Biology subjects

Bai, L.

Publications and source records attributed to Bai, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Wasabi leaf extract changes the expression levels of cytokine related genes in dermal papilla cells, which identified by the whole transcriptome

Wasabi is a traditional food in Asian area. Wasabi leaf extract derived compounds such as 6-methylsulfinylhexyl isothiocyanate (6-MSITC) have been reported to exert anti-proliferative effects on cancer cells. The antibacterial action of wasabi leaf extract has been reported previously. However, the detailed biological effects of wasabi leaf extract are not fully understood. To get a clue for the understanding, we used next-generation sequencing to identify the upregulated or downregulated genes in immortalized human dermal papilla cells. Differentially expressed genes were identified in human papilla cells in the presence or absence of wasabi leaf extract. The effects of 6-MSITC and isosaponarin were evaluated. We found that wasabi leaf extracts upregulated or downregulated the expression of cytokine-related genes. The identified expression changes will contribute to our understanding of the biological effects of wasabi.

cell biology↗

bioRxiv2025

Condensin Accelerates Long-Range Intra-Chromosomal Interactions

The 3D genome organization plays a key role in regulating interactions among chromosomal loci. While Chromosome Conformation Capture (3C)-based methods have provided static snapshots of chromatin architecture, the kinetics of chromosomal encounters in live cells remain poorly characterized. In this study, we employ Chemically Induced Chromosomal Interaction (CICI) to measure encounter times between multiple loci pairs in G1-arrested budding yeast. Our results show that chromosome motion closely follows the Rouse polymer model, with similar diffusion parameters at all tested loci. Surprisingly, we find that long-range intra-chromosomal encounters occur significantly faster than inter-chromosomal encounters at similar 3D distances. Using targeted depletion experiments, we identify condensin, but not cohesin, as the complex responsible for these rapid intra-chromosomal interactions. This is further supported by Hi-C analysis, which reveals that condensin promotes long-distance intra-chromosomal interactions in G1 yeast. Through polymer simulations, we estimate that condensin extrudes chromatin at [~]2 kb/s with a density of one complex per 1-2 Mb and a processivity of 120-220 kb. These findings uncover a novel role for condensin in shaping the interphase genome organization and provide new insights into chromosomal search dynamics in vivo.

molecular biology↗

bioRxiv2025

Glial betaPix is essential for blood vessel integrity in the zebrafish brain

The formation of blood-brain barrier and vascular integrity depends on the coordinative development of different cell types in the brain. Previous studies have shown that zebrafish bubblehead (bbh) mutant, which has mutation in the betaPix locus, develops spontaneous intracerebral hemorrhage during early development. However, it remains unclear in which brain cells betaPix may function. Here, we established a highly efficient conditional knockout method in zebrafish by using homology-directed repair (HDR)-mediated knockin and knockout technology, and generated betaPix conditional trap (betaPixct) allele in zebrafish. We found that betaPix in glia, but neither neurons, endothelial cells, nor pericytes, was critical for glial and vascular development and integrity, thus contributing to the formation of blood-brain barrier. Single-cell transcriptome profiling revealed that microtubule aggregation signaling stathmins and pro-angiogenic transcription factors Zfhx3/4 were down-regulated in glial and neuronal progenitors, and further genetic analysis suggested that betaPix may act upstream on the PAK1-Stathmin and Zfhx3/4-Vegfaa signaling to regulate glia migration and angiogenesis. Therefore, this work reveals that glial betaPix plays an important role in brain vascular development in zebrafish embryos and possibly human cells.

developmental biology↗

bioRxiv2025

scWGBS-GPT: A Foundation Model for Capturing Long-Range CpG Dependencies in Single-Cell Whole-Genome Bisulfite Sequencing to Enhance Epigenetic Analysis

Single-cell DNA methylomes are challenging to interpret because of sparse CpG coverage and the complexity of genome-wide sequences. We present scDNAm-GPT, a universal foundation model that uses context-aware CpG tokenization, a Mamba backbone, and cross-attention to capture both local and global DNA methylation patterns. Trained on over one million single cells from 35 human and mouse tissues, scDNAm-GPT enables accurate cell clustering, zero-shot prediction of CpG effects on gene expression, improved trajectory inference, and reference-free deconvolution of cell types from cell-free DNA. The model hierarchically learns regulatory features, and its attention maps highlight functionally relevant regions, demonstrating high biological interpretability. These results establish scDNAm-GPT as a scalable and generalizable framework for single-cell epigenomic analysis, offering new opportunities to dissect epigenetic regulation in health and disease. Code is available at GitHub (https://github.com/ChaoqiLiang/scDNAm-GPT).

