Biology subjects

Hu, W.

Publications and source records attributed to Hu, W..

At least 91 records · Page 5Linked to original sources

bioRxiv2024

Hormonal dynamics reveal a stimulatory role for secretoneurin in zebrafish ovulation

Surge release of luteinizing hormone (Lh) from the pituitary is essential for fertility as it triggers ovulation. While secretoneurin (SN) is a phylogenetically conserved secretogranin-2 derived peptide that stimulates Lh, its role in ovulation has not been established. To directly compare periovulatory changes in the classical hormones to the emerging reproductive neuropeptides SNa and SNb, simultaneous mass spectrometry measurement of 9 peptides and 5 steroids was conducted in female zebrafish. Regression analysis indicated that levels of SNa1-34 in the brain peaked when type 3 gonadotropin-releasing hormone (Gnrh3) increased (R2=0.71) at the time of the Lh surge, 3.5 h before ovulation. In contrast, levels of the naturally occurring derivative SNa1-14 were highest at ovulation, while SNb1-31 was invariable. The bioactivities of SNa1-34 and SNa1-14 were investigated. After injection of SNa1-34 in females that had been isolated from males, 61% (11/18) ovulated within 6 h, which was like the effects of the Lh analog human chorionic gonadotropin (hCG) (72%; 13/18 females). SNa1-34 could induce ovulation by stimulating time-dependent expression of gnrh3 in the brain, chorionic gonadotropin alpha (cga), luteinizing hormone b (lhb) subunit in pituitary, and the nuclear progesterone receptor (npr) in ovaries. In contrast, SNa1-14 exhibited far fewer effects on gene expression and did not induce ovulation. Our results support the proposal that SN is a reproductive hormone. Significance statementSecretogranin-2 is a secretory granule protein that is enzymatically processed to the bioactive neuropeptide secretoneurin. It is produced in hypothalamic neurons and anterior pituitary cells, and we provide in vivo evidence that secretoneurin plays an important role to induce ovulation. Secretoneurin levels in the brain increase concomitantly with gonadotropin-releasing hormone prior to ovulation in normal zebrafish. Injection of a synthetic secretoneurin peptide increased expression of reproduction-related genes at all levels of the hypothalamic-pituitary-ovarian axis. Secretoneurin stimulates ovulation in otherwise anovulatory females. Together these data place the evolutionarily conserved secretoneurin amongst other critical neuroendocrine regulators. Secretoneurin or synthetic agonists could be used to improve breeding in fish species, or to potentially help with infertility treatments

physiology↗

bioRxiv2024

Single-cell transcriptome unravels spermatogonial stem cells and dynamic heterogeneity of spermatogenesis in seasonal breeding teleost

Seasonal spermatogenesis in fish is driven by spermatogonial stem cells (SSCs), which undergo a complex cellular process to differentiate into mature sperm. In this study, we characterized spermatogenesis in the large yellow croaker (Larimichthys crocea), a marine fish of significant commercial value, based on a high-resolution single-cell RNA-seq atlas of testicular cells from three distinct developmental stages- juvenile, adult differentiating and regressed testes. We detailed continuous developmental trajectory of spermatogenic cells, from spermatogonia to spermatids, elucidating the molecular events involved in spermatogenesis. We uncovered dynamic heterogeneity in cellular compositions throughout the annual reproductive cycle, accompanied by strong molecular signatures within specific testicular cells. Notably, we identified a distinct population of SSCs and observed a critical metabolic transition from glycolysis to oxidative phosphorylation, enhancing our understanding of the biochemical and molecular characteristics of SSCs. Additionally, we elucidated the interactions between somatic cells and spermatogonia, illuminating the mechanisms that regulate SSCs development. Overall, this work enhances our understanding of spermatogenesis in seasonal breeding teleost and provides essential insights for the further conservation and culture of SSCs. Summary statementOur study reveals new insights into the development of spermatogonial stem cells (SSCs), potentially impacting further conservation and culture of SSCs in teleost.

developmental biology↗

bioRxiv2024

The genomic and epigenomic dynamics of hemizygous genes across crops with contrasting mating systems

