Biology subjects

Lei, M.

Publications and source records attributed to Lei, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Spatiotemporal atlas resolves the mesenchymal-epithelial stem cell axis governing human hair follicle aging and pathology

How adult stem cell populations coordinate tissue regeneration across physiological and pathological states remains unclear. Hair follicles contain epithelial and mesenchymal stem cells that codetermine hair regeneration. Here, we integrate a multimodal spatiotemporal atlas with functional validation to define the mesenchymal-epithelial stem cell dynamics governing human hair follicle homeostasis, aging, and androgenetic alopecia. Aging is characterized by passive depletion of hDSC-derived regenerative cues, whereas AGA involves a shift of hDSC toward an inhibitory signaling hub that promotes HFSC dysfunction. We further pinpoint hDSC-secreted PTN as a key regenerative factor that promotes hair growth and counteracts androgen-induced growth suppression. This study provides a holistic framework of adult stem cell crosstalk across physiological and pathological states, offering a mechanistic roadmap to reinstate tissue regeneration.

cell biology↗

bioRxiv2026

FXR-mediated recruitment of PPP1CB suppresses SMAD2/3 phosphorylation to mitigate pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal interstitial lung disease with limited treatment options and poorly understood molecular underpinnings. Dysregulated TGF-{beta}/SMAD signaling is a key driver of fibrotic remodeling, promoting persistent myofibroblast activation and excessive extracellular matrix deposition. Here we identify the Farnesoid X receptor (FXR), a bile acid activated nuclear receptor, as a previously unrecognized suppressor of pulmonary fibrosis. FXR expression is significantly reduced in lung tissues from patients with PF and in myofibroblasts derived from BLM-induced mouse models, correlating inversely with fibrosis severity. Genetic ablation of FXR exacerbates BLM-induced pulmonary fibrosis by promoting fibroblast hyperactivation and dysregulation of the TGF-{beta}/SMAD signaling pathway. Mechanistically, we identify PPP1CB as a previously unrecognized FXR-interacting protein in primary myofibroblasts derived from IPF patients. We further show that FXR both increases chromatin accessibility at the PPP1CB locus and assembles a functional complex with PPP1CB, which in turn promotes SMAD2/3 dephosphorylation and suppresses their nuclear translocation. Notably, the clinical-stage FXR agonist TERN101 exhibits potent therapeutic efficacy in a BLM-induced mouse pulmonary fibrosis model. These findings establish FXR as a critical antifibrotic regulator in lung tissue and suggest that pharmacological activation of FXR may offer a promising therapeutic strategy for IPF.

cell biology↗

bioRxiv2026

Molecular and Structural Basis of Cardiac Remodelling in Niemann-Pick Type C

Key Point SummaryNiemann-Pick disease type C (NPC) patients showed a high prevalence of ECG abnormalities, with additional echocardiographic evidence of altered left-ventricular structure and function. Npc1-/- mouse hearts exhibited age-associated glycosphingolipid accumulation accompanied by marked myocardial fibrosis and increased collagen deposition. Ex vivo electrophysiology revealed QT prolongation and atrioventricular conduction defects in Npc1-/- hearts, particularly under {beta}-adrenergic stress. Transcriptomic profiling identified inflammatory and fibrotic pathway activation consistent with the structural and electrophysiological abnormalities observed. Together, these findings demonstrate previously unrecognised cardiac involvement in NPC and support routine cardiac screening to improve clinical management. Niemann-Pick disease type C (NPC) is a rare autosomal recessive neurodegenerative lysosomal storage disease caused by pathogenic variants in NPC1 or NPC2. Sudden death can occur due to seizures, but cardiac involvement has not been well defined. We performed 12-lead electrocardiograms (ECG) in 14 adult NPC patients (8 male, 6 female). Cardiac structure and function were examined in Npc1-/- adult mouse hearts, alongside wild-type controls. Glycosphingolipid accumulation was quantified by high-performance liquid chromatography, fibrosis and collagen deposition were quantified using Massons Trichrome (M&T) and Picrosirius Red (PR) staining. Whole-heart morphology, including chamber size and wall thickness, was assessed. Ex vivo ECG recordings assessed conduction abnormalities and arrhythmias. RNA-seq transcriptomics characterised molecular pathways altered in Npc1-/- hearts. 8/14 patients showed ECG abnormalities including abnormal QRS transitions (N=8), increased QRS amplitude (N=4), fascicular block (N=2), and abnormal T wave inversion (N=1). 13 patients also had transthoracic echocardiograms identifying mildly impaired LV systolic function (N=2) and increased wall thickness/LV mass (N=4). In Npc1-/- mice, age-related glycosphingolipid accumulation was associated with pronounced ventricular fibrotic remodelling. There was a significant increase in stained connective tissue area and connective tissue to cardiac tissue ratio in both M&T and PR staining. ECG from Langendorff-perfused Npc1-/- hearts showed QT prolongation and atrioventricular conduction abnormalities under isoprenaline stress. Transcriptomics revealed major changes in Npc1-/- hearts, consistent with histological fibrosis and linking NPC to inflammation-driven remodelling and arrhythmogenesis. These findings support routine cardiac screening in NPC patients and highlight the need for further studies to improve management and treatment.

