nitrogen metabolism and a co-factor for enzymes involved in hormone and secondary product synthesis. Long-read sequencing of inbreds derived from the divergent IHP and ILP parental populations revealed promoter polymorphisms defining E1OGDH1 alleles and differed in E1OGDH1 expression in root tissue. Field experiments in IPSRI lines carrying IHP- or ILP-associated E1OGDH1 alleles showed differences in root architectural traits over two years. CRISPR-Cas9 knockout mutants confirmed a functional role for E1OGDH1 in whole-plant performance and nitrogen-responsive root development. Mutants were shorter, had reduced biomass, and exhibited altered architectural responses to soil nitrogen levels. Transcriptome analysis further showed that loss of E1OGDH1 altered basal and nitrogen-responsive expression of genes associated with root development and nitrogen uptake and metabolism. Together, these findings identify E1OGDH1 as a strong candidate quantitative regulator of maize RSA and nitrogen plasticity, suggesting that central carbon-nitrogen metabolic genes can contribute to root developmental responses relevant to NUpE.

plant biology↗

bioRxiv2026

CXCL12/CXCR4 Governs Lymphatic Valve Formation Through Flow Dependent AKT/FOXO1/FOXC2 Activation

BackgroundLymphatic valves are specialized structures within lymphatic vessels that ensure unidirectional lymph transport. Defective lymphatic valve formation is associated with lymphedema, a chronic disease characterized by impaired lymph drainage and the accumulation of protein-rich interstitial fluid. Lymphatic valves form during late embryonic stages in mice, with oscillatory shear stress implicated in regulating the molecular mechanisms which control lymphatic valve formation. However, the molecular mechanisms governing lymphatic valve formation remain incompletely understood. Although CXCR4 is regulated by shear stress in blood vessels, whether CXCL12/CXCR4 signaling regulates lymphatic valve formation and the underlying molecular mechanisms remain unknown. MethodsTo investigate the roles of CXCR4 in the regulation of lymphatic valve development, we utilized lymphatic endothelial cell (LEC)-specific Cxcr4 knockout (Flt4CreERT2, Cxcr4f/f) mice. To determine the source of CXCL12, major ligand for CXCR4 in the mesentery, we used global Cxcl12-/-, and Cxcl12-DsRed knock-in/knockout (KIKO) reporter mice, as well as conditional Cxcl12 knockout mouse lines. To determine the molecular mechanisms by which CXCL12/CXCR4 regulates lymphatic valve development, primary human dermal LECs were exposed to oscillatory shear stress (OSS) to mimic valve-associated flow, followed by analysis of downstream signaling pathways and valve related gene expression. ResultsLEC-specific loss of CXCR4 displayed impaired lymphatic valve development. Flt4CreERT2, Cxcr4f/f mice showed a significant reduction in valve numbers in embryonic mesenteric lymphatic vessels. Similarly, reduced valve numbers were observed in Cxcl12-/- embryos, indicating CXCL12/CXCR4 is required for embryonic mesentery collecting lymphatic valve formation. Cxcl12-DsRed KIKO mice revealed that blood vessels, opposed to nerves, were the major source of CXCL12 in the embryonic mesentery. In align with this finding, EC-specific Cxcl12 deletion recapitulated defective valve phenotypes observed in Cxcl12-/- embryos. Mechanistically, CXCR4 knockdown in primary human dermal LECs attenuated OSS induced phosphorylation of AKT and FOXO1, leading to increased nuclear localization of FOXO1 and reduced expression of FOXC2, an essential transcription factor governing lymphatic valve development. Consistent with these findings, lymphatic valves of LEC-Cxcr4 deficient mice exhibited increased FOXO1 nuclear localization. Importantly, pharmacological activation of AKT reduced FOXO1 nuclear accumulation and restored lymphatic valve numbers in LEC-Cxcr4 deficient mesenteric lymphatic vessels. ConclusionsOur findings reveal CXCL12/CXCR4 signaling acts as a critical regulator of lymphatic valve development. CXCL12/CXCR4 signaling integrates into the flow dependent AKT/FOXO1/FOXC2 signaling axis to coordinate lymphatic valve development and morphogenesis. Taken together, our study uncovers a previously unknown role of CXCL12/CXCR4 signaling pathway in the regulation of lymphatic valve development. Targeting CXCL12/CXCR4/AKT/FOXO1 axis may represent a promising therapeutic strategy for improving lymphatic valve development to improve lymphatic function for the treatment of lymphedema.