Hemizygous genes, which present on only one of the two homologous chromosomes of diploid organisms, have been mainly studied in the context of sex chromosomes and sex-linked genes. However, structural variants (SVs), such as a deletion/insertion of one allele, can lead to hemizygous genes, a phenomenon largely unexplored in plants. Here, we investigated the genomic and epigenomic landscapes of hemizygous genes across 22 genomes with varying propagation histories: eleven clonal lineages, seven outcrossed samples and four inbred and putatively homozygous genomes. We identified SVs leading to genic hemizygosity. As expected, very few genes (0.01%-1.2%) were hemizygous in the homozygous genomes, representing negative controls. Hemizygosity was appreciable among outcrossed lineages, averaging 8.7% of genes, but consistently elevated for the clonal samples at 13.8% genes, likely reflecting heterozygous SVs accumulation during clonal propagation. Compared to diploid genes, hemizygous genes were more often situated in centromeric than telomeric regions and underlying weaker purifying selection. They also had reduced levels of expression, averaging [~]20% of the expression levels of diploid genes, violating the evolutionary model of dosage compensation. We also detected higher DNA methylation levels, in hemizygous genes and transposable elements, which may contribute to the reduced expression of hemizygous genes. Finally, expression profiles showed that hemizygous genes were more specifically expressed in contexts related to fruit development, organ differentiation and stress responses. Overall, hemizygous genes accumulate in clonally propagated lineages and display distinct genetic, and epigenetic features compared to diploid genes, shedding new insights on genetic studies and breeding programs of clonal crops.

plant biology↗

bioRxiv2024

A conserved lysine/arginine-rich motif in potyviral 6K1 protein is key in engaging autophagy-mediated self-degradation for completing pepper veinal mottle virus infection

Potyviruses possess one positive-sense single-stranded RNA genome mainly with polyprotein processing as their gene expression strategy. The resulting polyproteins are proteolytically processed by three virus-encoded proteases into 11 or 12 mature proteins. One of such, 6-kDa peptide 1 (6K1), is an understudied viral factor. Its function in viral infection remains largely mysterious. This study is to reveal part of its roles by using pepper veinal mottle virus (PVMV) as a model virus. Alanine substitution screening analysis revealed that 15 out of 17 conserved residues across potyviral 6K1 sequences are essential for PVMV infection. However, 6K1 protein is less accumulated in virus-infected cells, even though P3-6K1 junction is efficiently processed by NIa-Pro for its release, indicating that 6K1 undergoes a self-degradation event. Mutating the cleavage site to prevent NIa-Pro processing abolishes viral infection, suggesting that the generation of 6K1 along with its degradation might be important for viral multiplication. We corroborated that cellular autophagy is engaged in 6K1s degradation. Individual engineering of the 15 6K1 variants into PVMV was performed to allow for their expression along with viral infection. Five of such variants, D30A, V32A, K34A, L36A, and L39A, significantly interfere with viral infection. The five residues are enclosed in a conserved lysine/arginine-rich motif; four of them appear to be crucial in engaging autophagy-mediated self-degradation. Based on these data, we envisaged a scenario that potyviral 6K1s interact with an unknown anti-viral component to be co-degraded by autophagy to promote viral infection. IMPORTANCEPotyvirus is the largest genus of plant-infecting RNA viruses, which encompasses socio-economically important virus species, such as Potato virus Y, Plum pox virus, and Soybean mosaic virus. Like all picorna-like viruses, potyviruses express their factors mainly via polyprotein processing. Theoretically, viral factors P3 through CP, including 6K1, should share an equivalent number of molecules. The 6K1 is small in size ([~]6 kDa) and conserved across potyviruses, but less accumulated in virus-infected cells. This study demonstrates that cellular autophagy is engaged in the degradation of 6K1 to promote viral infection. In particular, we found a conserved lysine/arginine-rich motif in 6K1s across potyviruses that is engaged in this degradation event. This finding reveals one facet of a small protein that help understand the pro-viral role of cellular autophagy in viral infection.

microbiology↗

bioRxiv2024

ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer's disease.