physiology↗

bioRxiv2026

Structural basis of substrate recognition and allosteric inhibition in human B0AT2

The SLC6 family is a major target for neuropsychiatric therapeutics. Human B0AT2 (SLC6A15) regulates amino acid homeostasis and glutamatergic transmission and is linked to major depressive disorder, yet its transport and inhibition mechanisms remain unclear. Here we report cryo-EM structures of B0AT2 in apo state and in complex with substrates (proline, leucine, methionine) and inhibitors (loratadine, tiagabine), capturing outward-open, early substrate-bound intermediate, outward-occluded, and inward-open conformations along the transport cycle. These structures reveal an early substrate-sensing mechanism at the substrate-binding pocket (S1), where a substrate-dependent rotameric switch of Phe308 remodels pocket geometry to tune substrate accommodation and selectivity. Loratadine stabilizes an outward-occluded state via allosteric inhibition at the extracellular S2 pocket, whereas tiagabine stabilizes the inward-open state through cooperative multi-site inhibition involving S1 and two previously unrecognized intracellular cavities (S3 and S4). Together with functional assays, these data define the molecular basis of B0AT2 substrate selectivity and state-dependent inhibition. Notably, the two intracellular cavities are conserved across SLC6 transporters, reflecting a shared intracellular vestibular architecture and enabling rational design of conformation-selective modulators for neuropsychiatric disorders.

biophysics↗

bioRxiv2026

NFIC-mediated CaSR endocytosis defines a hyperactive TOMM20highCHGAhigh oxyphil cell state as a pathological driver of autonomous secondary hyperparathyroidism

Secondary hyperparathyroidism (SHPT) is a debilitating complication of chronic kidney disease. Its clinical management is frequently compromised by calcimimetic resistance, a refractory state primarily driven by the progressive downregulation of the membrane calcium-sensing receptor (CaSR). Despite the centrality of CaSR as a therapeutic target, the mechanisms governing its aberrant expression and membrane localization remain incompletely elucidated. Here, we generated a single-cell transcriptomic atlas of human parathyroid tissues from SHPT and primary hyperparathyroidism (PHPT) patients, uncovering a unique stromal-immune niche that is specifically induced by uremic stress in SHPT. Our data also observed a striking dissociation between CaSR mRNA and its abundance as a membrane protein in SHPT tissues. Pseudotime trajectory analysis showed a progressive decline in CaSR pathway activity and a concomitant increase in endo-lysosomal activity along the trajectory, terminating in pathological oxyphil cells as the endpoint of chief cell differentiation in SHPT. Mechanistically, Nuclear Factor I C (NFIC) transcriptionally activated clathrin light chain B (CLTB) and Ras-related protein Rab7a (RAB7A) to trigger clathrin-mediated endocytosis and lysosomal degradation of CaSR, thus reducing its membrane abundance. This degradative program was further validated by multiplex immunofluorescence in TOMM20highCHGAhigh pathological oxyphil cells in human SHPT tissues. To translate these mechanistic findings into a clinically actionable strategy, we repurposed the clinically approved lysosomal inhibitor hydroxychloroquine (HCQ) to block this CaSR degradation pathway. In patient-derived xenograft (PDX) mouse models, co-administration of HCQ and cinacalcet acted synergistically to restore membrane CaSR expression, normalize serum PTH and calcium levels and suppress parathyroid tumor growth more effectively than monotherapies. Collectively, our single-cell-guided study identifies an NFIC-driven endo-lysosomal program as a previously unrecognized mechanism underlying CaSR downregulation and calcimimetic resistance in SHPT, and establishes HCQ repurposing as a clinically tractable therapeutic strategy for patients with refractory SHPT.

