Biology subjects

Yang, J.

Publications and source records attributed to Yang, J..

At least 541 records · Page 30Linked to original sources

bioRxiv2023

Regulatory variation controlling architectural pleiotropy in maize

An early event in plant organogenesis is establishment of a boundary between the meristem and differentiating lateral organ. In maize (Zea mays), evidence suggests a common gene network functions at boundaries of distinct organs and contributes to pleiotropy between leaf angle and tassel branch number, two agronomic traits. To uncover regulatory variation at the nexus of these two traits, we used regulatory network topologies derived from specific developmental contexts to guide multivariate genome-wide association analyses. In addition to defining network plasticity around core pleiotropic loci, we identified new transcription factors that contribute to phenotypic variation in canopy architecture, and structural variation that contributes to cis-regulatory control of pleiotropy between tassel branching and leaf angle across maize diversity. Results demonstrate the power of informing statistical genetics with context-specific developmental networks to pinpoint pleiotropic loci and their cis-regulatory components, which can be used to fine-tune plant architecture for crop improvement.

plant biology↗

bioRxiv2023

LncRNA SNHG16 modulates paclitaxel resistance in breast cancer by regulating Let-7a-5p/DUSP7

ObjectiveTo investigate the effect of long chain non coding RNA (lncRNA) small nucleolar RNA host gene 6 (SNHG16) on paclitaxel (PTX) resistance in breast cancer and to understand its underlying mechanism, to lay a foundation for decreasing the PTX resistance in breast cancer treatment and improving the therapeutic quality for breast cancer patients. MethodsPTX was used to induce the establishment of PTX resistant breast cancer cell lines; the control group (normal cultured MCF-7/PTX cells), si-NC group, si-SNHG16 group, si-SNHG16+anti miR-NC group, and si-SNHG16 +anti-Let-7a-5p group were set to compared the effect of SNHG16 on the PTX resistance in MCF-7 cells; MTT assay, Flow cytometry, and Transwell invasion assay were used to determine the PTX resistance, apoptosis, and invasion ability of MCF-7 cells in different groups, respectively; for further assess the effect of SNHG16 on the PTX resistance, nude mouse tumor transplantation experiment was used; and the potential mechanism of SNHG16 regulated the PTX resistance in MCF-7 cells was explored by double luciferase reporter gene detection method and gene silencing technology. ResultsThe expression of SNHG16 gene and DUSP7 protein in MCF-7 cell line was the highest, and the expression of Let-7a-5p was the lowest compared with the various breast cancer cell lines (human breast epithelial cell line MCF-10A and human breast cancer cell lines MDA-MB-468 and MDA-MB-453) (P<0.05); PTX could increase the expression of SNHG16 gene and DUSP7 protein, and reduce the expression of Let-7a-5pin MCF-7 cell line (P<0.05); the results of cell experiment and nude mouse transplantation tumor experiment demonstrated that inhibiting the expression of SNHG16 gene could reduce the invasive ability and promote cell apoptosis of MCF-7/PTX cells (P<0.05), and inhibit tumor growth and reduce the PTX resistance in breast cancer transplantation models; simultaneous inhibition of Let-7a-5p and SNHG16 had a weakening effect in MCF-7/PTX cells (P<0.05). Double luciferase reporter gene detection and gene silencing technology demonstrated that inhibiting SNHG16 gene expression could increase the expression of Let-7a-5p and decrease the expression of DUSP7 (P<0.05); inhibiting the Let-7a-5p gene could increase the expression of DUSP7. ConclusionsInhibiting SNHG16 gene could upregulate Let-7a-5p expression and downregulate the expression of DUSP7 to inhibit MCF-7 cell invasion, promote MCF-7 cell apoptosis, and reduce the PTX resistance in MCF-7 cells and nude mouse tumor transplantation models, those data demonstrated that SNHG16-Let-7a-5p-DUSP7 axis maybe a potential therapeutic strategy for decreasing the PTX resistance in breast cancer in the future.