bioinformatics↗

bioRxiv2025

Mapping the Landscape of Allele-Specific Expression In Porcine Genomes

Allele-specific expression (ASE) is the imbalanced expression of two alleles of the same locus. It is quite pervasive among mammals and is associated with healthy and economically relevant traits. ASE is often used to support the identification of variants related to gene expression (cis-eQTLs). Thus, profiling ASE represents a significant step in elucidating the mechanism underlying gene expression regulation. In this study, we developed an ASE pipeline using public available RNA-seq data and open-source software. Using this pipeline, we were able to profile pervasive allelic imbalance across 42 tissues and 34 breeds from the Farm-GTEX-pig consortium at both SNP and gene levels without the need for parental genotype or whole genome sequence data. ASE was widely, but not evenly, spread across the genome. We also observed considerable variation in ASE profiles among various tissues, in which the ASE fraction ranged from 1.3% to 54.1%. ASE tends to be highly tissue-specific, and the overlap across tissues is limited. The functional analysis of tissue-specific ASE sites indicates that they are involved in the critical maintenance of these tissues. Our ASE pipeline can be readily applied to other RNA-seq data sets for livestock, thereby significantly expanding its potential utility. The wealth of available ASE resources provides a solid foundation for identifying regulatory elements within the genome that drive complex traits in livestock, making our pipeline and results valuable resources for researchers in this field.

genomics↗

bioRxiv2025

From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models

Protein language models (pLMs) are powerful predictors of protein structure and function, learning through unsupervised training on millions of protein sequences. pLMs are thought to capture common motifs in protein sequences, but the specifics of pLM features are not well understood. Identifying these features would not only shed light on how pLMs work, but potentially uncover novel protein biology--studying the model to study the biology. Motivated by this, we train sparse autoencoders (SAEs) on the residual stream of a pLM, ESM-2. By characterizing SAE features, we determine that pLMs use a combination of generic features and family-specific features to represent a protein. In addition, we demonstrate how known sequence determinants of properties such as thermostability and subcellular localization can be identified by linear probing of SAE features. For predictive features without known functional associations, we hypothesize their role in unknown mechanisms and provide visualization tools to aid their interpretation. Our study gives a better understanding of the limitations of pLMs, and demonstrates how SAE features can be used to help generate hypotheses for biological mechanisms. We release our code, model weights and feature visualizer.

bioinformatics↗

bioRxiv2025

Drosophila larval gut transcriptome reveals a microbe-mediated intestinal tissue growth via Ecdysone during adaptive growth

Organ and systemic growth must remain coordinated during development, even under nutritional stress. In Drosophila larvae, the intestinal microbiota contributes to this coordination by promoting growth and maturation under chronic undernutrition. Using gnotobiotic models, we show that association with Lactiplantibacillus plantarum (Lp) selectively enhances midgut growth relatively to other organs, providing an adaptive mechanism that buffers the impact of dietary restriction. Transcriptomic profiling of larval midguts revealed a strong Ecdysone signaling signature upon Lp association. Functional analyses showed that local conversion of Ecdysone to its active form, 20-hydroxyecdysone, by the cytochrome P450 enzyme Shade, together with enterocyte Ecd receptor activity, is required for Lp-dependent intestinal and systemic growth. Pharmacological activation of Ecd signaling partially mimicked the bacterial effect, confirming its sufficiency to drive adaptive midgut expansion. Our results uncover an unexpected role of intestinal Ecd signaling in microbiota-driven developmental plasticity, revealing how commensal bacteria modulate local steroid signaling to fine-tune organismal growth and maturation.

cell biology↗

bioRxiv2025

Genomic Insights into the Demographic History and Local Adaptation of Wild Boars Across Eurasia

Wild boars exhibit genetic and phenotypic diversity shaped by migrations and local adaptations. Its expansion across Eurasia, especially in central Asia, remains underexplored. Here, we present newly sequenced whole-genome data of 47 wild boars from Eastern Asia, Central Asia, and Europe, combined with 49 existing genomes, creating a comprehensive dataset of 96 individuals. Our analyses show that Asian wild boars and Southeast Asian Suids split [~]3.6 Mya, with Central Asian and Southern Chinese ancestors diverging [~]1.8 Mya. The split between Central Asian and European-Near East ancestors occurred [~]0.9 Mya, followed by a European-Near East divergence [~]0.6 Mya. We identify signatures of local adaptation in Central Asian populations, including two positively selected variants in LPIN1, associated with cold adaptation, and a missense mutation in ALPK2, linked to meat traits. These findings provide insights into wild boar dispersal and adaptation, and shed light on domestic pigs breeding.