cell biology↗

bioRxiv2026

Specialised root hair cells facilitate rhizobial infection

Legumes establish symbiotic partnerships with soil bacteria that convert atmospheric nitrogen into plant-available forms. Symbiotic bacteria enter through root hairs following recognition by cell surface receptors that help identify compatible symbionts. However, many root hairs express these receptors, and it has long remained unclear why only a small fraction become infected. Here, we use single-cell transcriptomics to show that legumes pre-specify a rare root hair population for infection before bacterial contact. These susceptible root hairs represent less than one percent of the total, express infection-associated genes prior to encountering symbionts and are conserved in distantly related legumes. Their abundance is regulated by the hormone ethylene and correlates with infection capacity. Our findings reveal that root hair cells do not respond uniformly to symbionts but are instead transcriptionally specialised in advance to control infection entry points. This pre-specification provides a mechanism to balance symbiotic benefits against pathogen infection risks and may exemplify a more general strategy used by multicellular hosts to spatially restrict microbial access.

plant biology↗

bioRxiv2026

Histone H2BK120 ubiquitination modulates PRC1 activity and H2AK119ub deposition on nucleosomes

Polycomb group and Trithorax group complexes antagonistically regulate developmental gene expression, yet the mechanisms coordinating their interplay remain poorly understood. Here, we uncover a synergistic histone crosstalk in which H2BK120ub (histone H2B ubiquitination at lysine 120), a Trithorax-associated active mark, enhances Polycomb repressive complex 1 (PRC1) activity by directly binding specific PCGF subunits of PRC1 on the nucleosome surface, as shown in cryo-electron microscopy (cryo-EM) analysis. Beyond regulating enzymatic activity, H2BK120ub also modulates the competitive binding between the catalytic RNF2-BMI1 module and the RYBP subunit of noncanonical PRC1.4 complexes to nucleosomes, potentially restricting H2AK119ub (histone H2A ubiquitination at lysine 119) spreading to neighboring nucleosomes. In mouse embryonic stem cells, H2BK120ub directs the deposition of H2AK119ub within the gene bodies of a subset of developmental genes, which exhibit more rapid activation compared to canonical H3K4me3/H3K27me3 bivalent genes. These findings reveal a previously unrecognized mechanism that links active and repressive histone modifications, providing new insights into the intricate chromatin regulation of gene expression during development.

molecular biology↗

bioRxiv2025

DICAR-JP Regulates Ribosome Migration, a New Theory of Mitochondrial Protein Production