cancer biology↗

bioRxiv2023

VISTA: An integrated framework for structural variant discovery

Structural variation (SV), refers to insertions, deletions, inversions, and duplications in human genomes. With advances in whole genome sequencing (WGS) technologies, a plethora of SV detection methods have been developed. However, dissecting SVs from WGS data remains a challenge, with the majority of SV detection methods prone to a high false-positive rate, and no existing method able to precisely detect a full range of SVs present in a sample. Previous studies have shown that none of the existing SV callers can maintain high accuracy across various SV lengths and genomic coverages. Here, we report an integrated structural variant calling framework, VISTA (Variant Identification and Structural Variant Analysis) that leverages the results of individual callers using a novel and robust filtering and merging algorithm. In contrast to existing consensus-based tools which ignore the length and coverage, VISTA overcomes this limitation by executing various combinations of top-performing callers based on variant length and genomic coverage to generate SV events with high accuracy. We evaluated the performance of VISTA on using comprehensive gold-standard datasets across varying organisms and coverage. We benchmarked VISTA using the Genome-in-a-Bottle (GIAB) gold standard SV set, haplotype-resolved de novo assemblies from The Human Pangenome Reference Consortium (HPRC)1,2, along with an in-house PCR-validated mouse gold standard set. VISTA maintained the highest F1 score among top consensus-based tools measured using a comprehensive gold standard across both mouse and human genomes. VISTA also has an optimized mode, where the calls can be optimized for precision or recall. VISTA-optimized is able to attain 100% precision and the highest sensitivity among other variant callers. In conclusion, VISTA represents a significant advancement in structural variant calling, offering a robust and accurate framework that outperforms existing consensus-based tools and sets a new standard for SV detection in genomic research.

bioinformatics↗

bioRxiv2023

CD4+ T cell senescence is associated with reduced reactogenicity in severe/critical COVID-19

BackgroundAging is a critical risk factor for unfavorable clinical outcomes among COVID-19 patients and may affect vaccine efficacy. However, whether the senescence of T cells impact the progression to severe COVID-19 in the elderly individuals remains unclear. MethodsBy using flow cytometry, we analyzed the frequency of senescent T cells (Tsens) in the peripheral blood from 100 elderly patients hospitalized for COVID-19 and compared the difference between mild/moderate and severe/critical illness. We also assessed correlations between the percentage of Tsens and the quantity and quality of spike-specific antibodies by ELISA, neutralizing antibody test kit and Elispot assay respectively, cytokine production profile of COVID-19 reactive T cells as well as plasma soluble factors by cytometric bead array (CBA). ResultsWe found a significant elevated level of CD4+ Tsens in severe/critical disease compared to mild/moderate illness and patients with a higher level of CD4+ Tsens (>19.78%) showed a decreased survival rate as compared to those with a lower level (<19.78%), especially in the breakthrough infection. The percentage of CD4+ Tsens was negatively correlated with spike-specific antibody titers, neutralization ability and COVID-19 reactive IL-2+ CD4+ T cells. Additionally, IL-2 producing T cells and plasma levels of IL-2 were positively correlated with antibody levels. ConclusionOur data illustrated that the percentage of CD4+ Tsens in the peripheral blood could act as an efficient biomarker for the capacity of spike-specific antibody production and the prognosis of severe COVID-19, especially in the breakthrough infection. Therefore, restoration of the immune response of CD4+ Tsens is one of the key factors to prevent severe illness and improve vaccine efficacy in older adults.