evolutionary biology↗

bioRxiv2025

Native nucleosome-positioning elements for the investigation of nucleosome repositioning

Nucleosome repositioning is essential for establishing nucleosome-depleted regions (NDRs) to initiate transcription. This process has been extensively studied using structural, biochemical, and single-molecule approaches, which require homogenously positioned nucleosomes. This is often achieved using the Widom 601 sequence, a highly efficient nucleosome positioning element (NPE) selected for its unusually strong binding to the H3-H4 histone tetramer. Due to the artificial nature of 601, native NPEs are needed to explore the role of DNA sequence in nucleosome repositioning. Here, we characterize the position distributions and nucleosome formation free energy for a set of yeast native nucleosomes (YNNs) from Saccharomyces cerevisiae. We show these native NPEs can be used in biochemical studies of nucleosome repositioning by transcription factors (TFs) and the chromatin remodeler Chd1. TFs could directly reposition a fraction of nucleosomes containing native NPEs, but not 601-containing nucleosomes. In contrast, partial unwrapping was similar for 601 and native NPE sequences, and the rate of ATP-dependent remodeling by Chd1 was within the range of the fast and slow directions of the 601 nucleosomes. This set of native NPEs provides an alternative to the 601 NPE that can be used for probing the repositioning of nucleosomes that contain native DNA sequences.

molecular biology↗

bioRxiv2024

Hi-C Calibration by Chemically Induced Chromosomal Interactions

The genome-wide chromosome conformation capture method, Hi-C, has greatly advanced our understanding of genome organization. However, its quantitative properties, including sensitivity, bias, and linearity, remain challenging to assess. Measuring these properties in vivo is difficult due to the heterogenous and dynamic nature of chromosomal interactions. Here, using Chemically Induced Chromosomal Interaction (CICI) method, we create stable intra- and inter-chromosomal interactions in G1-phase budding yeast across a broad range of contact frequencies. Hi-C analysis of these engineered cell populations demonstrates that static intra-chromosomal loops do not generate Topologically Associated Domains (TADs) and only promote 3D proximity within [~]50kb flanking regions. At moderate sequencing depth, Hi-C is sensitive enough to detect interactions occurring in 5-10% of cells. It also shows no inherent bias toward intra-versus inter-chromosomal interactions. Furthermore, we observe a linear relationship between Hi-C signal intensity and contact frequency. These findings illuminate the intrinsic properties of the Hi-C assay and provide a robust framework for its calibration.

genomics↗

bioRxiv2024

High-Resolution Genome-Wide Mapping of Chromatin Accessibility and Torsional Stress

Torsional stress in chromatin plays a fundamental role in cellular functions, influencing key processes such as transcription, replication, and chromatin organization. Transcription and other processes may generate and be regulated by torsional stress. In the genome, the interplay of these processes creates complicated patterns of both positive (+) and negative (-) torsion. However, a challenge in generating an accurate torsion map is determining the zero-torsion baseline signal, which is conflated with chromatin accessibility. Here, we introduce a high-resolution method based on the intercalator trimethylpsoralen (TMP) to address this challenge. We describe a method to establish the zero-torsion baseline while preserving the chromatin state of the genome of S. cerevisiae. This approach enables both high-resolution mapping of accessibility and torsional stress in chromatin in the cell. Our analysis shows transcription-generated torsional domains consistent with the twin-supercoiled-domain model of transcription and suggests a role for torsional stress in recruiting topoisomerases and in regulating 3D genome architecture via cohesin. Significantly, we reveal that insulator sequence-specific transcription factors decouple torsion between divergent promoters, whereas torsion spreads between divergent promoters lacking these factors, suggesting that torsion serves as a regulatory mechanism in these regions. Although insulators are known to decouple gene expression, our finding provides a physical explanation of how such decoupling may occur. This new method provides a potential path forward for using TMP to measure torsional stress in the genome without the confounding contribution of accessibility in chromatin.

genomics↗

bioRxiv2024

Episodic Transport of Protein Aggregates Achieves a Positive Size Selectivity in Aggresome Formation

Eukaryotic cells direct toxic misfolded proteins to various protein quality control pathways based on their chemical features and aggregation status. Aggregated proteins are targeted to selective autophagy or specifically sequestered into the "aggresome," a perinuclear inclusion at the microtubule-organizing center (MTOC). However, the mechanism for selectively sequestering protein aggregates into the aggresome remains unclear. To investigate aggresome formation, we reconstituted MTOC-directed aggregate transport in Xenopus laevis egg extract using AgDD, a chemically inducible aggregation system. High-resolution single-particle tracking revealed that dynein-mediated transport of aggregates was highly episodic, with average velocity positively correlated with aggregate size. Our mechanistic model suggests that the recurrent formation of the dynein transport complex biases larger aggregates towards the active transport state, compensating for the slowdown due to viscosity. Both episodic transport and positive size selectivity are specifically associated with aggresome-dynein adaptors. Coupling conventional dynein-activating adaptors to the aggregates perturbs aggresome formation and reverses size selectivity.

