Biology subjects

wang, w.

Publications and source records attributed to wang, w..

9 recordsLinked to original sources

bioRxiv2025

The Notch/snRNA negative feedback regulation and its implications in Alzheimer's disease

Alzheimers disease (AD) is a multifactorial disorder whose hallmark lesions have been recognized for more than a century, yet its molecular pathobiology remains fragmentary. During our AD research, we discovered a direct mechanistic axis that links the Notch signalling pathway -- a crucial regulator of cell differentiation and proliferation--with the small nuclear RNAs (snRNAs) that drive pre-mRNA splicing. For the first time, our discovery unifies two previously siloed paradigms -- cell signal transduction and RNA splicing, expanding the fundamental knowledge of gene expression and its regulation. The first contribution of the present study is the discovery and validation of the Notch/snRNA negative feedback regulation. More implications include: (1) it reframes splicing-related diseases as dynamic consequences of pathway dysregulation rather than static snRNA-gene mutations; (2) it explains why global splicing abnormalities appear in AD, aging, and cancer even when snRNA genes themselves are not mutated; and (3) it provides an immediate, druggable "splicing rheostat" for any Notch-hyperactive disorder, such as AD.

cell biology↗

bioRxiv2024

scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse

Extrachromosomal circular DNA (eccDNA), an extrachromosomal circular structured DNA, is extensively found in eukaryotes. Exploring eccDNA at the single-cell level contributes to understanding heterogeneity, evolution, development, and specific functions within cells. Nevertheless, the high-throughput identification methods for single-cell eccDNA are complex, and currently mature and widely applicable technologies are lacking. Those factors have led to a scarcity of resources for studying eccDNA at the single-cell level. Therefore, using available single-cell whole-genome sequencing (WGS) data, we have constructed a comprehensive eccDNA database named scEccDNAdb (https://lcbb.swjtu.edu.cn/scEccDNAdb/). Presently, scEccDNAdb comprises 3,195,464 single-cell eccDNA entries from both disease/health human and mouse samples, which provides comprehensive annotations including oncogenes, typical enhancers, super-enhancers, CTCF binding sites, SNPs, chromatin accessibility, eQTLs, transcription factor binding sites, motifs, and SVs. Additionally, it provides nine online analysis and visualization tools, facilitating the generation of publication-quality figures for eccDNA analysis through the upload of customized files. Overall, scEccDNAdb represents the first comprehensive database known to us for exploring and analyzing single-cell eccDNA data in diverse cell types, tissues, and species. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/604058v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@bd23f8org.highwire.dtl.DTLVardef@1847c7eorg.highwire.dtl.DTLVardef@109717forg.highwire.dtl.DTLVardef@fa56b7_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2021

Efficacy of recombinant NP-M1 and NP-M1-CRT DNA vaccines against Influenza A viruses in mice C57/BL6

Effective vaccination against the influenza virus remains a challenge because of antigenic shift and drift in influenza viruses. Conservation is an important feature of the Nucleoprotein (NP) and Matrix protein 1(M1) qualifying them as potential candidates for developing a universal vaccine against the influenza A virus. Carliticulin (CRT), a member of heat shock protein (HSP) family, are conserved and widely distributed in many microorganisms and mammalian cells. In this study, a plasmid vector encoding the NP-M1-CRT sequence was constructed and compared with the NP-M1 sequence with respect to immunogenicity and protective efficacy in a murine model. The potency of the created construct for provoking humoral, cellular immune responses, and its protective immunity against the lethal influenza virus infection were then compared with commercial split vaccine and then evaluated in a murine model system. NP-M1-CRT as a DNA vaccine combined with in vivo electroporation could significantly improve the immunogenicity of constructed vectors. Serological evaluations demonstrated the potency of our approach to provoke strong anti-NP specific antibody responses. Furthermore, our strategy of immunization in prime-boost groups were able to provide protection against lethal viral challenge using H1N1 subtype. The ease of production of these types of vectors and the fact that they would not require annual updating and manufacturing may provide an alternative cost-effective approach to limit the spread of potential pandemic influenza viruses.

molecular biology↗

bioRxiv2021

Reg4 defenses the intestine against Salmonella infection via binding the flagellin

Salmonella Typhimurium is gram-negative flagellated bacteria that can cause food-borne gastroenteritis and diarrhea in humans and animals. The regenerating islet-derived family member 4 (Reg4) is overexpressed in the gastrointestinal tract during intestinal inflammation. However, the role of Reg4 in the intestinal inflammation induced by Salmonella Typhimurium is largely unknown. In this study, we reported for the first time that Reg4 has bactericidal activity against intestinal infection caused by Salmonella Typhimurium. In vivo, Reg4 could reduce the colonization of Salmonella Typhimurium and attenuate intestinal inflammation in the Salmonella Typhimurium-infected model. Additionally, the mice with the epithelial cell specific deletion of Reg4 (Reg4{Delta}IEC) exhibited more severe intestinal inflammation and more colonization of Salmonella Typhimurium. However, the administration of Reg4 could reverse these negative impacts. In vitro, Reg4 protein was showed to inhibit the growth of Salmonella Typhimurium. We further investigate the function motif of Reg4 and find that the "HDPQK" motif in Reg4 is essential to its bactericidal activity. Reg4 exerted the bactericidal effect by binding to the flagellin of Salmonella Typhimurium and suppressing its motility, adhesion, and invasion to the intestinal epithelia. In conclusion, our findings identify Reg4 as a novel antimicrobial peptide against infection by Salmonella Typhimurium and explore its possible mechanism, which may be of great significance for developing novel agents against flagellated micro pathogens.