immunology↗

bioRxiv2023

Structure of the human outer kinetochore KMN network complex

Faithful chromosome segregation requires robust, load-bearing attachments of chromosomes to the mitotic spindle, a function accomplished by large macromolecular complexes termed kinetochores. In most eukaryotes, the constitutive centromere-associated network (CCAN) complex of the inner kinetochore recruits to centromeres the ten-subunit outer kinetochore KMN network, which comprises the KNL1C, MIS12C and NDC80C complexes. The KMN network directly attaches CCAN to microtubules through MIS12C and NDC80C. Here, we determined a high-resolution cryo-EM structure of the human KMN network. This showed an intricate and extensive assembly of KMN subunits, with the central MIS12C forming rigid interfaces with NDC80C and KNL1C. The redundancy and strength of inter-subunit connections explains how KMN withstands strong forces applied during chromosome segregation. We also observed that unphosphorylated MIS12C exists in an auto-inhibited state that suppresses its capacity to interact with CCAN. Ser100 and Ser109 of the N-terminal segment of the MIS12C subunit Dsn1, two key targets of Aurora B kinase, directly stabilize this auto-inhibition. Our work provides a molecular mechanism for how selectively relieving this auto-inhibition through Ser100 and Ser109 phosphorylation would restrict outer kinetochore assembly to functional centromeres during cell division.

cell biology↗

bioRxiv2023

Anopheles gambiae mosGILT regulates innate immune genes and zpg expression

Gene-edited mosquitoes lacking a gamma-interferon-inducible lysosomal thiol reductase-like protein, namely (mosGILTnull) have lower Plasmodium infection, which is linked to impaired ovarian development and immune activation. The transcriptome of mosGILTnull A. gambiae was therefore compared to wild type (WT) by RNA-sequencing to delineate mosGILT-dependent pathways. Compared to WT mosquitoes, mosGILTnull A. gambiae demonstrated altered expression of genes related to oogenesis, 20-hydroxyecdysone synthesis, as well as immune-related genes. Serendipitously, the zero population growth gene, zpg, an essential regulator of germ cell development was found to be one of the most downregulated genes in mosGILTnull mosquitoes. These results provide the crucial missing link between two previous studies on the role of zpg and mosGILT in ovarian development. This study further demonstrates that mosGILT has the potential to serve as a target for the biological control of mosquito vectors and to influence the Plasmodium life cycle within the vector.

genomics↗

bioRxiv2023

BacScan: An Unbiased and Genome-Wide Approach to Identify Bacterial Highly Immunogenic Proteins

Bacterial pathogens are the second leading cause of death worldwide. However, the development of bacterial vaccines has been challenged by the presence of multiple serotypes and the lack of cross-protection between serotypes. Therefore, there is an urgent need to identify protective antigens conserved across serotypes in order to develop a broadly protective vaccine. Here, we have developed an unbiased and genome-wide technique, BacScan, which uses bacterial-specific serum to rapidly identify highly conserved immunogenic proteins by combining phage display, immunoprecipitation, and next-generation sequencing. As a proof of concept, we identified 19 highly immunogenic proteins from Streptococcus suis core proteins. Immunoreactivity analysis of mouse, pig, and human sera indicated that 2 proteins could be the potential targets for the development of serological diagnostics. Eight proteins provided 20%-100% protection against S. suis challenge in immunized animals, indicating the potential vaccine targets. BacScan can be applied to any bacterial pathogen and has the potential to accelerate the development of a broadly protective bacterial vaccine. TeaserA novel method to identify the highly conserved immunogenic bacterial proteins as targets for the development a broadly protective bacterial vaccine.

microbiology↗

bioRxiv2023

Mecp2 Fine-tunes Quiescence Exit by Targeting Nuclear Receptors

Quiescence (G0) maintenance and exit are crucial for tissue homeostasis and regeneration in mammals. Here, we show that methyl-CpG binding protein 2 (Mecp2) expression is cell cycle-dependent and negatively regulates quiescence exit in cultured cells and in an injury-induced liver regeneration mouse model. Specifically, acute reduction of Mecp2 is required for efficient quiescence exit, as deletion of Mecp2 accelerates, while overexpression of Mecp2 delays quiescence exit, and forced expression of Mecp2 after Mecp2 conditional knockout rescues cell cycle reentry. The E3 ligase Nedd4 mediates the ubiquitination and degradation of Mecp2, and thus facilitates quiescence exit. Genome-wide study uncovered the dual role of Mecp2 in preventing quiescence exit by transcriptionally activating metabolic genes while repressing proliferation-associated genes. Particularly, disruption of two nuclear receptors (NRs), Rara or Nr1h3, accelerates quiescence exit, mimicking the Mecp2 depletion phenotype. Our studies unravel a previously unrecognized role for Mecp2 as an essential regulator of quiescence exit and tissue regeneration.