cell biology↗

bioRxiv2024

Structural details of helix-mediated TDP-43 C-terminal domain multimerization

The primarily disordered C-terminal domain (CTD) of TAR DNA binding protein-43 (TDP-43), a key nuclear protein in RNA metabolism, forms neuronal inclusions in several neurodegenerative diseases. A conserved region (CR, spanning residues 319-341) in CTD forms transient helix-helix contacts important for its higher-order oligomerization and function that are disrupted by ALS-associated mutations. However, the structural details of CR assembly and the explanation for several ALS-associated variants impact on phase separation and function remain unclear due to challenges in analyzing the dynamic association of TDP-43 CTD using traditional structural biology approaches. By employing an integrative approach, combining biophysical experiments, biochemical assays, AlphaFold2-Multimer (AF2-Multimer), and atomistic simulations, we generated structural models of helical oligomerization of TDP-43 CR. Using NMR, we first established that the native state of TDP-43 CR under physiological conditions is -helical. Next, alanine scanning mutagenesis revealed that while hydrophobic residues in the CR are important for CR assembly, phase separation and TDP-43 nuclear retention function, polar residues down regulate these processes. Finally, pairing AF2-Multimer modeling with AAMD simulations indicated that dynamic, oligomeric assemblies of TDP-43 that are stabilized by a methionine-rich core with specific contributions from a tryptophan/leucine pair. In conclusion, our results advance the structural understanding of the mechanisms driving TDP-43 function and provide a window into the initial stages of its conversion into pathogenic aggregates.

biochemistry↗

bioRxiv2024

The Prefrontal Cortex to the Hippocampus Glutamatergic Pathway Regulates Reward Effects of Methamphetamine

Methamphetamine (METH) induces reward effects. The prefrontal cortex (PFC) plays a role in regulating top-down. The hippocampus is closely involved reward memory. However, the direct projects from the PFC to the hippocampus have not been studied well. Here, we use conditioned place preference (CPP), a recombinant adeno-associated virus 2/9 (rAAV2/9) and optogenetic approaches to explore a role in METH-CPP for a novel pathway projecting from the medial prefrontal prelimbic cortex (PrL) directly to the dorsal hippocampus CA1 (dCA1). Expressing CaMKII-ChR2 or CaMKII-eNpHR3.0 in the PrL and optically stimulating in the dCA1 blocks or enhances METH-CPP, respectively. Moreover, silencing the PrL to dCA1 glutamatergic pathway with tetanus neurotoxin (TeNT) enhances METH-CPP. These results identify a novel PrL-to-dCA1 glutamatergic pathway regulating METH-CPP.

neuroscience↗

bioRxiv2024

Targeting CD19 for the treatment of B-cell related autoimmune diseases with a novel T cell engager

Autoimmune disorder, affecting more than twenty million in United States and billions of people worldwide, occurs when human immune system mistakenly attacks its own body. Autoreactive B cells, particularly the autoantibodies they produce, play a critical role in the etiology, progress, prognosis, and pathogenesis of multiple autoimmune diseases. While targeting B cells medicines, such as anti-CD19 or anti-CD20 monoclonal antibodies have produced promise in both pre-clinic models and some clinic practices, many patients failed to respond, ended less satisfactory outcome, or relapsed to monoclonal antibody therapies. Novel therapies are desperately needed to fight this challenge. In this study, based upon a symmetrical format, namely fusion of IgG and scFv technology (FIST), an anti-CD19xCD3 T cell engager (TCE) YK012, developed to treat B-cell malignancies such as precursor pre-B acute lymphatic leukemia (ALL) and non-Hodgkins lymphoma (NHL), was expanded to explore the treatment of autoimmune diseases by bringing T cells to CD19 positive B cells, including autoreactive B cell populations. Even as bivalent binding to CD3, YK012 has so significantly reduced binding affinity to TCR compared to other TCEs that, free YK012 alone does activate T cells at all. In contrast, in the presence of CD19-expressing Raji target cells and mediated by YK012, T cells can be activated in a dose-dependent manner, measured by upregulation of NFAT-reporter, CD25, IFN-{gamma} and granzyme B expression. Crosslinking of B cell with T cell by YK012, the conjugation elicited T cell-mediated potent but mild cytotoxicity only to CD19-positive Raji cells. Additionally, YK012 elicited much reduced cytokines release in vitro compared to that of Blincyto(R) biosimilar, implying a potentially me-better therapeutics replacement in clinics for B-cell related diseases. In two in vivo pharmacological studies, YK012 alleviated the pathology symptoms of a collagen-induced arthritis model and almost completely depleted the peripheral B cell in human stem cell-transplanted murine model. In summary, this study demonstrated that YK012, a FIST platform designed TCE, has the potential to treat B cell-mediated diseases including autoimmune indications with possible better efficacy and less side effects in clinical practices.

