Biology subjects

Guo, L.

Publications and source records attributed to Guo, L..

At least 217 records · Page 12Linked to original sources

bioRxiv2020

LiBis: An ultrasensitive alignment method for low-input bisulfite sequencing

The cell-free DNA (cfDNA) methylation profile in liquid biopsies has been utilized to diagnose early-stage disease and estimate therapy response. However, in typical clinical settings, only very small amounts of cfDNA can be purified. Whole-genome bisulfite sequencing (WGBS) is the gold standard to measure DNA methylation; however, WGBS using small amounts of fragmented DNA introduces a critical challenge for data analysis, namely a low mapping ratio. This, in turn, generates low sequencing depth and low coverage for CpG sites genome wide. The lack of informative CpGs has become a bottleneck for the clinical application of cfDNA-based WGBS assays. Hence, we developed LiBis (Low-input Bisulfite Sequencing), a novel method for low-input WGBS data alignment. By dynamically clipping initially unmapped reads and remapping clipped fragments, we judiciously rescued those reads and uniquely aligned them to the genome. By substantially increasing the mapping ratio by up to 88%, LiBis dramatically improved the number of informative CpGs and the precision in quantifying the methylation status of individual CpG sites. The high sensitivity and cost effectiveness afforded by LiBis for low-input samples will allow the discovery of genetic and epigenetic features suitable for downstream analysis and biomarker identification using liquid biopsy.Competing Interest StatementThe authors have declared no competing interest.List of AbbreviationsLiBislow-input bisulfite sequencing alignmentcfDNAcell-free DNAWGBSwhole-genome bisulfite sequencingCpGcytosine nucleotide followed by a guanine nucleotidectDNAcirculating tumor DNAHTMLHyperText Markup LanguageHPVHuman papillomavirusView Full Text

bioinformatics↗

bioRxiv2020

Mammalian ATG9s drive the autophagosome formation by binding to LC3

The autophagosome is a membranous organelle that executes macroautophagy (call autophagy hereafter for the sake of brevity). Although the biogenesis of autophagosome depends on continuous acquirement of necessary membrane components to support its growth, the underlying mechanism has remained uncertain. Herein, we report that the mammalian ATG9 family members (maATG9s) play master roles in this process. We show that maATG9s directly localize to the growing autophagosomal membrane through their Ubiquitin-interacting motives (UIMs), which interact with the UIM docking site (UDS) on LC3, a component of the autophagosomal membrane. Interrupting the UIM-UDS interaction abrogates the maATG9s-LC3 binding, the localization of maATG9s to the growing autophagosome, and the autophagosome formation. Collectively, our findings show the first evidence that maATG9s act as primary autophagosomal membrane components to drive the autophagosome formation. As autophagy has been implicated in many human diseases, the identified maATG9s-LC3 interaction may serve as a target for manipulating pathological autophagosome formation.