microbiology↗

bioRxiv2021

The haplotype-based analysis of Aegilops tauschii introgression into hard red winter wheat and its impact on productivity traits

Introgression from wild relatives have a great potential to broaden beneficial allelic diversity available for crop improvement in breeding programs. Here, we assessed the impact of introgression from 21 diverse accessions of Aegilops tauschii, the diploid ancestor of the wheat D genome, into six hard red winter wheat cultivars on yield and yield component traits. We used 5.2 million imputed D genome SNPs identified by whole-genome sequencing of parental lines and the sequence-based genotyping of introgression population including 351 BC1F3:5 lines. Phenotyping data collected from the irrigated and non-irrigated field trials revealed that up to 23% of the introgression lines produce more grain than the parents and check cultivars. Based on sixteen yield stability statistics, the yield of twelve introgression lines (3.4%) was stable across treatments, years and locations; five of these lines were also high yielding, producing 9.8% more grain than the average yield of check cultivars. The most significant SNP-trait and haplotype-trait associations were identified on chromosome arms 2DS and 6DL for spikelet number per spike (SNS), on chromosome arms 2DS, 3DS, 5DS and 7DS for grain length and on chromosome arms 1DL, 2DS, 6DL and 7DS for grain width. Introgression of haplotypes from Ae. tauschii parents was associated with increase in SNS, which positively correlated with heading date, whereas haplotypes from hexaploid wheat parents were associated with increased grain width. We show that haplotypes on 2DS associated with increased spikelet number and heading date are linked with multiple introgressed alleles of Ppd-D1 identified by the whole-genome sequencing of the Ae. tauschii parents. While some introgressed haplotypes exhibited significant pleiotropic effects with the direction of effects on the yield component traits being largely consistent with the previously reported trade-offs, there were haplotype combinations associated with the positive trends in yield. The characterized repertoire of the introgressed haplotypes derived from Ae. tauschii accessions with the combined positive effects on yield and yield components traits in elite germplasm provides a valuable source of alleles for improving the productivity of winter wheat by optimizing the contribution of component traits to yield.

genetics↗

bioRxiv2020

The COMPASS-like complex modulates fungal development and pathogenesis by regulating H3K4me3-mediated targeted gene expression in Magnaporthe oryzae

Histone H3K4 methylation is catalysed by the multi-protein complex known as the Set1/COMPASS or MLL/COMPASS-like complex, an element that is highly evolutionarily conserved from yeast to humans. However, the components and mechanisms by which the COMPASS-like complex targets the H3K4 methylation of plant pathogenic genes in fungi remain elusive. Here we present a comprehensive analysis combining biochemical, molecular, and genome-wide approaches to characterize the roles of the COMPASS-like family in Magnaporthe oryzae, a model plant fungal pathogen. We purified and identified six conserved subunits of COMPASS from the rice blast fungus M. oryzae, i.e., MoBre2 (Cps60/ASH2L), MoSpp1 (Cps40/Cfp1), MoSwd2 (Cps35), MoSdc1 (Cps25/DPY30), MoSet1 (MLL/ALL) and MoRbBP5 (Cps50), using an affinity tag on MoBre2. We determined the SPRY domain of MoBre2 can recognize directly with DPY30 domain of MoSdc1 in vitro. Furthermore, we found that deletion of the genes encoding COMPASS subunits of MoBre2, MoSpp1 and MoSwd2 caused similar defects regarding invasive hyphal development and pathogenicity. Genome-wide profiling of H3K4me3 revealed that the it has remarkable co-occupancy at the TSS regions of target genes. Significantly, these target genes are often involved in spore germination and pathogenesis. Decreased gene expression caused by the deletion of MoBre2, MoSwd2 or MoSpp1 gene was highly correlated with decrease in H3K4me3. Taken together, these results suggest that MoBre2, MoSpp1, and MoSwd2 function as a whole COMPASS complex, contributing to fungal development and pathogenesis by regulating H3K4me3-targeted genes in M. oryzae.

microbiology↗

bioRxiv2019

The draft nuclear genome assembly of Eucalyptus pauciflora: new approaches to comparing de novo assemblies