Multimodal measurements have become widespread in genomics, however measuring open chromatin accessibility and splicing simultaneously in frozen brain tissues remains unconquered. Hence, we devised Single-Cell-ISOform-RNA sequencing coupled with the Assay-for-Transposase-Accessible-Chromatin (ScISOr-ATAC). We utilized ScISOr-ATAC to assess whether chromatin and splicing alterations in the brain convergently affect the same cell types or divergently different ones. We applied ScISOr-ATAC to three major conditions: comparing (i) the Rhesus macaque (Macaca mulatta) prefrontal cortex (PFC) and visual cortex (VIS), (ii) cross species divergence of Rhesus macaque versus human PFC, as well as (iii) dysregulation in Alzheimers disease in human PFC. We found that among cortical-layer biased excitatory neuron subtypes, splicing is highly brain-region specific for L3-5/L6 IT_RORB neurons, moderately specific in L2-3 IT_CUX2.RORB neurons and unspecific in L2-3 IT_CUX2 neurons. In contrast, at the chromatin level, L2-3 IT_CUX2.RORB neurons show the highest brain-region specificity compared to other subtypes. Likewise, when comparing human and macaque PFC, strong evolutionary divergence on one molecular modality does not necessarily imply strong such divergence on another molecular level in the same cell type. Finally, in Alzheimers disease, oligodendrocytes show convergently high dysregulation in both chromatin and splicing. However, chromatin and splicing dysregulation most strongly affect distinct oligodendrocyte subtypes. Overall, these results indicate that chromatin and splicing can show convergent or divergent results depending on the performed comparison, justifying the need for their concurrent measurement to investigate complex systems. Taken together, ScISOr-ATAC allows for the characterization of single-cell splicing and chromatin patterns and the comparison of sample groups in frozen brain samples.

genomics↗

bioRxiv2024

GhCPK28 negatively regulates the immune response by phosphorylating GhTIFY3b

The soil-borne fungus Verticillium dahliae (V. dahliae) seriously inhibits cotton (Gossypium hirsutum) growth and productivity. The immune system of cotton against this pathogen is largely unknown. Here we investigated the involvement of Ca2+-dependent protein kinases (CPKs) in this immunity. One CPK coding gene GhCPK28 had reduced expression after infection by V. dahliae in cotton. Knocking down of the GhCPK28 by virus induced gene silencing led to enhanced resistance to V. dahliae which is accompanied by a higher ROS accumulation and systemic acquired response. GhCPK28 was found to phosphorylate a TIFY family protein GhTIFY3b and reduce its stability. Silencing GhTIFY3b increased the susceptibility of cotton to V. dahliae. Together, this study indicate that GhCPK28 is a negative regulator of defense against V. dahliae infection and the GhTIFY3b might be a target protein of its activity. It sheds light on the immune system against V. dahliae and provides candidate genes for improving resistance against Verticillium wilt in cotton.

plant biology↗

bioRxiv2024

A CANCER PERSISTENT DNA REPAIR CIRCUIT DRIVEN BY MDM2, MDM4 (MDMX), AND MUTANT P53 FOR RECRUITMENT OF MDC1 AND 53BP1 TO CHROMATIN

The influence of the metastasis promoting proteins mutant p53 (mtp53) and MDM2 on Cancer Persistent Repair (CPR) to promote cancer cell survival is understudied. Interactions between the DNA repair choice protein 53BP1 and wild type tumor suppressor protein p53 (wtp53) regulates cell cycle control. Cancer cells often express elevated levels of transcriptionally inactive missense mutant p53 (mtp53) that interacts with MDM2 and MDM4/MDMX (herein called MDMX). The ability of mtp53 to maintain a 53BP1 interaction while in the context of interactions with MDM2 and MDMX has not been described. We asked if MDM2 regulates chromatin-based phosphorylation events in the context of mtp53 by comparing the chromatin of T47D breast cancer cells with and without MDM2 in a phospho-peptide stable isotope labeling in cell culture (SILAC) screen. We found reduced phospho-53BP1 chromatin association, which we confirmed by chromatin fractionation and immunofluorescence in multiple breast cancer cell lines. We used the Proximity Ligation Assay (PLA) in breast cancer cell lines and detected 53BP1 in close proximity to mtp53, MDM2, and the DNA repair protein MDC1. Through disruption of the mtp53-MDM2 interaction, by either Nutlin 3a or a mtp53 R273H C-terminal deletion, we uncovered that mtp53 was required for MDM2-53BP1 interaction foci. Our data suggests that mtp53 works with MDM2 and 53BP1 to promote CPR and cell survival.