cell biology↗

bioRxiv2020

Deficiency in reverse cholesterol transport in mice augments sepsis

BackgroundSepsis claims over 215,000 lives and costs $16.7 billion per year in America alone. Recent studies revealed that HDL receptor scavenger receptor BI (SR-BI or Scarb1) plays a critical protective role in sepsis. Using Scarb1I179N mice, a mutant SR-BI mouse model with 90% depletion in hepatic SR-BI, we previously reported that the mutant mice are susceptible to cecal ligation and puncture (CLP)-induced sepsis. However, using a hypo-AlbCreSR-BIfl/fl mouse model, Hubys group showed that the liver-specific SR-BI KO mice are not more susceptible to CLP-induced sepsis. In this study, we generated a new floxed SR-BI mouse model to clarify the contribution of hepatic SR-BI in sepsis. SR-BI is known as a receptor that plays a key role in reverse cholesterol transport (RCT) by uptaking cholesterol to the liver. So, our established AlbCreSR-BIfl/fl mice (liver-specific SR-BI KO) is an RCT deficiency mice model that can be used to understand the mechanisms of RCT protecting against sepsis and may provide new insight into the pathogenesis of sepsis. Methods and ResultsWe generated SR-BIfl/fl mice by flanking exon 2. We bred the floxed mice with AlbCre mice to generate AlbCreSR-BIfl/fl mice (liver-specific SR-BI KO mice), then the mice were backcrossed to C57BL/6J for 10 generations. As shown in Fig 1, the liver SR-BI expression was normal in SR-BIfl/fl mice as compared to C57BL/6J (B6) mice, but completely depleted in AlbCreSR-BIfl/fl mice. Using this liver-specific SR-BI KO model, we observed that a deficiency in RCT rendered the mice highly susceptible to CLP-induced sepsis as shown by 80% and 14.3% survival of SR-BIfl/fl and AlbCreSR-BIfl/fl mice, respectively. We found aggravated inflammatory cytokine production, altered leukocyte recruitment and slightly increased in the blood and peritoneal bacteria. Moreover, we found RCT deficiency mice increased both free and total cholesterol levels in serum and showed severer hemolysis in AlbCreSR-BIfl/fl mice than SR-BIfl/fl mice during CLP-induced sepsis. Importantly, when we fed AlbCreSR-BIfl/fl mice with probucol to decrease the cholesterol level in serum before performing CLP, the survival rate of AlbCreSR-BIfl/fl mice improved to 88.9%. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/051250v1_fig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@80f819org.highwire.dtl.DTLVardef@12064dborg.highwire.dtl.DTLVardef@1bd8e72org.highwire.dtl.DTLVardef@1d30b5e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO Mice deficient in hepatic SR-BI are susceptible to CLP-induced septic death. A, PCR genotyping of AlbCreSR-BIfl/fl mice using tail DNA. B, Western blot analysis of SR-BI expression in the liver; C, survival analysis. AlbCreSR-BIfl/fl (n = 14) and SR-BIfl/fl mice (n = 10) were treated with CLP (23G needle, half ligation) and survival was observed for 7 days. The data were expressed as the percentage of mice surviving at indicated times, and survival was analyzed by Log-Rank x2 test. D, AlbCreSR-BIfl/fl and SR-BIfl/fl mice were treated with CLP for the indicated times, and kidney injury was assessed by measuring blood urea nitrogen (BUN) levels; and E, liver injury was assessed by measuring serum alanine aminotransferase (ALT) levels. n = 6 - 7 each group, mean {+/-} SEM. C_FIG ConclusionsDeficiency RCT resulting in abnormal metabolism of cholesterol and lipid metabolism is a risk factor in sepsis and maintain normal metabolism of cholesterol may provide a new insight for sepsis therapies.

molecular biology↗

bioRxiv2020

Relative adrenal insufficiency is a risk factor and an endotype of sepsis - A proof of concept study to support a precision medicine approach for glucocorticoid sepsis therapy

Rational25-60% of septic patients experience relative adrenal insufficiency (RAI) and glucocorticoid (GC) is frequently used in septic patients. However, the efficacy of GC therapy and whether the GC therapy should be based on the status of RAI are highly controversial. Critical barriers include technical limitations in properly identifying RAI in septic patients and a lack of RAI animal model. ObjectivesWe established a new RAI animal model to test our hypothesis that precision medicine approach should be used for GC sepsis therapy - only applying GC to a subgroup of septic mice with RAI. MethodsWe generated SF1CreSR-BIfl/fl conditional knockout mice. The mice exhibited specific depletion of SR-BI expression in adrenal gland, resulting in a lack of production of inducible GC in response to ACTH stimulation or sepsis, but the mice had normal basal GC levels. Mice were treated with cecal ligation and puncture to develop sepsis. Mice were also supplemented with or without GC to study the effect of GC in sepsis therapy. Plasma and organs were collected for biochemical assays. BODIPY FL-conjugated Escherichia coli was used for phagocytosis assay. Macrophages were used to study effects of GC on inflammatory responses. Measurements and Main ResultsUsing SF1CreSR-BIfl/fl mice as a RAI model, we found that mice with RAI were susceptible to CLP-induced sepsis compared to controls (6.7% survival in SF1CreSR-BIfl/fl mice versus 86.4% in SR-BIfl/fl mice; p=0.0001). Supplementation of hydrocortisone significantly improved survival in CLP-treated SF1CreSR-BIfl/fl mice. Surprisingly, wild type mice receiving GC treatment exhibited significantly less survival compared to wild type mice without GC treatment. We further found that, in contrast to wild type mice which displayed a well-controlled systemic inflammatory response, the mice with RAI featured a persisted systemic response as shown by high levels of plasma inflammatory cytokines/chemokines 20 hours post CLP, and supplementation of GC kept the inflammatory response under control. In vitro analysis revealed that stress level of GC is required to suppress inflammatory response through modulating MAPK signaling in macrophages. ConclusionsWe demonstrate that RAI is a risk factor and an endotype for sepsis, and GC treatment benefits mice with RAI but harms mice without RAI. We further demonstrate that inducible GC functions to keep the systemic inflammatory response under control through modulating MAPK signaling, but mice with RAI lose such protection and supplementation of GC regains the protection. Our study provides a proof of concept to support the use of a precision medicine approach for sepsis therapy - selectively applying GC therapy for a subgroup of patients with RAI.