cell biology↗

bioRxiv2023

Endothelial SARS-CoV-2 infection is not the underlying cause of COVID19-associated vascular pathology in mice

Endothelial damage and vascular pathology have been recognized as major features of COVID-19 since the beginning of the pandemic. Two main theories regarding how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) damages endothelial cells and causes vascular pathology have been proposed: direct viral infection of endothelial cells or indirect damage mediated by circulating inflammatory molecules and immune mechanisms. However, these proposed mechanisms remain largely untested in vivo. Here, we utilized a set of new mouse genetic tools1 developed in our lab to test both the necessity and sufficiency of endothelial human angiotensin-converting enzyme 2 (hACE2) in COVID19 pathogenesis. Our results demonstrate that endothelial ACE2 and direct infection of vascular endothelial cells does not contribute significantly to the diverse vascular pathology associated with COVID-19.

pathology↗

bioRxiv2023

Mechanism of outer kinetochore assembly on microtubules and its regulation by mitotic error correction

Kinetochores couple chromosomes to the mitotic spindle and transduce the energy of microtubule depolymerization to segregate the genome during cell division. Kinetochore - microtubule attachments are often initially erroneous and subject to a mitotic error correction (EC) mechanism that drives their turnover until biorientation is achieved. How this is accomplished and regulated, and how kinetochore-mediated chromosome segregation occurs at a molecular level remain major outstanding questions. Here we describe the cryo-electron microscopy (cryo-EM) structure of the budding yeast outer kinetochore Ndc80 and Dam1 ring complexes assembled onto microtubules. We observe coordinated interactions of the outer kinetochore complexes through multiple interfaces, in addition to a short staple within the Dam1 subunit that facilitates Dam1c ring assembly. Perturbation of these interfaces results in loss of yeast viability. Force-rupture assays indicated this is a consequence of substantial reductions in kinetochore - microtubule binding strength. EC-mediated phosphorylation of Ndc80c-Dam1c interfaces would drive complex disassembly, whereas Dam1 staple phosphorylation would promote Dam1c ring disassembly, explaining how kinetochore - microtubule attachments are destabilized and reset by the EC mechanism. One-Sentence SummaryPhosphorylation disrupts the outer kinetochore to regulate kinetochore-microtubule attachments in mitotic error correction.

molecular biology↗

bioRxiv2023

Habitat correlates of cave-dwelling: A radiation-scale analysis of skin traits and comparative transcriptomics of the Sinocyclocheilus cavefish