BackgroundDICAR plays a cardioprotection of diabetic models. DICAR-JP, a short sequence of DICAR, may represent DICARs active functional domain. NAC is necessary for the heart tissue development. Addtionally, OGDHL is a metabolism regulator. In this study, we examine a new mechanism of DICAR via NAC/OGDHL on regulating cardiomyocyte metabolism in DCM. We also sought to elucidate the function of DICAR/DICAR-JP in modulating NAC-dependent production of OGDHL nascent peptides and their mitochondrial translocation, and we also aimed to optimize the DICAR-JP sequence to be better therapy on DCM. MethodsSPR was to investigate the binding interaction between DICAR-JP and NAC. The function of DICAR-JP and DICAR-JP45 on OGDHL nascent peptide transfection was detected by in vitro translation approach. Biotin-DICAR-JP was transfected to study the function of DICAR-JP, NAC and OGDHL. Untargeted metabolomics was utilized to characterize the metabolic reprogramming of cardiomyocytes. AAV9-DICAR-JP and DICAR-JP45 were constructed and administered to db/db mice for 1-2 months to assess their cardioprotective effects detected by Echocardiography confirmed mouse cardiac function. ResultsOur findings demonstrated that DICAR-JP be the functional domain that interacts with NAC to regulate OGDHL nascent peptide expression. Disruption of OGDHL expression reversed the metabolic reprogramming observed in diabetic cardiomyocytes, highlighting its crucial role in maintaining cardiac metabolic homeostasis. DICAR-JP facilitated the translocation of OGDHL nascent peptides from the cytoplasm to the mitochondria, leading us to hypothesize that DICAR-JP plays a key role in regulating ribosomal migration from the endoplasmic reticulum to the mitochondria. We refer to this process as the Ribosome Migration. In our studies using AAV9-mediated DICAR-JP and DICAR-JP45 overexpression in heart tissue. DICAR-JP and DICAR-JP45 both exhibited significant cardioprotective effects against diabetic cardiomyopathy (DCM), comparable to those observed with Empagliflozin. ConclusionsIn a conclusion, we propose a new endogenous nucleic acid candidate drug library, and a new molecular framework, the Ribosome Migration, which implicates the DICAR-JP/NAC/OGDHL nascent peptide axis in metabolic reprogramming related to DCM. This theory constructs a new mitochondrion protein from nuclear original protein. Moreover, DICAR-JP45 shows strong potential as a nucleic acid-based therapeutic candidate for treating DCM. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSDICAR is a new protective circular noncoding RNA for diabetic cardiomyopathy. NAC is located in ribosome and regulates new peptide production, which is also a key factor in heart tissue development. OGDHL can regulate different energy metabolism in mitochondria. What New Information Does This Article Contribute?DICAR-JP is the functional domain that interacts with NAC to regulate OGDHL nascent peptide expression. There is an interaction between DICAR-JP and NAC. DICAR-JP sequence is protected by NAC and NAC function is mediated by DICAR-JP. We called this RNA functional domain. OGDHL expression reversed the metabolic reprogramming observed in diabetic cardiomyocytes, highlighting its crucial role in maintaining cardiac metabolic homeostasis. DICAR-JP takes part in tanscription and translocation of OGDHL nascent peptides from the cytoplasm to the mitochondria via plasma ribosome. We call this process the Ribosome Migration Theory. DICAR-JP and DICAR-JP45 both exhibited significant cardioprotective effects against diabetic cardiomyopathy (DCM), comparable to those observed with Dapagliflozin (DAPA). Our study revealed a novel molecular framework, the Ribosome Migration Theory, which implicates the DICAR-JP/NAC/OGDHL nascent peptide axis in metabolic reprogramming related to DCM. Moreover, DICAR-JP45 shows strong potential as a nucleic acid-based therapeutic candidate for treating DCM.

pharmacology and toxicology↗

bioRxiv2025

RNA-triggered fluorescence controlled by RNA switches for real-time RNA expression tracking in living plants

Real-time visualization of RNA dynamics across spatial scales in living plants is desirable yet remains challenging, hindered by the absence of imaging tools that simultaneously offer high sensitivity and deployability in whole living plants. Here, we engineered a modular, RNA-triggered fluorescence (RTF) reporter system de novo for spatiotemporal imaging of RNA from cellular to whole-plant scales in vivo. This system integrates three functional modules: a target-specific allosteric RNA switch, a degradable adapter for background suppression, and a fluorescent reporter. All components are stably expressed from a single vector and assemble in vivo, enabling uniform deployment throughout entire plants. The modified RTF (RTFst) achieves single-molecule sensitivity (signal-to-noise ratio >60) for dynamic tracking of developmentally regulated, tissue-specific, circadian, and stress-responsive mRNAs. Crucially, it enables the first direct, real-time observation of graft-transmissible mRNA trafficking across tissue scales and cross-kingdom transfer of the aphid-secreted long non-coding RNA Ya1 to plant cells. RTF establishes a versatile platform for studying gene regulation, signaling, and transcript mobility in plants, with broad applicability in synthetic biology and crop improvement.

molecular biology↗

bioRxiv2025

KIDINS220 and InsP8 safeguard the stepwise regulation of phosphate exporter XPR1

XPR1 is emerging as the only known inorganic phosphate (Pi) exporter in humans, critical for Pi homeostasis, with its activity stimulated by inositol pyrophosphate InsP8 and regulated by neuronal scaffold protein KIDINS220. Our structural studies reveal InsP8 specifically activates XPR1 in a stepwise manner, involving profound SPX domain movements. Each XPR1 subunit functions with four gating states, in which Pi permeates a constriction site via a "knock-kiss-kick" process. In contrast, KIDINS220 delicately stabilizes XPR1 in a closed conformation through multiple mechanisms, one of which involves trapping the XPR1 1 helix--critical for InsP8 binding--within an interaction hub. InsP8 serves as a key to release KIDINS220s restraint, reinforcing a "key-to-locks" mechanism to safeguard the stepwise activation. Additionally, our study provides direct structural insights into XPR1-associated neuronal disorders and highlights the evolutionary conservation and divergence among XPR1 orthologues, offering a comprehensive understanding of Pi homeostasis across species.