immunology↗

bioRxiv2020

Deletion of the mitochondrial matrix protein cyclophilin-D prevents parvalbumin interneuron dysfunction and cognitive deficits in a mouse model of NMDA hypofunction

Redox dysregulation and oxidative stress are final common pathways in the pathophysiology of a variety of psychiatric disorders, including schizophrenia. Oxidative stress causes dysfunction of GABAergic parvalbumin-positive interneurons (PVI), which are crucial for the coordination of neuronal synchrony during sensory- and cognitive-processing. Mitochondria are the main source of reactive oxygen species (ROS) in neurons and they control synaptic activity through their roles in energy production and intracellular calcium homeostasis. We have previously shown that in male mice transient blockade of NMDA receptors during development (subcutaneous injections of 30 mg/kg ketamine (KET) on postnatal days 7, 9, and 11) results in long-lasting alterations in synaptic transmission and reduced parvalbumin expression in the adult prefrontal cortex (PFC), contributing to a behavioral phenotype that mimics multiple symptoms associated with schizophrenia. These changes correlate with oxidative stress and impaired mitochondrial function in both PVI and pyramidal cells. Here, we show that genetic deletion (Ppif-/-) of the mitochondrial matrix protein cyclophilin D (CypD) prevents perinatal KET-induced increases in ROS and the resulting deficits in PVI function, and changes in excitatory and inhibitory synaptic transmission in the PFC. Deletion of CypD also prevented KET-induced behavioral deficits in cognitive flexibility, social interaction, and novel object recognition. Taken together, these data highlight how mitochondrial activity may play an integral role in modulating PVI-mediated cognitive processes. Significance StatementMitochondria are important modulators of oxidative stress and cell function, yet how mitochondrial dysfunction affects cell activity and synaptic transmission in psychiatric illnesses is not well understood. NMDA receptor blockade with ketamine during development causes oxidative stress, dysfunction of parvalbumin-positive interneurons (PVI), and long-lasting physiological and behavioral changes. Here we show that mice deficient for the mitochondrial matrix protein cyclophilin D show robust protection from PVI dysfunction following perinatal NMDAR-blockade. Mitochondria serve as an essential node for a number of stress-induced signaling pathways and our experiments suggest that failure of mitochondrial redox regulation can contribute to PVI dysfunction.

neuroscience↗

bioRxiv2020

SARS-CoV-2 detection with CRISPR diagnostics

The novel coronavirus (CoV) disease termed COVID-19 (Coronavirus Disease-19) caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) is causing a massive pandemic worldwide, threatening public health systems across the globe. During this ongoing COVID-19 outbreak, nucleic acid detection has played an important role in early diagnosis. Here we report a SARS-CoV-2 detection protocol using a CRISPR-based CRISPR diagnostic platform - CDetection (Cas12b-mediated DNA detection). By combining sample treatment protocols and nucleic acid amplification methods with CDetection, we have established an integrated viral nucleic acid detection platform - CASdetec (CRISPR-assisted detection). The detection limit of CASdetec for SARS-CoV-2 pseudovirus is 1 x 104 copies/mL, with no cross reactivity observed. Our assay design and optimization process can provide guidance for future CRISPR-based nucleic acid detection assay development and optimization.

