Biology subjects

Gu, Y.

Publications and source records attributed to Gu, Y..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Collective biosynthesis of plant spirooxindole alkaloids through enzyme discovery and engineering

Collective synthesis is a well-established strategy to produce natural product collections from common intermediates. Extending this concept to enzymatic systems, collective biosynthesis offers a sustainable approach to diverse molecular collections but faces distinct challenges, including incomplete pathway knowledge and narrow substrate specificity of biosynthetic enzymes. Here, we overcome these limitations through enzyme discovery and protein engineering to achieve collective biosynthesis of spirooxindole alkaloids, an important class of natural products with diverse biological activities. We identified two key enzymes that catalyze enzymatic epimerization, working sequentially with a previously discovered cytochrome P450 enzyme to fully elucidate the biosynthetic pathway of pentacyclic spirooxindole alkaloids. Structure-guided engineering expanded substrate scope, enabling collective biosynthesis of 12 tetracyclic and pentacyclic spirooxindole natural products. We also generated new-to-nature fluorinated and deuterated derivatives through precursor-directed biosynthesis. This work provides crucial insights into plant spirooxindole alkaloid biosynthesis while establishing a powerful approach for sustainable production of complex natural products.

biochemistry↗

bioRxiv2025

Single-Cell Genomics Elucidates Molecular Variations and Regulatory Mechanisms in Circulating Immune Cells

The human peripheral blood displays diverse molecular characteristics across populations, understanding the drivers and underlying mechanisms of which remains challenging. Here, we introduce the Chinese Immune Multi-Omics Atlas (CIMA), elucidating sex-, age-, and genetic-related molecular variations by analyzing multi-omics data from 428 adults with over 10 million immune cells. CIMA generated an enhancer-driven gene regulatory network, identifying 237 high-quality regulons and revealing cell type-specific regulatory mechanisms. Additionally, 11,521 lead cis-expression quantitative trait loci (eQTLs) and 46,339 chromatin accessibility QTLs (caQTLs) were identified at cell type level. CIMA also uncovered pleiotropic associations among immune-related disease risk loci, eQTLs, and caQTLs in a cell type-specific manner. Lastly, a novel cell language model, CIMA-CLM, was developed to predict chromatin accessibility and noncoding variant effects using chromatin sequences and gene expressions. This work represents a population-scale multi-omics resource of human immune cells, providing a valuable reference for future investigation of immune-related diseases.

immunology↗

bioRxiv2025

Niacin protects against vascular calcification via enhanced SIRT1 and SIRT6 signaling and promoted VSMC autophagy

BackgroundVascular calcification (VC) is a common pathologic state that often accompanies calcium-phosphorus metabolism disorder and chronic kidney diseases (CKDs) in aging individuals. Vascular smooth muscle cell (VSMC) has been widely acknowledged as one of the main cell types that involved in this process. Niacin, a lipid-lowering reagent, has been demonstrated to be beneficial in atherosclerotic disease. The correlation and mechanism between niacin and vascular calcification have not been reported so far. Methods and resultsRCS analysis based on large clinical databases indicated that diet that riches in niacin can protect against abdominal artery calcification (AAC). Our data showed that niacin treatment remarkably reduced VSMC osteogenic differentiation and senescence-associated markers under osteogenic stimulation. Moreover, niacin treatment alleviated CKD and vitamin D3-induced vascular calcification in C57BL/6J mice. Mechanistically, we for the first time demonstrated that niacin supplementation inhibited vascular calcification via maintaining both Sirtuin 1 (SIRT1) and Sirtuin 6 (SIRT6) levels. Moreover, we verified that niacin activated SIRT1 and SIRT6 promoted VSMC autophagy flux. ConclusionsThese findings may help to develop novel therapeutic strategies in the treatment and prevention of vascular calcification.

cell biology↗

bioRxiv2025

Absolute Quantification of Aging-Associated Glycans in IgG for Biological Age Prediction: Insights from Glycomics and Transcriptomics