molecular biology↗

bioRxiv2025

EPSD 2.0: An Updated Database of Protein Phosphorylation Sites across Eukaryotic Species

As one of the most crucial post-translational modifications (PTMs), protein phosphorylation regulates a broad range of biological processes in eukaryotes. Biocuration, integration and annotation of reported phosphorylation events will deliver a valuable resource for the community. Here, we present an updated database, the eukaryotic phosphorylation site database 2.0 (EPSD 2.0), which includes 2,769,163 experimentally identified phosphorylation sites (p-sites) in 362,707 phosphoproteins from 223 eukaryotes. From the literature, 873,718 new p-sites identified through high-throughput phosphoproteomic research were first collected, and 1,078,888 original phosphopeptides together with primary references were reserved. Then, this dataset was merged into EPSD 1.0, comprising 1,616,804 p-sites within 209,326 proteins across 68 eukaryotic organisms [1]. We also integrated 362,190 additional known p-sites from 10 public databases. After redundancy clearance, we manually re-checked each p-site and annotated 88,074 functional events for 32,762 p-sites, covering 58 types of downstream effects on phosphoproteins, and regulatory impacts on 107 biological processes. In addition, phosphoproteins and p-sites in 8 model organisms were meticulously annotated utilizing information supplied by 100 external platforms encompassing 15 areas. These areas included kinase/phosphatase, transcription regulators, three-dimensional structures, physicochemical characteristics, genomic variations, functional descriptions, protein domains, molecular interactions, drug-target associations, disease-related data, orthologs, transcript expression levels, proteomics, subcellular localization, and regulatory pathways. We expect that EPSD 2.0 will become a useful database supporting comprehensive studies on phosphorylation in eukaryotes. The EPSD 2.0 database is freely accessible online at https://epsd.biocuckoo.cn/.

bioinformatics↗

bioRxiv2024

Natural genetic and transcriptomic variation in photosynthesis associated pathways contribute to adaptive traits variation in worldwide Arabidopsis thaliana population

Photosynthesis is the most important reaction underlying carbon fixation. Despite its potential in boosting carbon assimilation, nature variations underlying genes in photosynthesis pathway and their role in adaptive traits variation remains elusive. In this study, we investigated the genetic, transcriptomic variation of 1103 genes in photosynthesis associated pathways, including 82 photosynthesis core genes, 24 plastid-encoded RNA polymerase related genes, 2 nucleus-encoded RNA polymerase-related genes, 34 photomorphogenesis-related genes, 40 genes involved in transcription and translation (TAC) and 938 other nuclear-encoded chloroplast-targeted genes. By de novo assembling the chloroplast genomes of 28 representative accessions and leveraging whole-genome, transcriptome sequencing data from the 1001 Genome Project, we revealed extensive natural genetic and transcriptome variations these genes in worldwide Arabidopsis thaliana population. 34.0% of them were identified with regulatory variations in expression quantitative locus mapping (eQTL) mapping, including key components of Rubisco (RBCS1B, RBCS2B), and Rubisco activase (RCA). Genome-wide and transcriptome-wide association analysis (GWAS/TWAS) showed that these genetic and transcriptomic variations made considerable contribution to variation of adaptive traits. Overall, our study provides insight into the natural genetic variation of these genes among worldwide Arabidopsis thaliana accessions and their role in complex traits variation and adaptation.