molecular biology↗

bioRxiv2020

Mechanism of auxin and GA crosstalk in diploid strawberry fruit initiation

Strawberry, a high value fruit crop, has recently become amenable for genetic studies due to genomic resources and CRISPR/CAS9 tools. Unlike ovary-derived botanical fruits, strawberry is an accessory fruit derived from receptacle, the stem tip subtending floral organs. Although both botanical and accessory fruits initiate development in response to auxin and GA released from seeds, the downstream auxin and GA signaling mechanisms underlying accessory fruit development remain unknown. Using wild strawberry, we performed in depth molecular characterizations of accessory fruit development. We show that auxin signaling proteins FveARF8/FveARF6 are bound and hence inhibited by FveIAA4 and FveRGA1, repressors in auxin and GA signaling pathways. This inhibition is relieved post-fertilization or by the application of GA or auxin. Mutants of FveRGA1 developed parthenocarpic fruit suggesting a conserved function of DELLA proteins in fruit set. Further, FveARF8 was found to repress the expression of a GA receptor gene GID1c to control fruits sensitivity to GA, revealing a novel crosstalk mechanism. We demonstrate that consensus co-expression network provides a powerful tool for non-model species in the selection of interacting genes for functional studies. These findings will facilitate the improvement of strawberry fruit productivity and quality by guiding future production of parthenocarpic fruit. One sentence summaryGenome editing and network analysis are applied to investigating the mechanism of accessory fruit initiation in the wild strawberry, revealing conserved as well as novel crosstalk mechanisms. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Zhongchi Liu (zliu@umd.edu)

plant biology↗

bioRxiv2020

Partnership between epigenetic reader BRD4 and transcription factor CEBPD

Vascular smooth muscle cell (SMC) state/phenotype transitions underlie neointimal hyperplasia (IH) predisposing to cardiovascular diseases. Bromodomain protein BRD4 is a histone acetylation reader and enhancer mark that co-activates transcription elongation. CCAAT enhancer binding protein delta (CEBPD) is a transcription factor typically studied in adipogenesis and immune cell differentiation. Here we investigated the association between BRD4 and CEBPD in SMC state transition. Chromatin immunoprecipitation sequencing (ChIPseq) showed enrichment of BRD4 and histone acetylation (H3K27ac) at Cebpd and enhancer in rat carotid arteries undergoing IH. In vitro, BRD4 silencing with siRNA reduced SMC expression of CEBPD. Bromodomain-1 but not bromodoamin-2 accounted for this BRD4 function. Endogenous BRD4 co-IPed with CEBPD; Cebpd promoter and enhancer DNA fragments co-IPed with CEBPD or endogenous BRD4 (ChIP-qPCR). These co-IPs were abolished by the BRD4 bromodomain blocker JQ1. TNF upregulated both BRD4 and CEBPD. Silencing CEBPD averted TNF-induced inflammatory SMC state transition (heightened IL-1{beta}, IL6, and MCP-1 mRNA levels), so did JQ1. CEBPD overexpression increased PDGFR preferentially over PDGFR{beta}; so did TNF, and JQ1 abolished TNFs effect. Our data reveal a BRD4/CEBPD partnership that promotes CEBPDs own transcription and inflammatory SMC state transition, thus shedding new light on epigenetic reader and transcription factor cooperative actions in SMC pathobiology.

cell biology↗

bioRxiv2020

Blunted Diurnal Firing in Lateral Habenula Projections to Dorsal Raphe Nucleus and Delayed Photoentrainment in Stress-Susceptible Mice.

Daily rhythms are disrupted in patients suffering from mood disorders. The lateral habenula (LHb) and dorsal raphe nucleus (DRN) contribute to circadian timekeeping and regulate mood. Thus, pathophysiology in these nuclei may be responsible for aberrations in daily rhythms during mood disorders. Using the chronic social defeat stress (CSDS) paradigm and in-vitro slice electrophysiology we measured the effects of stress on diurnal rhythms in firing of LHb cells projecting to the DRN (cellsLHb[->]DRN) and DRN cells alone. We also performed optogenetic experiments to investigate if increased firing in cellsLHb[->]DRN during exposure to subthreshold social defeat stress (SSDS), induces stress-susceptibility. Last we investigated whether exposure to CSDS affected the ability of mice to phototentrain to a new LD cycle. The cellsLHb[->]DRN and DRN cells alone of stress-susceptible mice express greater blunted diurnal firing compared to stress-naive (control) and stress-resilient mice. Day-time optogenetic activation of cellsLHb[->]DRN during SSDS induces stress-susceptibility which shows the direct correlation between increased activity in this circuit and putative mood disorders. Finally, we found that stress-susceptible mice are slower, while stress-resilient mice are faster, at photoentraining to a new LD cycle. Our findings suggest that CSDS induces blunted daily rhythms in firing in cellsLHb[->]DRN and slow rate of photoentrainment in susceptible-mice. In contrast, resilientmice may undergo homeostatic adaptations that maintain daily rhythms in firing in cellsLHb[->]DRN and also show rapid photoentrainment to a new LD-cycle.