Immunoglobulin G (IgG) N-glycans have been identified as associated with aging; however, previous studies predominantly quantified changes based on the relative percentages of each glycan within the total glycan pool, neglecting the absolute concentration changes of individual glycans. Additionally, relative quantification can limit practical applications, as these often require absolute concentration measurements for consistent and interpretable biomarker values. In this study, we introduce a novel strategy for discovering aging-associated IgG glycans and establishing a prediction model based on their absolute concentration alteration. We employed a glycome quantification technology to identify the alteration in IgG glycan amount in natural aging and anti-aging (caloric restriction) models, discovering aging-related glycans. The glycomics analysis revealed key features: downregulation of bisected glycan GP3 (F(6)A2B) and upregulation of digalactosylated glycan GP8 (F(6)A2G2). These glycan changes showed significant fold changes from an early stage. Using external standards of these two glycans, we subsequently measured the absolute concentrations of them, allowing us to establish a predictive model, abGlycoAge, for biological aging. The abGlycoAge index suggested a younger state under caloric restriction, with an average age reduction of 3.9-14 weeks. Additionally, we performed RNA sequencing on splenic B cells of mice, suggesting Derl3, Smarcb1, Ankrd55, Tbkbp1 and Slc38a10 could contribute to the alteration of GP3 and GP8 in aging. This analysis enhances our understanding of glycan alterations, accounts for individual variability, and aids in designing effective anti-aging strategies. These findings highlight the crucial roles of the GP3 and GP8 as potential biomarkers for aging and health.

biochemistry↗

bioRxiv2024

The genetic architecture of cortical similarity networks

The genetic architecture of human brain networks is central to understanding the organization and evolution of the cortex, the causal relationships between brain structure and function, and the pathogenesis of heritable neuropsychiatric disorders. However, the current understanding of the genetics of brain networks remains fragmented. Here, we investigated common genetic effects on Morphometric INverse Divergence (MIND), a biologically-validated, heritable, and multimodal MRI metric of inter-areal similarity and connectivity. Using a discovery dataset (N>30,000 adults), we estimated subject-specific MIND networks from the multivariate distributions of four MRI features at each of 23 cortical areas and performed genome-wide association studies (GWAS) at each of the 276 inter-areal edges. These edge-level genetic effects were highly replicated by parallel GWAS of an independent validation dataset (N>18,000 adults). We found that strong genetic correlations between multiple edges were largely reducible to two gradients of genetically-determined cortical similarity, each of which was aligned with geodesic distance from one of the two phylogenetically primitive areas (paleocortex and archicortex) predicted by the dual origin theory of cortical evolution. Genetic MIND gradients were more heritable than comparable gradients derived from GWAS of functional MRI connectivity networks; and the paleocortical trend was genetically correlated with, and causally predictive of, functional connectivity. Finally, we identified multiple global and local genetic correlations between both MIND gradients and nine clinical diagnoses or biomedical traits, indicating that the normative genetic architecture of human brain networks is pleiotropically associated with inherited risk of neuropsychiatric disorders and systemic metabolic and immune traits. These results provide fresh insight into the dual origins of the human cortex and their implications for brain function and health.

neuroscience↗

bioRxiv2024

Spatial-DC: a robust deep learning-based method for deconvolution of spatial proteomics

Spatial proteomics studies the spatial distribution of proteins within cells or tissues, providing a new perspective for comprehending cellular processes and disease mechanisms. One important challenge of current spatial proteomics technologies is low resolution, resulting in multiple cells in each spatial proteomics spot. While methods have been proposed to infer the composition of potential cell types in such spots for spatial transcriptomics, the depressed correlation and divergent quantification between transcriptome and proteome limits their capability in spatial proteomics. To enhance the utility of spatial proteomics data, we propose Spatial-DC (Spatial Digital Cytometry), a deep learning-based framework that infers cell-type composition in each spot and reconstructs spatially and cell-type resolved proteomic profiles. We achieve this by utilizing transfer learning and self-supervised learning with graph convolutional networks (GCN), which enables the incorporation of target spatial proteomics with reference single-cell or single-cell-type proteomics data. Through extensive simulations of spatial proteomics data, we demonstrate that Spatial-DC outperforms eight state-of-the-art methods in estimating cell-type composition and provides meaningful reconstructions of proteomic profiles for individual cell types. We apply Spatial-DC to different tissues measured using both multiplexed antibody-based and mass spectrometry (MS)-based spatial proteomics technologies. The results showcase Spatial-DCs superior sensitivity in providing more refined cell-type distribution maps compared to cell-type-specific marker-based distributions and its feasibility in reconstructing spatially and cell-type resolved proteomic profiles from real-world spatial proteomics data. Moreover, we validate Spatial-DC with a newly self-collected pancreatic cancer spatial proteomics data characterized by complex tumor microenvironment (TME) and identify the signaling direction and strength at both spatial and cell-type levels within the TME, suggesting cell-type-specific and spatially-resolved interactions linked to tumor outcomes. Our results highlight Spatial-DC as a versatile tool for the deconvolution of spatial proteomics data across various tissue slices, providing a reliable foundation for downstream analysis.