developmental biology↗

bioRxiv2026

Promoter architecture decodes response regulator phosphorylation into distinct transcriptional logics in Pseudomonas aeruginosa

Two-component systems convert environmental signals into transcriptional responses, but how one response-regulator phosphorylation state produces different outputs at different promoters remains unclear. Here we show that promoter architecture determines how the ParR response regulator in Pseudomonas aeruginosa interprets phosphorylation. Phenotypic, transcriptomic, biochemical and promoter-engineering analyses showed that phosphorylation of the conserved ParR receiver residue Asp57 lowered DNA-occupancy thresholds across target promoters. Individual promoters, however, converted this shared increase in binding into activation, repression or phosphorylation-dependent sign switching. Chromosomally D57 ParR variants reproduced these behaviours at endogenous loci and altered antibiotic susceptibility, biofilm formation and virulence-associated phenotypes. Mapping and engineering of representative promoters identified a two-tier cis-regulatory code: half-site sequence compatibility determines productive ParR engagement, whereas spacer length determines regulatory sign and magnitude. Spacer swaps were sufficient to reprogram promoter logic between regulatory modes. These findings separate regulator state from promoter decoding and show how bacterial promoter architecture can diversify the outputs of a shared phosphorylation signal. ImportancePseudomonas aeruginosa is an opportunistic pathogen that survives antimicrobial treatment and adapts to diverse host environments by rapidly changing gene expression. How a single sensory pathway generates different, and sometimes opposing, responses across many genes has remained unclear. We show that the regulatory protein ParR does not impose one fixed transcriptional program. Instead, the DNA architecture of each target promoter determines whether the same phosphorylation signal activates, represses, or reverses gene expression. The sequence and spacing of ParR recognition sites form a compact regulatory code, and changing spacer length alone can reprogram promoter behavior. Different ParR states were also associated with changes in antibiotic susceptibility, biofilm formation, and virulence-associated phenotypes. Our findings explain how one bacterial signaling pathway can generate diverse physiological outcomes without additional regulators and provide a framework for understanding regulatory flexibility in Pseudomonas aeruginosa and for engineering genetic circuits with multiple outputs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/740031v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1b6ec28org.highwire.dtl.DTLVardef@4a3f2eorg.highwire.dtl.DTLVardef@79e528org.highwire.dtl.DTLVardef@b3aa77_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Reconstructing sequence-grammar trajectories enables interpretable and tunable cis- regulatory element design

Designing synthetic cis-regulatory elements (CREs) with cell-type-specific activity remains challenging, and optimization is usually treated as a black box, obscuring how regulatory grammar emerges and why design trajectories fail. Here, we present GO-CRE (Guided Optimization of Cis-Regulatory Elements), which combines efficient sequence generation, predictor-guided reinforcement learning, and trajectory-level interpretation. GO-CRE reconstructs iterative sequence changes in a shared sequence-grammar landscape and identifies coordinated update programs corresponding to search, commitment, and optimization. Productive trajectories in HepG2 and K562 progressively acquired cell-type-associated grammar, whereas SK-N-SH trajectories remained confined to local basins. In HepG2, trajectory analysis revealed a low-complexity polyG trap; introducing a polyG penalty redirected optimization toward HNF/FOXA-associated features. Final designs retained sequence diversity while converging on cell-type-associated motif patterns. Lentiviral MPRA validated cell-type-specific activity in K562 and HepG2 and showed higher average activity of HepG2 designs than endogenous CREs. Together, these findings establish sequence-grammar trajectory reconstruction as a basis for interpretable and tunable synthetic CRE design.

genomics↗