With 78 species, Sinocyclocheilus cavefish constitute the largest cavefish radiation in the world. They exhibit remarkable morphological diversity across three habitat types: surface (Surface morphs, Normal-eyed, variably colored), exclusively-cave-dwelling (Stygobitic morphs, Eyeless, depigmented), and intermediate between cave and surface (Stygophilic morphs, Micro-eyed, partially depigmented). Distinctive traits of Sinocyclocheilus include variations in eye and skin conditions associated with their habitat, despite the role of the skin in sensing environmental changes, its habitat correlates are less understood, compared to the well-studied eye conditions. Here, we analyzed the correlation between Sinocyclocheilus skin morphology and its habitat, utilizing morphological and transcriptomics-based methods. We generated RNA-sequencing data for nine species and integrated those with existing data from five additional species. These 14 species represent the primary clades and major habitats of these cavefish. Data on skin color and scale morphology were generated and 7374 orthologous genes were identified. Using a comparative transcriptomics approach, we identified 1,348 differentially expressed genes (DEGs) in the three morphotypes. GO and KEGG enrichment analyses suggest that these species have evolved different strategies for energy metabolism, immunity, and oxidative stress in different habitats. We also found 329 positive selection genes (PSGs) in the skin of these species that are mainly involved in immunity, apoptosis, and necrosis, indicating potential adaptations to their habitats. The maximum likelihood phylogenetic tree, based on 1369 single-copy orthologous genes of the species, was largely concordant with the currently established RAD-seq and mt-DNA based phylogenies, but with a few exceptions. Species with higher cave dependence present lighter coloration, fewer dark blotches, and diminished scale morphology and coverage. PCA and cluster analysis suggested that cave-dwelling species, characterized by the absence of black blotches, have similar expression patterns, indicating convergence in cave adaptation. Variations in tyrosine metabolism may explain pigmentation differences among species in diverse habitats. Our study highlights the significance of habitat in shaping skin metabolism, pigmentation variation, and morphology while offering insights into the molecular mechanisms driving these habitat-specific adaptations in Sinocyclocheilus. These findings underscore the transcriptional variation in adapting to diverse environments and contribute to future studies on the evolution and ecology of cavefish.

evolutionary biology↗

bioRxiv2023

Multigenerational effects of tire wear particle leachate through trophic transfer from producer to primary consumer

Tire wear particle (TWP) and their leachate have been known toxic for aquatic organism due to additives released from the rubber matrix. However, it is not clear whether the ecotoxicity of TWP leachate could be transferred through algae-zooplankton food chain especially after multi generations. In this work, the effect of different concentrations TWP leachate on growth of microalgae, Chlorella pyrenoidesa, was studied. Subsequently, those algae were fed to zooplankton rotifer, Brachionus calyciflorus, which continuously lasted for ten generations to explore multigenerational accumulation of TWP leachate ecotoxicity through food-chain transfer. The results showed that the TWP leachate displayed growth inhibition for algae with evident concentration effect. For rotifer fed with those contaminated microalgae, though the first two generations showed hormesis, the ecotoxicity exhibited after 2 generations, characterized by reduction of lifespan and offspring number. The ecological effects of TWP leachate were transferred from algae to rotifer. In addition, the ecotoxicity gradually aggravated along with generation passage and exposure concentration of algae. What was even more, population passage of rotifer collapsed totally with no offspring after 5-generations feed by algae exposed to high concentration TWP leachate. Based on those, it is summarized that the ecological effects of TWP leachate indeed can be transferred from low to high trophic level in food chain, and accumulate across generations passage. The indirect non-contact exposure through food chain should be considered at the risk assessment of TWP. Single generation exposure will underestimate their ecological risk from long term.

ecology↗

bioRxiv2023

Malaria resistance-related biological adaptation and complex evolutionary footprints of Tai-Kadai people inferred from 796 genomes

Pathogen-host adaptative interaction and complex population demographical processes, including admixture, drift and Darwen selection, have considerably shaped the Neolithic-to-Modern Western Eurasian population structure and genetic susceptibility to modern human diseases. However, the genetic footprints of evolutionary events in East Asia keep unknown as the underrepresentation of genomic diversity and the design of large-scale population studies. We reported one aggregated database of genome-wide-SNP variations from 796 Tai-Kadai (TK) genomes, including Bouyei first reported here, to explore the genetic history, population structure and biological adaptative features of TK-speaking people from Southern China and Southeast Asia. We found geography-related population substructure among TK-speaking people using the state-of-the-art population genetic structure reconstruction techniques based on the allele frequency spectrum and haplotype-resolved phased fragments. We found that the Northern TK-speaking people from Guizhou harboured one TK-dominant ancestry maximised in Bouyei people, and the Southern one from Thailand obtained more influences from Southeast Asians and indigenous people. We reconstructed the fitted admixture models and demographic graphs, which showed that TK-speaking people received gene flow from ancient rice farmer-related lineages related to the Hmong-Mien and Austroasiatic people and Northern millet farmers associated with the Sino-Tibetan people. Biological adaptation focused on our identified unique TK lineages related to Bouyei showed many adaptive signatures conferring Malaria resistance and low-rate lipid metabolism. Further gene enrichment, the allele frequency distribution of derived alleles, and their correlation with the incidence of Malaria further confirmed that CR1 played an essential role in the resistance of Malaria in the ancient "Baiyue" tribes.