bioinformatics↗

bioRxiv2024

A genome-scale single cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines

Population-scale resources of genetic, molecular, and cellular information form the basis for understanding human genomes, charting the heritable basis of disease, and tracing the effects of mutations. Pooled perturbation assays applied to cellular models, probing the effect of many perturbations coupled with an scRNA-seq readout (Perturb-seq), are especially potent references for interpreting disease-linked mutations or gene expression changes. However, the utility of existing maps has been limited by the comprehensiveness of perturbations possible, and the relevance of their cell line context. Here, we present the first genome-scale CRISPR interference (CRISPRi) perturbation map with single-cell RNA sequencing readout across many human genetic backgrounds in human pluripotent cells. To do so, we establish large-scale CRISPRi screening in human induced pluripotent stem cells from healthy donors, using over 20,000 guide RNAs to target 7,226 genes across 34 cell lines from 26 genetic backgrounds, and gather expression data from nearly 2 million cells. We comprehensively map trans expression changes induced by the target knockdowns, which complement co-expression patterns in unperturbed cells and facilitate the functional annotation of target genes to biological processes and complexes. Consistency of targeting protein complex members point to protein complexes as a nexus for aggregating transcriptional variation, revealing novel interaction partners. We characterise variation in perturbation effects across donors, with expression quantitative trait loci linked to higher genetic modulation of perturbation effects but overall low replication of trans effects due to knockdown of their corresponding cis regulators. This study pioneers population-scale CRISPR perturbations with single cell readouts that will fuel foundation models for the future of effective modulation of cellular disease phenotypes.

genetics↗

bioRxiv2024

Structural diversity and oligomerization of bacterial ubiquitin-like proteins

Bacteria possess a variety of operons with homology to eukaryotic ubiquitination pathways that encode predicted E1, E2, E3, deubiquitinase, and ubiquitin-like proteins. Some of these pathways have recently been shown to function in anti-bacteriophage immunity, but the biological functions of others remain unknown. Here, we show that ubiquitin-like proteins in two bacterial operon families show surprising architectural diversity, possessing one to three {beta}-grasp domains preceded by diverse N-terminal domains. We find that a large group of bacterial ubiquitin-like proteins possess three {beta}-grasp domains and form homodimers and helical filaments mediated by conserved Ca2+ ion binding sites. Our findings highlight a distinctive mode of self-assembly for ubiquitin-like proteins, and suggest that Ca2+-mediated ubiquitin-like protein filament assembly and/or disassembly enables cells to sense and respond to stress conditions that alter intracellular metal ion concentration.

biochemistry↗

bioRxiv2024

Characteristic of KPC-14, a KPC Variant Conferring Resistance to Ceftazidime-Avibactam in the Extensively Drug-resistant ST463 Pseudomonas aeruginosa Clinical Isolate