cancer biology↗

bioRxiv2024

"Hitting Two Birds with One Stone" Design of Intestinal Integrin-Targeting and Redox Homeostasis-Regulating Oral Nanotherapy for Ulcerative Colitis

Designing highly efficient orally administrated nanotherapeutics with specific inflammatory site-targeting functions in the gastrointestinal (GI) tract for ulcerative colitis (UC) management is a significant challenge. Straightforward and adaptable modular multifunctional nanotherapeutics represent groundbreaking advancements and are crucial to promoting broad application in both academic research and clinical practice. In this study, we focused on exploring a specific targeting modular and functional oral nanotherapy, serving as "one stone", for the directed localization of inflammation and the regulation of redox homeostasis, thereby achieving effects against "two birds" for UC treatment. The designed nanotherapeutic agent OPNs@LMWH, which has a core-shell structure composed of oxidation-sensitive {varepsilon}-polylysine nanoparticles (OPNs) in the core and low-molecular-weight heparin (LMWH) in the shell, exhibited specific active targeting effects and therapeutic efficacy simultaneously. We qualitatively and quantificationally confirmed that OPNs@LMWH possessed high integrin M-mediated immune cellular uptake efficiency and preferentially accumulated in inflamed lesions. Compared with bare OPNs, OPNs@LMWH exhibited enhanced intracellular reactive oxygen species (ROS) scavenging and anti-inflammatory effects. After oral administration of OPNs@LMWH to mice with dextran sulfate sodium (DSS)-induced colitis, robust resilience was observed. OPNs@LMWH effectively ameliorated oxidative stress and inhibited the activation of inflammation-associated signalling pathways while simultaneously bolstering the protective mechanisms of the colonic epithelium. Overall, these findings underscore the compelling dual functionalities of OPNs@LMWH, which enable effective oral delivery to inflamed sites, thereby facilitating precise UC management.

bioengineering↗

bioRxiv2024

Integrated Analyses of Multi-omic Data Derived from Paired Primary Lung Cancer and Brain Metastasis Reveals the Metabolic Vulnerability as a Novel Therapeutic Target

Lung cancer brain metastases (LC-BrMs) are frequently associated with dismal mortality rates in patients with lung cancer; however, standard of care therapies for LC-BrMs are still limited in their efficacy. A deep understanding of molecular mechanisms and tumor microenvironment of LC-BrMs will provide us with new insights into developing novel therapeutics for treating patients with LC-BrMs. Here, we performed integrated analyses of genomic, transcriptomic, proteomic and metabolomic data which were derived from a total number of 174 patients with paired and unpaired primary lung cancer and LC-BrM, spanning four published and two newly generated patient cohorts on both bulk and single cell levels. We uncovered that LC-BrMs exhibited significantly higher intra-tumor heterogeneity. We also observed that mutations in a subset of genes were almost always shared by both primary lung cancers and LC-BrM lesions, including TTN, TP53, MUC16, LRP1B, RYR2, and EGFR. In addition, the genome-wide landscape of somatic copy number alterations was similar between primary lung cancers and LC-BrM lesions. Nevertheless, several regions of focal amplification were significantly enriched in LC-BrMs, including 5p15.33 and 20q13.33. Intriguingly, integrated analyses of transcriptomic, proteomic and metabolomic data revealed mitochondrial-specific metabolism was activated but tumor immune microenvironment was suppressed in LC-BrMs. Subsequently, we validated our results by conducting real-time quantitative reverse transcription PCR experiments, immunohistochemistry and multiplexed immunofluorescence staining of patients paired tumor specimens. Patients with a higher expression of mitochondrial metabolism genes but a lower expression of immune genes in their LC-BrM lesions tended to have a worse survival outcome. Therapeutically, targeting oxidative phosphorylation with gamitrinib in patient-derived organoids specific to LC-BrMs induced apoptosis and inhibited cell proliferation. The combination of gamitrinib plus anti-PD-1 immunotherapy significantly improved survival of mice bearing LC-BrMs. In conclusion, our findings not only provide comprehensive and integrated perspectives of molecular underpinnings of LC-BrMs but also contribute to the development of a potential, rationale-based combinatorial therapeutic strategy with the goal of translating it into clinical trials for patients with LC-BrMs.