genetics↗

bioRxiv2023

Transcriptome brings variations of gene expression, alternative splicing, and structural variations into gene-scale trait dissection in soybean

Genome-wide association study (GWAS) identifies trait-associated loci, but due in part to slow decay of linkage disequilibrium (LD), identifying the causal genes can be a bottleneck. Transcriptome-wide association study (TWAS) addresses this by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci (eQTLs) with GWAS results. Here, we used self-pollinated soybean as a model to evaluate the application of TWAS in the genetic dissection of traits in plant species that exhibit slow LD decay. The first RNA-Seq analysis of a soybean diversity panel was conducted, which identified the genetic regulation of 29,286 genes. Different TWAS solutions were less affected by LD and robust with source of expression that identified known genes related to traits from different development stages and tissues. A novel gene named pod color L2 was identified via TWAS and functionally validated by genome editing. Our introduction of the new exon proportion feature significantly improves the capture of expression variations resulting from structural variations and alternative splicing. As a result, the genes identified by our TWAS approach exhibited a diverse range of causal variations, including SNP, insertion/deletion, gene fusion, copy number variation, and alternative splicing. Using our TWAS approach, we identified genes associated with flowering time, including both previously known candidates and novel genes that had not been linked to this trait before, providing complementary insights with GWAS. In summary, this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.

genetics↗

bioRxiv2023

Degradation of amyloid beta species by multi-copper oxidases

Reduction of the production of amyloid beta (A{beta}) species has been intensively investigated as potential therapeutic approaches for Alzheimers disease (AD). However, the degradation of A{beta} species, another potential beneficial approach, has been far less explored. In this study, we discovered that ceruloplasmin (CP), an important multi-copper oxidase (MCO) in human blood, could degrade A{beta} peptides. We also found that the presence of Vitamin C could enhance the degrading effect in a concentration-dependent manner. We then validated the CP-A{beta} interaction using total internal reflection fluorescence (TIRF) microscopy, fluorescence photometer, and fluorescence polarization measurement. Based on the above discovery, we hypothesized that other MCOs had similar A{beta}-degrading functions. Indeed, we found that other MCOs could induce A{beta} degradation as well. Remarkably, we revealed that ascorbate oxidase (AO) had the strongest degrading effect among the tested MCOs. Using induced pluripotent stem (iPS) neuron cells, we observed that AO could rescue neuron toxicity which induced by A{beta} oligomers. In addition, our electrophysiological analysis with brain slices suggested that AO could prevent an A{beta}-induced deficit in synaptic transmission in the hippocampus. To the best of our knowledge, our report is the first to demonstrate that MCOs have a degrading function for peptides/proteins. Further investigations are warranted to explore the possible benefits of MCOs for future AD treatment.

neuroscience↗

bioRxiv2023

In Vivo Three-dimensional Brain Imaging with Chemiluminescence Probes in Alzheimers Disease Models