We studied two KPC-14 variants from clinical Pseudomonas aeruginosa isolates, C137 and C159, to better understand genomic diversity, mechanisms, and genes that confer antibiotic resistance and pathogenicity. C137 and C159, a sequence type 463 ExoU-positive multidrug-resistant strain, were concurrently resistant to carbapenems and ceftazidime-avibactam (CZA). Both strains possessed five intrinsic antimicrobial resistance genes (fosA, catB7, crpP, blaPAO, and a blaOXA-486 variant), as well as the blaKPC-14 gene in the chromosome. In strain C137, blaKPC-14 gene was situated on the plasmid pC137. KPC-14-harbouring transformants of pC137 exhibited resistance to CZA and restored sensitivity to carbapenems, signifying a "see-saw" effect. Both strains demonstrated the expression of the blaKPC-14 gene, concurrent inactivation of the outer membrane protein OprD, overexpression of the efflux pump MexX, and a pronounced capacity for biofilm formation. The genomic environment of KPC-14 consisted of IS26/IS26/TnpR_Tn3/ISKpn27/ISKpn6/IS26, which was classified as pseudo-compound transposons (PCTs). Plasmid pC137 closely resembled the previously described plasmid p94, which possesses the same genomic architecture, implying that IS26-mediated PCTs may store a variety of resistance genes, including blaKPC-2 and KPC variants, and were currently disseminating in the region. The KPC-14 variant presents significant challenges for clinical treatment. The blaKPC-14 gene, carried by the PCTs, was integrated into the chromosome, exhibiting stability throughout bacterial inheritance. Our research highlights the necessity for improved clinical surveillance of Klebsiella pneumoniae carbapenemase-producing P. aeruginosa.

molecular biology↗

bioRxiv2024

RBPMS and RBPMS2 Cooperate to Safeguard Cardiac Splicing

BackgroundMutations in cardiac splicing factors (SFs) cause cardiomyopathy and congenital heart disease, underscoring the critical role of SFs in cardiac development and disease. Cardiac SFs are implicated to cooperatively regulate the splicing of essential cardiac genes, but the functional importance of their collaboration remains unclear. RNA Binding Protein with Multiple Splicing (RBPMS) and RBPMS2 are SFs involved in heart development and exhibit similar splicing regulatory activities in vitro, but it is unknown whether they cooperate to regulate splicing in vivo. MethodsRbpms and Rbpms2 single or double cardiomyocyte (CM)-specific knockout (KO) mice were generated and analyzed for cardiac phenotypes. RNA sequencing was performed to assess gene expression and splicing changes in single and double KOs. In silico analyses were used to dissect the mechanisms underlying distinct and overlapping roles of RBPMS and RBPMS2 in heart development. ResultsMice lacking both RBPMS and RBPMS2 in CMs died before embryonic day 13.5 and developed sarcomere disarray, whereas Rbpms or Rbpms2 single CM-specific KO mice had normal sarcomere assembly and survived to adulthood. Defective sarcomere assembly is likely owing to the widespread mis-splicing of genes essential for cardiac contraction in double KO mice, underscoring the overlapping role of RBPMS and RBPMS2 in splicing regulation. Mechanistically, we found RBPMS and RBPMS collectively promote cardiac splicing program while repressing non-cardiac splicing programs. Moreover, RNA splicing maps suggested that the binding location of RBPMS and RBPMS2 on pre-mRNA dictates whether they function as splicing activators or repressors. Lastly, the requirement for RBPMS and/or RBPMS2 for splicing regulation arises from intrinsic features of the target exons. ConclusionsOur results demonstrate that RBPMS and RBPMS2 work in concert to safeguard the splicing of genes essential for cardiac contraction, highlighting the importance of SF collaboration in maintaining cardiac splicing signature, which should be taken into consideration when devising future therapeutic approaches through modulating the activity of SFs. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSO_LIMutations in cardiac splicing factors (SFs) cause cardiomyopathy and congenital heart disease, and the splicing of cardiac genes is regulated by multiple SFs. However, the functional importance of the collaboration among specific cardiac SFs is unknown. C_LIO_LIRBPMS has emerged as a cardiac SF for sarcomere genes but is not required for sarcomere assembly. C_LIO_LIRBPMS2 can substitute RBPMS in in vitro splicing assays, yet its role in mammalian cardiomyocytes (CMs) remains unclear. C_LI What New Information Does This Article Contribute?O_LIRBPMS and RBPMS2 have both distinct and overlapping roles in CMs. C_LIO_LIRBPMS and RBPMS2 collectively contribute to the maintenance of cardiac splicing program, which is essential for sarcomere assembly and embryonic survival. C_LIO_LIRNA splicing map of RBPMS and RBPMS2 reveals that they can function either as splicing activators or repressors, depending on their binding locations on pre-mRNA. C_LI This study provides compelling evidence of cooperation between cardiac splicing factors during heart development, which, to our knowledge, has not been demonstrated in vivo. Rbpms and Rbpms2 CM-specific double KO mice die in utero and exhibit sarcomere disarray, whereas single KO mice survive to adulthood with normal sarcomere structure but manifest distinct cardiac phenotypes, suggesting RBPMS and RBPMS2 possess both distinct and overlapping functions in CMs. Although mis-splicing in cardiac genes can be seen in all three KOs, the splicing signature of double KO hearts drastically shifts towards non-cardiac tissues, including more prominent mis-splicing in genes related to cardiac contractile function. Our study further reveals that the splicing regulation of RBPMS and RBPMS2 has the characteristics of "positional effects", i.e., the binding location on pre-mRNA dictates whether they function as splicing activators or repressors; and the intrinsic features of the target exon determine the requirement for one or two RBPMS proteins for splicing regulation. Our study sheds light on the functional importance of cardiac SF cooperation in maintaining cardiac splicing signature during heart development.