neuroscience↗

bioRxiv2020

Angioplasty-induced epigenomic remodeling entails BRD4 and EZH2 hierarchical regulations

Atherosclerosis is commonly treated with angioplasty which, however, evokes neointimal hyperplasia (IH) and recurrent stenotic diseases. Epigenomic investigation was lacking on post-angioplasty IH. The histone acetylation reader BRD4 and H3K27me3 writer EZH2 are potent epigenetic factors; their relationship is little understood. Through genome-wide survey in the rat angioplasty model, we studied BRD4 and EZH2 functional regulations involved in IH. We performed chromatin immunoprecipitation sequencing (ChIPseq) using rat carotid arteries. While H3K27me3 ChIPseq signal prevalently intensified in balloon-injured (vs uninjured) arteries, BRD4 and H3K27ac became more enriched at Ezh2. Indeed, BRD4-siRNA or CRISPR-deletion of BRD4-associated enhancer abated the smooth muscle cell (SMC) expression of EZH2, and SMC-specific BRD4 knockout in BRD4fl/fl; Myh11CreERT2 mice reduced both H3K27me3 and IH in wire-injured femoral arteries. In accordance, post-angioplasty IH was exacerbated and mitigated, respectively, by lentiviral expression and pharmacological inhibition of EZH2/1; EZH2 (or EZH1) loss- and gain-of-function respectively attenuated and aggravated pro-IH SMC proliferative behaviors. Furthermore, while H3K27me3 ChIPseq signal magnified at P57 and ebbed at Ccnd1 and Uhrf1 after injury, silencing either EZH2 or EZH1 in SMCs up-regulated P57 and down-regulated Ccnd1 and Uhrf1. In summary, our results reveal an upsurge of EZH2/H3K27me3 after angioplasty, BRD4s control over EZH2 expression, and non-redundant EZH2/1 functions. As such, this study unravels angioplasty-induced loci-specific H3K27me3/ac redistribution in the epigenomic landscape rationalizing BRD4/EZH2-governed pro-IH regulations.

pathology↗

bioRxiv2020

Transcriptional repression of Myc underlies AGO1's tumour suppressor function

Here we report novel tumour suppressor activity for the Drosophila Argonaute family RNA binding protein AGO1, a component of the miRNA-dependent RNA-induced silencing complex (RISC). The mechanism for growth inhibition does not, however, involve canonical roles as part of the RISC; rather AGO1 controls cell and tissue growth by functioning as a direct transcriptional repressor of the master regulator of growth, Myc. AGO1 depletion in wing imaginal discs drives a significant increase in ribosome biogenesis, nucleolar expansion, and cell growth in a manner dependent on Myc abundance. Moreover, increased Myc promoter activity and elevated Myc mRNA in AGO1 depleted animals requires RNA Pol II transcription. Further support for transcriptional AGO1 functions is provided by physical interaction with the RNA Pol II transcriptional machinery (chromatin remodelling factors and Mediator Complex), punctate nuclear localisation in euchromatic regions and overlap with Polycomb Group transcriptional silencing loci. Moreover, significant AGO1 enrichment is observed on the Myc promoter and AGO1 interacts with the Myc transcriptional activator Psi. Together our data show AGO1 functions outside of the RISC to repress Myc transcription and inhibit developmental cell and tissue growth.