cancer biology↗

bioRxiv2023

SpatialPPI: three-dimensional space protein-protein interaction prediction with AlphaFold Multimer

The rapid advancement of protein sequencing technology has resulted in a gap between proteins with identified sequences and those with mapped structures. Although sequence-based predictions offer insights, they can be incomplete due to the absence of structural details. On the other hand, structure-based methods face challenges with newly sequenced proteins. AlphaFold emerges as a potential solution, especially in predicting protein-protein interactions. This research delves into using deep neural networks, specifically analyzing protein complex structures as predicted by AlphaFold Multimer. By transforming atomic coordinates and utilizing sophisticated image processing techniques, the study extracts vital 3D structural details from protein complexes. Recognizing the significance of evaluating residue distances in protein interactions, the study leverages image recognition approaches, notably integrating DenseNet and ResNet within 3D convolutional networks for protein 3D structure analysis. When benchmarked against leading protein-protein interaction prediction methods like SpeedPPI, D-script, DeepTrio, and PEPPI, our proposed method, named SpatialPPI, exhibits notable efficacy, emphasizing the promising role of 3D spatial processing in advancing the realm of structural biology. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/571766v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@14fa761org.highwire.dtl.DTLVardef@761293org.highwire.dtl.DTLVardef@1bd9508org.highwire.dtl.DTLVardef@1837a8e_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

Structure basis for recognition of 26RFa by the pyroglutamylated RFamide peptide receptor

The neuropeptide 26RFa, a member of the RF-amide peptide family, activates the pyroglutamylated RF-amide peptide receptor (QRFPR), a class A GPCR. The 26RFa/QRFPR system plays critical roles in energy homeostasis, making QRFPR an attractive drug target for treating obesity, diabetes, and eating disorders. However, the lack of structural information has hindered our understanding of the peptide recognition and regulatory mechanism of QRFPR, impeding drug design efforts. In this study, we determined the cryo-EM structure of the Gq-coupled QRFPR bound to 26RFa. The structure reveals a unique assembly mode of the receptor extracellular regions and the peptide N-terminus and elucidates the recognition mechanism of the C-terminal heptapeptide of 26RFa within the transmembrane binding pocket of QRFPR. The study also clarifies the similarities and distinctions in the binding pattern of the RF-amide moiety in five RF-amide peptides and the RY-amide segment in neuropeptide Y. These findings deepen our understanding of the RF-amide peptides recognition, aiding in the rational design of drugs targeting QRFPR and other RF-amide receptors.

biophysics↗

bioRxiv2023

TIPE drives a cancer stem-like phenotype by promoting glycolysis via PKM2/HIF-1alpha axis in melanoma

TIPE (TNFAIP8) has been identified as an oncogene and participates in tumor biology. However, how its role in the metabolism of tumor cells during melanoma development remains unclear. Here, we demonstrated that TIPE promoted glycolysis by interacting with pyruvate kinase M2 (PKM2) in melanoma. We found that TIPE induced PKM2 dimerization, thereby facilitating its translocation from the cytoplasm to the nucleus. TIPE-mediated PKM2 dimerization consequently promoted HIF-1 activation and glycolysis, which contributed to melanoma progression and increased its stemness features. Notably, TIPE specifically phosphorylated PKM2 at Ser 37 in an ERK-dependent manner. Consistently, the expression of TIPE was positively correlated with the levels of PKM2 Ser37 phosphorylation and cancer stem cell markers in melanoma tissues from clinical samples and tumor bearing mice. In summary, our findings indicate that the TIPE/PKM2/HIF-1 signaling pathway plays a pivotal role in promoting cancer stem cell properties by facilitating the glycolysis, which would provide a promising therapeutic target for melanoma intervention.