developmental biology↗

bioRxiv2024

NOLC1 Suppresses Immuno-chemotherapy by Inhibiting p53-mediated Ferroptosis in Gastric Cancer

Gastric cancer (GC) is one of the most malignant cancers, and cisplatin (Cis)-based chemotherapy remains the main clinical treatment for GC. However, Cis resistance often occurs, largely limiting its therapeutic efficacy in tumors. Therefore, a better understanding of the drug resistance mechanism could reveal new approaches for improving GC treatment efficacy. Here, we define the integrative role of nucleolar and coiled-body phosphoprotein 1 (NOLC1), a molecular chaperone that is significantly upregulated in GC tissues and Cis-resistant GC cells. Knocking down NOLC1 increased GC sensitivity to Cis by regulating ferroptosis. Mechanistically, NOLC1 binds to the p53 DNA binding domain (DBD), decreasing p53 nuclear accumulation stimulated by Cis and suppressing p53 transcriptional functions. Then, the p53-mediated ferroptosis is suppressed. Furthermore, the silence of NOLC1 promoted ferroptosis-induced immunogenic cell death (ICD) and reprogrammed the immunosuppressive tumor microenvironment, thereby increasing sensitivity to anti-programmed cell death-1 (PD-1) therapy plus Cis. The combination of anti-PD-1 plus Cis effectively inhibited GC growth without significant side effects. In summary, our findings reveal that targeting NOLC1 may be a novel therapeutic strategy for GC and may increase the efficacy of chemotherapy combined with immune checkpoint inhibitor (ICI) therapy.

cancer biology↗

bioRxiv2024

DSA-DeepFM: A Dual-Stage Attention-Enhanced DeepFM Model for Predicting Anticancer Synergistic Drug Combinations

MotivationDrug combinations are crucial in combating drug resistance, reducing toxicity, and improving therapeutic outcomes in the treatment of complex diseases. As the number of available drugs grows, the potential combinations increase exponentially, making it impractical to rely solely on biological experiments to identify synergistic drug pairs. Consequently, machine learning methods are increasingly used to systematically screen for synergistic drug combinations. However, most current approaches prioritize predictive performance by integrating auxiliary information or increasing model complexity. By overlooking the biological mechanisms behind feature interactions, their effectiveness in predicting drug synergy can be limited. ResultsWe present DSA-DeepFM, a deep learning model that integrates a dual-stage attention (DSA) mechanism with Factorization Machines (FMs) to improve drug synergy prediction by addressing complex biological feature interactions. The model incorporates categorical and auxiliary numerical inputs, embedding them into high-dimensional spaces and then fusing them through the DSA mechanism to capture both field-aware and embedding-aware patterns. These patterns are then processed by a DeepFM module, which captures low-order and high-order feature interactions before making final predictions. Validation testing demonstrates that DSA-DeepFM significantly outperforms traditional machine learning and state-of-the-art deep learning models. Additionally, t-SNE visualizations confirm the models discriminative power at various stages. As a case study, we use our model to identify eight novel synergistic drug combinations, three of which are well-supported by existing wet-lab experiments, underscoring its practical utility and potential for future applications.