plant biology↗

bioRxiv2024

Single-Molecule Barcoding Technology for Single-Cell Genomics

Recent advances in barcoding technologies have significantly enhanced the scalability of single-cell genomic experiments. However, large-scale experiments are still rare due to high costs, complex logistics, and laborintensive procedures. To facilitate the routine application of the largest scalability, it is critical to simplify the production and use of barcoding reagents. Here, we introduce AmpliDrop, a technology that initiates the barcoding process using a pool of inexpensive single-copy barcodes and integrates barcode multiplicity generation with tagging of cellular content into a single reaction driven by DNA polymerase during library preparation. The barcoding reactions are compartmentalized using an electronic pipette or a robotic or standalone liquid handling system. These innovations eliminate the need for barcoded beads and complex combinatorial indexing workflows and provide flexibility for a wide range of scales and tube formats, as well as compatibility with automation. We show that AmpliDrop is capable of capturing transcriptomes and chromatin accessibility, and it can also be adapted for user-customized applications, including antibody-based protein detection, bacterial or viral DNA detection, and CRISPR perturbations without dual guide RNA-expression vectors. We validated AmpliDrop by investigating the influence of short-term static culturing on cell composition in human forebrain organoids, revealing metabolic reprogramming in lineage progenitors.

molecular biology↗

bioRxiv2024

Lysosomal signalling pathways influence heart rhythm, and regulate atrial function

In the heart, endogenous nicotinic acid adenine dinucleotide phosphate (NAADP) triggers lysosomal calcium (Ca2+) release to augment sarcoplasmic reticulum (SR) Ca2+ sequestration, producing larger Ca2+ transients. However, the role of lysosomal Ca2+ signals in pacemaker activity, a distinct Ca2+-operated function of the sinoatrial node (SAN), or in the atrial myocardium has not been investigated. Pharmacological or genetic ablation of the NAADP pathway inhibits the spontaneous beating rate response to beta-adrenergic stimulation in intact SAN. We found intracellular signaling microdomains between lysosomes and neighboring SR or mitochondria in mouse, and goat tissue. The spatial relationship between lysosomes and other Ca2+-handling organelles are altered in goat atrial fibrillation. Furthermore, we demonstrate atrial myocytes produce cAMP in response to lysosomal signaling, adding a novel trigger for cyclic nucleotide signaling. Our findings support the hypothesis that lysosomal Ca2+ signaling contributes to regulation of cardiomyocyte cAMP levels and pacemaker activity.

physiology↗

bioRxiv2024

Isoform-specific N-linked glycosylation of voltage-gated sodium channel alpha-subunits alters beta-subunit binding sites

HighlightsO_LIThree N-linked glycosylation sites conserved among all Nav channels C_LIO_LIGlycan modelling and molecular dynamics simulations highlight 3D landscape C_LIO_LIUnique Nav1.5 N-linked glycans may prevent binding to Ig-domains of {beta}1 and {beta}3 C_LIO_LIUnique Nav1.8 N-linked glycan may prevent binding to Ig-domains of {beta}2 and {beta}4 C_LIO_LIN-linked glycans likely contribute to supra-molecular clustering of Nav channels C_LI Voltage-gated sodium channel -subunits (Nav1.1-1.9) initiate and propagate action potentials in neurons and myocytes. The Nav {beta}-subunits ({beta}1-4) have been shown to modulate -subunit properties. Homo-oligomerization of {beta}-subunits on neighboring or opposing plasma membranes has been suggested to facilitate cis or trans interactions, respectively. The interactions between several Nav channel isoforms and {beta}-subunits have been determined using cryogenic electron microscopy (cryo-EM). Interestingly, the Nav cryo-EM structures reveal the presence of N-linked glycosylation sites. However, only the first glycan moieties are typically resolved at each site due to the flexibility of mature glycan trees. Thus, existing cryo-EM structures may risk de-emphasizing the structural implications of glycans on the Nav channels. Herein, molecular modelling and all-atom molecular dynamics simulations were applied to investigate the conformational landscape of N-linked glycans on Nav channel surfaces. The simulations revealed that negatively-charged sialic acid residues of two glycan sites may interact with voltage-sensing domains. Notably, two Nav1.5 isoform-specific glycans extensively cover the -subunit region that, in other Nav channel -subunit isoforms, corresponds to the binding site for the {beta}1-(and likely {beta}3-) subunit immunoglobulin (Ig) domain. Nav1.8 contains a unique N-linked glycosylation site that likely prevents its interaction with the {beta}2 and {beta}4-subunit Ig domain. These isoform-specific glycans may have evolved to facilitate specific functional interactions, for example by redirecting {beta}-subunit Ig-domains outwards to permit cis or trans supra-clustering within specialized cellular compartments such as the cardiomyocyte perinexal space. Further experimental work is necessary to validate these predictions.