Optical three-dimensional (3D) molecular imaging is highly desirable for providing precise distribution of the target-of-interest in disease models. However, such 3D imaging is still far from wide applications in biomedical research; 3D brain optical molecular imaging, in particular, has rarely been reported. In this report, we designed chemiluminescence probes with high quantum yields (QY), relatively long emission wavelengths, and high signal-to-noise ratios (SNRs) to fulfill the requirements for 3D brain imaging in vivo. With assistance from density-function theory (DFT) computation, we designed ADLumin-Xs by locking up the rotation of the double-bond via fusing the furan ring to the phenyl ring. Our results showed that ADLumin-5 had a high quantum yield of chemiluminescence and could bind to amyloid beta (A{beta}). Remarkably, ADLumin-5s radiance intensity in brain areas could reach 4x107 photon/s/cm2/sr, which is probably 100-fold higher than most chemiluminescence probes for in vivo imaging. Because of its strong emission, we demonstrated that ADLumin-5 could be used for in vivo 3D brain imaging in transgenic mouse models of Alzheimers disease (AD). Significance StatementAlthough MRI, PET, CT, and SPECT have been routinely used for 3D imaging, including 3D brain imaging, they are considerably expensive. Optical imaging is largely low-cost and high throughput. However, the 3D capacity of optical imaging is always limited. Obviously, optical 3D molecular imaging is highly challenging, particularly for 3D brain imaging. In this report, we provided the first example of 3D brain imaging with chemiluminescence probes ADLumin-Xs, which have advantages in quantum yields (QY), emission wavelengths, and signal-to-noise ratios (SNRs) to fulfill the requirements for 3D brain imaging. And we believe that such 3D capacity is potentially a game-changer for brain molecular imaging in preclinical studies.

bioengineering↗

bioRxiv2023

Bestrophin-4 relays Hes4 and interacts with Twist1 to suppress epithelial-to-mesenchymal transition in colorectal cancer cells

AbstractBestrophin isoform 4 (BEST4) is a newly identified subtype of the calcium-activated chloride channel family. Analysis of colonic epithelial cell diversity by single cell RNA-sequencing has revealed the existence of a cluster of BEST4+ mature colonocytes in humans. However, if the role of BEST4 is involved in regulating tumour progression remains largely unknown. In this study, we demonstrate that BEST4 overexpression attenuates cell proliferation, colony formation, and mobility in colorectal cancer (CRC) in vitro, and impedes the tumor growth and the liver metastasis in vivo. BEST4 is coexpressed with hairy/enhancer of split 4 (Hes4) in the nucleus of cells, and Hes4 signals BEST4 by interacting with the upstream region of the BEST4 promoter. BEST4 is epistatic to Hes4 and downregulates Twist1, thereby inhibiting epithelial-to-mesenchymal transition (EMT) in CRC. Conversely, knockout of BEST4 using CRISPR/Cas9 in CRC cells revitalises tumor growth and induces EMT. Furthermore, the low level of the BEST4 mRNA is correlated with advanced and the worse prognosis, suggesting its potential role in regulating CRC progression.

cancer biology↗

bioRxiv2023

Comprehensive Assessment of Eleven de novo HiFi Assemblers on Complex Eukaryotic Genomes and Metagenomes

BackgroundPacific Bioscience HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (less than 0.01% sequencing error). While several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. ResultsWe evaluated the performance of eleven de novo HiFi assemblers on (i) real data for three eukaryotic genomes, (ii) 34 synthetic datasets with different ploidy, sequencing coverage levels, heterozygosity rates and sequencing error rates, (iii) one real metagenomic dataset, and (iv) five synthetic metagenomic datasets with different composition abundance and heterozygosity rates. The nine assemblers were evaluated using QUAST (Quality Assessment Tool) and BUSCO (Benchmarking Universal Single-Copy Ortholog). We also used several additional criteria, namely, completion rate, single-copy completion rate, duplicated completion rate, average proportion of largest category, average distance difference, quality value, run-time and memory utilization. On complex eukaryotic genomes, Hifiasm had a clear advantage over the other assemblers in all tested experiments. On synthetic datasets, Hifiasm, HiCanu, and HiFlye performed equally well. Shasta and Peregrine had good performance across varying ploidy, but required high computational resources. On metagenomic datasets, Hifiasm-meta demonstrated a clear advantage over other assemblers. ConclusionWe carried out a comprehensive benchmarking study of commonly used assemblers on complex eukaryotic genomes and metagenomes. Our study will help the research community to choose the most appropriate assembler for their data and identify possible improvements in assembly algorithms.

genomics↗