bioinformatics↗

bioRxiv2024

Spatiotemporal map of the developing human reproductive tract at single-cell resolution

The human reproductive tract plays an essential role in species perpetuation. Its development involves complex processes of sex specification, tissue patterning and morphogenesis, which, if disrupted, can cause lifelong health issues, including infertility. Here, we generated an extensive single-cell and spatial multi-omic atlas of the human reproductive tract during prenatal development, which allowed us to answer questions that smaller-scale, organ-focused experiments could not address before. We identified potential regulators of sexual dimorphism in reproductive organs, pinpointing novel genes involved in urethral canalisation of the penis, with relevance to hypospadias. By combining histological features with gene expression data, we defined the transcription factors and cell signalling events required for the regionalisation of the Mullerian and Wolffian ducts. This led to a refinement of how the HOX code is established in the distinct reproductive organs, including increased expression of thoracic HOX genes in the rostral mesenchyme of the fallopian tube and epididymis. Our study further revealed that the epithelial regionalisation of the fallopian tube and epididymis required for sperm maturation in adulthood is established early in development. In contrast, later events in gestation or postnatally are necessary for the regionalisation of the uterocervical canal epithelium. By mapping sex-specific reproductive tract regionalisation and differentiation at the cellular level, our study offers valuable insights into the causes and potential treatments of reproductive disorders.

developmental biology↗

bioRxiv2024

Comparative spatiotemporal single cell transcriptomes reveal rewiring of pre-existing regulations during emergence of Kranz anatomy in C4 grasses

Many of the worlds most productive food and bioenergy crops use C4 photosynthesis, which have high photosynthetic efficiency due to a Kranz anatomy-based CO2 concentrating mechanism. Here, we took a comparative transcriptomics approach using single cell spatial transcriptomes of leaf primordia for maize (Zea mays) and single cell RNA-seq (scRNA-seq) atlases of corresponding leaf tissues for three C4 species (Zea mays, Sorghum bicolor, Setaria viridis) and one C3 rice (Oryza sativa) to study regulatory networks involved in the development and evolution of Kranz anatomy. We show that the formation of Kranz anatomy involves extensive recruitment and modification of pre-existing regulatory modules, especially the SHR-SCR module and the auxin signaling pathway. Members of the INDETERMINATE DOMAIN (IDD) family transcription factors, including IDD7 and IDDP1, contribute to the modification of the involved modules. These extensive recruitment and modification of existing genetic regulatory programs underlie the repeated emergence of C4 photosynthesis during evolution.

plant biology↗

bioRxiv2024

Cluster Assembly Dynamics Drive Fidelity of Planar Cell Polarity Polarization

In planar cell polarity (PCP) signaling, distinct molecular subcomplexes segregate to opposite sides of each cell, where they interact across intercellular junctions to form asymmetric clusters. Although proximal-distal asymmetry within PCP clusters is the defining feature of PCP signaling, the mechanism by which this asymmetry develops remains unclear. Here, we developed a method to count the number of monomers of core PCP proteins within individual clusters in live animals and used it to infer the underlying molecular dynamics of cluster assembly and polarization. Measurements over time and space in wild type and in strategically chosen mutants demonstrate that cluster assembly is required for polarization, and together with mathematical modeling provide evidence that clusters become increasingly asymmetric and correctly oriented as they increase in size. We propose that cluster assembly dynamics amplify weak and noisy inputs into a robust cellular output, in this case cell and tissue-level polarization.

cell biology↗

bioRxiv2024

Antisense oligonucleotide targeting pathogenic sense repeat RNA in C9ORF72 suppresses production of antisense-dependent dipeptide repeat proteins implicated in ALS/FTD