cancer biology↗

bioRxiv2023

Heparan sulfate dependent phase separation of CCL5 and its chemotactic activity

Secreted chemokines form concentration gradients in target tissues to control migratory directions and patterns of immune cells in response to inflammatory stimulation; however, how the gradients are formed is much debated. Heparan sulfate (HS) binds to chemokines and modulates their activities. In this study, we investigated the roles of HS in the gradient formation and chemoattractant activity of CCL5 that is known to bind to HS. CCL5 and heparin underwent liquid-liquid phase separation (LLPS) and formed gradient, which was confirmed using CCL5 immobilized on heparin-beads. The biological implication of HS in CCL5 gradient formation was established in CHO-K1 (wild type) and CHO-677 (lacking HS) cells by Transwell assay. The effect of HS on CCL5 chemoattractant activity was further proved by Transwell assay of human peripheral blood cells. Finally, peritoneal injection of the chemokines into mice showed reduced recruitment of inflammatory cells either by mutant CCL5 (lacking heparin binding sequence) or by addition of heparin to wild type CCL5. Our experimental data propose that co-phase separation of CCL5 with HS establishes a specific chemokine concentration gradient to trigger directional cell migration. The results warrant further investigation on other heparin binding chemokines and allows for a more elaborate insight into disease process and new treatment strategies.

cell biology↗

bioRxiv2023

Mechanisms of ligand recognition and activation of melanin-concentrating hormone receptors

Melanin-concentrating hormone (MCH) is a cyclic neuropeptide that regulates food intake, energy balance, and other physiological functions by stimulating MCHR1 and MCHR2 receptors, both of which are class A G protein-coupled receptors. MCHR1 can couple with multiple G-proteins, including Gi/o, Gq/11, and Gs, while MCHR2 only couple to Gq/11. Here we present cryo-electron microscopy structures of MCH-activated MCHR1 with Gi and MCH-activated MCHR2 with Gq complexes, at the global resolutions of 3.01 [A] and 2.40 [A], respectively. These structures reveal that MCH adopts a consistent cysteine-mediated hairpin loop configuration in both receptors. A central arginine from the LGRVY core motif between the two cysteines of MCH penetrates deeply into the transmembrane pocket, triggering receptor activation. Integrated with mutational and functional insights, our findings elucidate the molecular underpinnings of ligand recognition and MCH receptor activation, offering a structured foundation for targeted drug design.

molecular biology↗

bioRxiv2023

Human disturbance increases spatiotemporal associations among mountain forest terrestrial mammal species

Spatial and temporal associations between sympatric species underpin biotic interactions, structure ecological assemblages, and sustain ecosystem functioning and stability. However, the resilience of interspecific spatiotemporal associations to human activity remains poorly understood, particularly in mountain forests where anthropogenic impacts are often pervasive. Here we applied context-dependent Joint Species Distribution Models to a systematic camera-trap survey dataset from a global biodiversity hotspot in eastern Himalaya to understand how prominent human activities in mountain forests influence species associations within terrestrial mammal communities. We obtained 10,388 independent detections of 17 focal species (12 carnivores and five ungulates) from 322 stations over 43,163 camera days of effort. We identified a higher incidence of positive associations in habitats with higher levels of human modification (87 %) and human presence (83 %) compared to those located in habitats with lower human modification (64 %) and human presence (65 %) levels. We also detected a significant reduction of pairwise encounter time at increasing levels of human disturbance, corresponding to more frequent encounters between pairs of species. Our findings indicate that human activities can push mammals together into more frequent encounters and associations, which likely influences the coexistence and persistence of wildlife, with potential far-ranging ecological consequences.

ecology↗

bioRxiv2023

Molecular principles of CRISPR-Cas13 mismatch intolerance enable selective silencing of point-mutated oncogenic RNA with single-base precision