biochemistry↗

bioRxiv2023

Comprehensive analyses of 1771 transcriptome from seven tissues enhance genetic and biological interpretations of maize complex traits

By analyzing 1771 RNA-seq datasets from seven tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation and evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex trait. Using transcriptome-wide association analysis, we linked tissue-specific expression variation of 45 genes to variation of 11 agronomic traits. Through integrative analyses of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and candidate genes for a number of agronomic traits, including leaf during the day for anthesis-silking interval (GRMZM2G093210), leaf during the day for kernel Zeinoxanthin level (GRMZM2G143202), and root for ear height (GRMZM2G700665), highlighting the contribution from tissue-specific gene expression to variation of agronomic trait. Our findings provide novel insights into the genetic and biological mechanisms underlying complex traits in maize, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.

genetics↗

bioRxiv2023

Mechanisms underlying the therapeutic effects of Semen Cuscutae in treating Recurrent Spontaneous Abortion based on Network Pharmacology and Molecular Docking

BackgroundThis paper aims to analyze the active components of SC by network pharmacology and screen the most stable compounds with TNF-a by molecular docking, to explore the mechanism of SC treatment of RSA and provide theoretical basis for drug development. MethodsActive compounds of SC and the potential inflammatory targets of RSA were obtained from the Traditional Chinese Medicine Systematic Pharmacology Database and GeneCard, respectively. The interaction network of RSA-SC-target gene was accomplished and Visualizing by STRING database and Cytoscape software.GO and KEGG pathway enrichment analyses were obtained from DAVID to further explore the RSA mechanism and therapeutic effects of SC. Interactions between TNF- and active compounds were analyzed by molecular docking. Results10 active ingredients and 128 target genes were screened from SC, and 79 of them intersected with RSA target inflammatory genes,which were considered to be potential therapeutic targets. Network pharmacological analysis showed that Sesamin, matrine, matrol and other SC active components had good correlation with the inflammatory target genes of RSA.Related genes include PGR, PTGS1, PTGS2, TGFB1 and CHRNA7. Multiple signaling pathways are involved in RSA pathogenesis,sunh as TNF- signaling pathway, HIF-1 signaling pathway, estrogen signaling pathway, proteoglycans in cancer, FoxO signaling pathway, etc. Molecular docking results suggested that sesamin was the most appropriate natural TNFis. ConclusionOur findings provide an important role and basis for further research on the molecular mechanism of SC treatment of RSA and drug development of TNFis.

bioinformatics↗

bioRxiv2023

Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method

In the human genome, heterozygous sites are genomic positions with different alleles inherited from each parent. On average, there is a heterozygous site every 1-2 kilobases (kb). Resolving whether two alleles in neighboring heterozygous positions are physically linked--that is, phased--is possible with a short-read sequencer if the sequencing library captures long-range information. TELL-Seq is a library preparation method based on millions of barcoded micro-sized beads that enables instrument-free phasing of a whole human genome in a single PCR tube. TELL-Seq incorporates a unique molecular identifier (barcode) to the short reads generated from the same high-molecular-weight (HMW) DNA fragment (known as linked-reads). However, genome-scale TELL-Seq is not cost-effective for applications focusing on a single locus or a few loci. Here, we present an optimized TELL-Seq protocol that enables the cost-effective phasing of enriched loci (targets) of varying sizes, purity levels, and heterozygosity. Targeted TELL-Seq maximizes linked-read efficiency and library yield while minimizing input requirements, fragment collisions on microbeads, and sequencing burden. To validate the targeted protocol, we phased seven 180-200 kb loci enriched by CRISPR/Cas9-mediated excision coupled with pulse-field electrophoresis, four 20 kb loci enriched by CRISPR/Cas9-mediated protection from exonuclease digestion, and six 2-13 kb loci amplified by PCR. The selected targets have clinical and research relevance (BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, PMS2, SCN5A-SCN10A, and PKI3CA). These analyses reveal that targeted TELL-Seq provides a reliable way of phasing allelic variants within targets (2-200 kb in length) with the low cost and high accuracy of short-read sequencing.

genomics↗