BackgroundSelecting the best genome assembly from a collection of draft assemblies for the same species remains a difficult task. Here, we combine new and existing approaches to help to address this, using the non-model plant Eucalyptus pauciflora (snow gum) as a test case. Eucalyptus pauciflora is a long-lived tree with high economic and ecological importance. Currently, little genomic information for Eucalyptus pauciflora is available.\n\nFindingsWe generated high coverage of long-(Nanopore, 174x) and short-(Illumina, 228x) read data from a single Eucalyptus pauciflora individual and compared assemblies from four assemblers with a variety of settings: Canu, Flye, Marvel, and MaSuRCA. A key component of our approach is to keep a randomly selected collection of ~10% of both long- and short-reads separate from the assemblies to use as a validation set with which to assess the assemblies. Using this validation set along with a range of existing tools, we compared the assemblies in eight ways: contig N50, BUSCO scores, LAI scores, assembly ploidy, base-level error rate, computing genome assembly likelihoods, structural variation and genome sequence similarity. Our result showed that MaSuRCA generated the best assembly, which is 594.87 Mb in size, with a contig N50 of 3.23 Mb, and an estimated error rate of ~0.006 errors per base.\n\nConclusionsWe report a draft genome of Eucalyptus pauciflora, which will be a valuable resource for further genomic studies of eucalypts. These approaches for assessing and comparing genomes should help in assessing and choosing among many potential genome assemblies for a single species.

genomics↗

bioRxiv2018

Gene editing and mutagenesis reveal inter-cultivar differences and additivity in the contribution of TaGW2 homoeologues to grain size and weight in wheat

The TaGW2 gene homoeologues have been reported to be negative regulators of grain size (GS) and thousand grain weight (TGW) in wheat. However, the contribution of each homoeologue to trait variation among different wheat cultivars is not well documented. We used the CRISPR-Cas9 system and TILLING to mutagenize each homoeologous gene copy in cultivars Bobwhite and Paragon, respectively. Plants carrying single-copy nonsense mutations in different genomes showed different levels of GS/TGW increase, with TGW increasing by an average of 5.5% (edited lines) and 5.3% (TILLING mutants). In any combination, the double homoeologue mutants showed higher phenotypic effects than the respective single-genome mutants. The double mutants had on average 12.1% (edited) and 10.5% (TILLING) higher TGW with respect to wild-type lines. The highest increase in GS and TGW was shown for triple mutants of both cultivars, with increases of 16.3% (edited) and 20.7% (TILLING) in TGW. The additive effects of the TaGW2 homoeologues were also demonstrated by the negative correlation between the functional gene copy number and GS/TGW in Bobwhite mutants and an F2 population. The highest single-genome increases in GS and TGW in Paragon and Bobwhite were obtained by mutations in the B and D genomes, respectively. These inter-cultivar differences in the phenotypic effects between the TaGW2 gene homoeologues coincide with inter-cultivar differences in the homoeologue expression levels. These results indicate that GS/TGW variation in wheat can be modulated by the dosage of homoeologous genes with inter-cultivar differences in the magnitude of the individual homoeologue effects.

genetics↗

bioRxiv2018

Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

BackgroundChloroplasts are organelles that conduct photosynthesis in plant and algal cells. Chloroplast genomes code for around 130 genes, and the information they contain is widely used in agriculture and studies of evolution and ecology. Correctly assembling complete chloroplast genomes can be challenging because the chloroplast genome contains a pair of long inverted repeats (10-30 kb). The advent of long-read sequencing technologies should alleviate this problem by providing sufficient information to completely span the inverted repeat regions. Yet, long-reads tend to have higher error rates than short-reads, and relatively little is known about the best way to combine long- and short-reads to obtain the most accurate chloroplast genome assemblies. Using Eucalyptus pauciflora, the snow gum, as a test case, we evaluated the effect of multiple parameters, such as different coverage of long (Oxford nanopore) and short (Illumina) reads, different long-read lengths, different assembly pipelines, and different genome polishing steps, with a view to determining the most accurate and efficient approach to chloroplast genome assembly.\n\nResultsHybrid assemblies combining at least 20x coverage of both long-reads and short-reads generated a single contig spanning the entire chloroplast genome with few or no detectable errors. Short-read-only assemblies generated three contigs representing the long single copy, short single copy and inverted repeat regions of the chloroplast genome. These contigs contained few single-base errors but tended to exclude several bases at the beginning or end of each contig. Long-read-only assemblies tended to create multiple contigs with a much higher single-base error rate, even after polishing. The chloroplast genome of Eucalyptus pauciflora is 159,942 bp, contains 131 genes of known function, and confirms the phylogenetic position of Eucalyptus pauciflora as a close relative of Eucalyptus regnans.\n\nConclusionsOur results suggest that very accurate assemblies of chloroplast genomes can be achieved using a combination of at least 20x coverage of long- and short-reads respectively, provided that the long-reads contain at least ~5x coverage of reads longer than the inverted repeat region. We show that further increases in coverage give little or no improvement in accuracy, and that hybrid assemblies are more accurate than long-read-only or short-read-only assemblies.

genomics↗