Single nucleotide variants (SNVs) are extremely prevalent in human cancers. For instance, KRAS mutations occur in over 90% of pancreatic cancers and [~]40% of colorectal cancers. Virtually all KRAS mutations are SNVs, most of which remain clinically unactionable. The programmable RNA nuclease CRISPR-Cas13 has been deployed to specifically target RNAs such as overexpressed oncogenes and fusion transcripts. However, silencing oncogenic SNVs with single-base precision remains extremely challenging due to the intrinsic mismatch tolerance of Cas13. Here, we developed a comprehensive mutagenesis analysis of target-spacer interactions at single-nucleotide resolution, which revealed key spacer nucleotide positions intolerant to mismatches. We show that introducing synthetic mismatches at these precise positions enables de nova design of CRISPR RNA (crRNA) with strong preferential silencing of SNV transcripts. We demonstrate that our top-performing crRNAs possess prominent SNV-selectivity with dose-dependent silencing activity against all KRAS G12 variants at both the RNA and protein levels with minimal off-target silencing of wildtype KRAS. We applied these design principles to effectively silence oncogenic NRAS G12D and BRAF V600E transcripts, underscoring the adaptability of this platform to silence various SNVs. These findings demonstrate that the CRISPR Cas13 system can be reprogrammed to target mutant transcripts with single-base precision, showcasing the tremendous potential of this tool in personalized transcriptome editing. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/557083v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@20a7b3org.highwire.dtl.DTLVardef@1e1f79corg.highwire.dtl.DTLVardef@4724c1org.highwire.dtl.DTLVardef@be3063_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

High-throughput and genome-scale targeted mutagenesis using CRISPR in a non-model multicellular organism, Bombyx mori

Large-scale genetic mutant libraries are powerful approaches to interrogating genotype-phenotype correlations and identifying genes responsible for certain environmental stimuli, both of which are the central goal of life science study. We produced the first large-scale CRISPR/Cas9-induced library in a non-model multicellular organism, Bombyx mori. We developed a piggyBac-delivered binary genome editing strategy, which can simultaneously meet the requirements of mixed microinjection, efficient multi-purpose genetic operation, and preservation of growth-defect lines. We constructed a single-guide RNA (sgRNA) plasmid library containing 92,917 sgRNAs targeting promoters and exons of 14,645 protein-coding genes, established 1726 transgenic sgRNA lines following microinjection of 66,650 embryos, and generated 300 mutant lines with diverse phenotypic changes. Phenomic characterization of mutant lines identified a large set of genes responsible for visual phenotypic or economically valuable trait changes. Next, we performed pooled context-specific positive screens for tolerance to environmental pollute cadmium exposure, and identified KWMTBOMO12902 as a strong candidate gene for breeding applications in sericulture industry. Collectively, our results provide a novel and versatile approach for functional B. mori genomics, and a powerful resource for identifying key candidate genes potential for improving various economic traits. This study also demonstrates the effectiveness, practicality, and convenience of large-scale mutant libraries in other non-model organisms.

genomics↗

bioRxiv2023

Ubiquitination-mediated Golgi-to-endosome sorting determines the poison-antidote duality of wtf meiotic drivers

Killer meiotic drivers (KMDs) skew allele transmission in their favor by killing meiotic progeny not inheriting the driver allele. Despite their widespread presence in eukaryotes, the molecular mechanisms behind their selfish behavior are poorly understood. Here we investigate how the toxin and antidote products of a fission yeast wtf-family KMD gene can act antagonistically. Both the toxin and the antidote are multi-transmembrane proteins, differing only in their N-terminal cytosolic tails. We find that the antidote employs N-terminal PY motifs (Leu/Pro-Pro-X-Tyr) to bind Rsp5/NEDD4 family ubiquitin ligases, which ubiquitinate the antidote. Mutating PY motifs or attaching a deubiquitinating enzyme transforms the antidote into a toxic protein. Ubiquitination promotes the transport of the antidote from the trans-Golgi network to the endosome, thereby preventing it from causing toxicity. A physical interaction between the antidote and the toxin enables the ubiquitinated antidote to translocate the toxin to the endosome and neutralize its toxicity. We propose that post-translational modification-mediated protein localization and/or activity changes may be a common mechanism governing the antagonistic duality of single-gene KMDs.

cell biology↗