immunology↗

bioRxiv2024

Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression

Some transcription factors (TFs) can form liquid-liquid phase separated (LLPS) condensates. However, the functions of these TF condensates in 3D genome organization and gene regulation remain elusive. In response to methionine (met) starvation, budding yeast TF Met4 and a few co-activators, including Met32, induce a set of genes involved in met biosynthesis. Here, we show that the endogenous Met4 and Met32 form co-localized puncta-like structures in yeast nuclei upon met depletion. Recombinant Met4 and Met32 form mixed droplets with LLPS properties in vitro. In relation to chromatin, Met4 puncta co-localize with target genes, and at least a subset of these target genes is clustered in 3D in a Met4-dependent manner. A MET3pr-GFP reporter inserted near several native Met4 binding sites becomes co-localized with Met4 puncta and displays enhanced transcriptional activity. A Met4 variant with a partial truncation of an intrinsically disordered region (IDR) shows less puncta formation, and this mutant selectively reduces the reporter activity near Met4 binding sites to the basal level. Overall, these results support a model where Met4 and co-activators form condensates to bring multiple target genes into a vicinity with higher local TF concentrations, which facilitates a strong response to methionine depletion.

genetics↗

bioRxiv2023

DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions

3C-based methods have significantly advanced our understanding of 3D genome organization. However, it remains a formidable task to precisely capture long-range chromosomal interactions between individual loci, such as those between promoters and distal enhancers. Here, we present Methyltransferase Targeting-based chromosome Architecture Capture (MTAC), a method that maps the contacts between a target site (viewpoint) and the rest of the genome in budding yeast with high resolution and sensitivity. MTAC detects hundreds of intra-and inter-chromosomal interactions within nucleosome-depleted regions (NDRs) that cannot be captured by 4C, Hi-C, or Micro-C. By applying MTAC to various viewpoints, we find that 1) tethering to the nuclear pore complex (NPC) is a major mechanism that mediates long-distance chromosomal interactions in yeast, 2) genes co-regulated by methionine assemble into inter-chromosomal clusters near NPCs upon activation, 3) mediated by condensin, the mating locus forms a highly specific interaction with the recombination enhancer (RE) in a mating-type specific manner, and 4) correlation of MTAC signals among NDRs reveal spatial mixing and segregation of the genome. Overall, these results demonstrate MTAC as a powerful tool to resolve fine-scale long-distance chromosomal interactions and provide insights into the 3D genome organization.

molecular biology↗

bioRxiv2023

Serine hydroxymethyl transferase is a binding target of caprylic acid: Uncovering a novel molecular target for a herbicide and for producing caprylic acid-tolerant crops

Identification of new binding targets is essential for the development of herbicides and phytotoxin-tolerant crops. Caprylic acid (CAP) is a safe and non-selective bio-herbicide in uncultivated areas. However, the herbicidal action of CAP remains unclear. Herein, metabolomic and proteomic profiling indicated that a serine hydroxymethyl transferase in Conyza canadensis (CcSHMT1) is a promising candidate binding targeted for CAP. The protein abundance and activity of CcSHMT1 were decreased in a time- and dosage-dependent manners after CAP treatment. CAP competes with phenyl-serine at the binding sites, decreasing the enzymatic activity of CcSHMT1. Overexpression of CcSHMT1, AtSHMT1 and OsSHMT1 in Arabidopsis or rice endowed plants with high tolerance to CAP treatment, whereas the knockout of osshmt1 led to death of plants under normal atmospheric conditions. Furthermore, T194A, T194A/ M195V and D209N Osshmt1 mutant plants derived from base editing exhibited tolerance to CAP. CAP bound to CcSHMT1 with high affinity, and Ala191 in the key domains of N-terminus was identified to be critical for the binding site of CAP. Collectively, our findings demonstrate that CcSHMT1 is a binding target for herbicidal activity of CAP. This study marks a key step in the druggability of SHMT inhibitors and represents an attractive target for phytotoxin-tolerant crops.

plant biology↗