A six nucleotide repeat expansion in intron-1 of the C9ORF72 gene is the most common genetic mutation affecting individuals with Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Bi-directional transcription of the repeat expansion generates sense and antisense repeat RNAs that can then be translated in all reading frames to produce six distinct dipeptide repeat (DPR) proteins with unique termini. The precise site of translation initiation of these proteins within the C9ORF72 repeat expansion remains elusive. We used CRISPR-Cas9 genome editing and steric-blocking antisense oligonucleotides (ASOs) to investigate the contribution of different AUG codons in the antisense repeat RNA to the production of DPR proteins, poly(GP) and poly(PR) in C9ORF72 expansion carrier motor neurons and lymphoblast cells. We then utilized ASOs targeting C9ORF72 sense repeat RNA to examine whether sense or antisense RNA is the major source of the poly(GP) protein - a question for which conflicting evidence exists. We found that these ASOs reduced the intended sense RNA target, but also the antisense RNA, thus preventing the production of poly(PR). Our data highlights the importance of the sequences preceding the antisense CCCCGG repeat expansion for the synthesis of antisense DPR proteins and supports the use of sense C9ORF72 ASOs to prevent the accumulation of both sense- and antisense-dependent DPR proteins in C9ORF72 ALS/FTD.

neuroscience↗

bioRxiv2024

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes

BackgroundThe agamid dragon lizard Pogona vitticeps is one of the most popular domesticated reptiles to be kept as pets worldwide. The capacity of breeding in captivity also makes it emerging as a model species for a range of scientific research, especially for the studies of sex chromosome origin and sex determination mechanisms. ResultsBy leveraging the CycloneSEQ and DNBSEQ sequencing technologies, we conducted whole genome and long-range sequencing for a captive-bred ZZ male to construct a chromosome-scale reference genome for P. vitticeps. The new reference genome is [~]1.8 Gb in length, with a contig N50 of 202.5 Mb and all contigs anchored onto 16 chromosomes. Genome annotation assisted by long-read RNA sequencing greatly expanded the P. vitticeps lncRNA catalog. With the chromosome-scale genome, we were able to characterize the whole Z sex chromosome for the first time. We found that over 80% of the Z chromosome remains as pseudo-autosomal region (PAR) where recombination is not suppressed. The sexually differentiated region (SDR) is small and occupied mostly by transposons, yet it aggregates genes involved in male development, such as AMH, AMHR2 and BMPR1A. Finally, by tracking the evolutionary origin and developmental expression of the SDR genes, we proposed a model for the origin of P. vitticeps sex chromosomes which considered the Z-linked AMH as the master sex-determining gene. ConclusionsOur study provides novel insights into the sex chromosome origin and sex determination of this model lizard. The near-complete P. vitticeps reference genome will also benefit future study of amniote evolution and may facilitate genome-assisted breeding.

genomics↗

bioRxiv2024

Deciphering the Cell Specific Transcript Heterogeneity and Alternative Splicing during the Early Embryonic Development of Zebrafish

Cell fate determination during early embryonic development is a complex process modulated by gene expression. The intricate interplay of transcriptional and post-transcriptional regulation is integral to the developmental trajectory of embryogenesis, yet how RNA processing may contribute to early development programming is largely elusive. Leveraging recent technological advances in single-molecule nanopore sequencing, we developed a single-cell long-read transcriptome sequencing technology, allowing a clear view of transcript diversity during zebrafish embryogenesis during pre- and post-zygotic genome activation (ZGA). A closer examination of the dynamic transcript usage and potential alternative splicing revealed that abundant stage-specific transcripts with differential coding potentials are involved in distinct biological functions. Specifically, we identified two cell populations at the onset of ZGA based on isoform diversity instead of gene profiling, which followed divergent developmental trajectories toward the ectoderm and the presumptive ectoderm. These two populations of cells were characterized by divergent splicing regulations linked to differential RNA-binding proteins, including SNRPA and SFPQ. Altogether, using the single-cell long-read transcriptome sequencing strategy, we work has revealed the cell-specific transcriptome dynamics contributing to the cell fate determination during embryogenesis.

developmental biology↗