developmental biology↗

bioRxiv2020

The Pathogenicity of 2019 Novel Coronavirus in hACE2 Transgenic Mice

Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) caused the Corona Virus Disease 2019 (COVID-19) cases in China has become a public health emergency of international concern (PHEIC). Based on angiotensin converting enzyme 2 (ACE2) as cell entry receptor of SARS-CoV, we used the hACE2 transgenic mice infected with SARS-CoV-2 to study the pathogenicity of the virus. Weight loss and virus replication in lung were observed in hACE2 mice infected with SARS-CoV-2. The typical histopathology was interstitial pneumonia with infiltration of significant lymphocytes and monocytes in alveolar interstitium, and accumulation of macrophages in alveolar cavities. Viral antigens were observed in the bronchial epithelial cells, alveolar macrophages and alveolar epithelia. The phenomenon was not found in wild type mice with SARS-CoV-2 infection. The pathogenicity of SARS-CoV-2 in hACE2 mice was clarified and the Kochs postulates were fulfilled as well, and the mouse model may facilitate the development of therapeutics and vaccines against SARS-CoV-2.

microbiology↗

bioRxiv2020

Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single nucleotide polymorphism (SNP). In recent years there have been a number of studies associating large, chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloging small (30 to 10,000 bp) to mid-scale (10,000 bp to 30,000 bp) SV and their impact on evolution and adaptation related traits in plants. This might be attributed to complex and highly-duplicated nature of plant genomes, which makes them difficult to assess using high-throughput genome screening methods. Here we describe how long-read sequencing technologies can overcome this problem, revealing a surprisingly high level of widespread, small to mid-scale SV in a major allopolyploid crop species, Brassica napus. We found that up to 10% of all genes were affected by small to mid-scale SV events. Nearly half of these SV events ranged between 100 bp to 1000 bp, which makes them challenging to detect using short read Illumina sequencing. Examples demonstrating the contribution of such SV towards eco-geographical adaptation and disease resistance in oilseed rape suggest that revisiting complex plant genomes using medium-coverage, long-read sequencing might reveal unexpected levels of functional gene variation, with major implications for trait regulation and crop improvement.

genomics↗

bioRxiv2020

Efficient long fragment editing technique enables rapid construction of genetically stable bacterial strains

Bacteria are versatile living systems that enhance our understanding of nature and enable biosynthesis of valuable chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable strains. However, the existing genome editing methods cannot meet the needs of engineers. We herein report an efficient long fragment editing method for large-scale and scarless genome engineering in Escherichia coli. The method enabled us to insert DNA fragments up to 12 kb into the genome and to delete DNA fragments up to 186.7 kb from the genome, with positive rates over 95%. We applied this method for E. coli genome simplification, resulting in 12 individual deletion mutants and four cumulative deletion mutants. The simplest genome lost a total of 370.6 kb of DNA sequence containing 364 open reading frames. Additionally, we applied this technique to metabolic engineering and obtained a genetically stable plasmid-independent isobutanol production strain that produced 1.3 g/L isobutanol via shake-flask fermentation. These results suggest that the method is a powerful genome engineering tool, highlighting its potential to be applied in synthetic biology and metabolic engineering.

bioengineering↗

bioRxiv2020

MSIsensor-pro: fast, accurate and matched-normal-sample-free detection of microsatellite instability

We developed MSIsensor-pro (https://github.com/xjtu-omics/msisensor-pro), an open-source single sample microsatellite instability (MSI) scoring method for research and clinical applications. MSIsensor-pro introduces a multinomial distribution model to quantify polymerase slippages for each tumor sample and a discriminative sites selection method to enable MSI detection without matched normal samples. For samples of various sequencing depths and tumor purities, MSIsensor-pro significantly outperformed the current leading methods in terms of both accuracy and computational cost.

bioinformatics↗

bioRxiv2019

Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

We present a chromosome-scale annotated assembly of the rye (Secale cereale L. inbred line Lo7) genome, which we use to explore Triticeae genomic evolution, and ryes superior disease and stress tolerance. The rye genome shares chromosome-level organization with other Triticeae cereals, but exhibits unique retrotransposon dynamics and structural features. Crop improvement in rye, as well as in wheat and triticale, will profit from investigations of rye gene families implicated in pathogen resistance, low temperature tolerance, and fertility control systems for hybrid breeding. We show that rye introgressions in wheat breeding panels can be characterised in high-throughput to predict the yield effects and trade-offs of rye chromatin.

genomics↗

bioRxiv2019

Na2CO3-Responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics

Alkali-salinity exerts severe osmotic, ionic and high-pH stresses to plants. To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species (ROS) homeostasis, physiological and diverse quantitative proteomics analyses of alkaligrass (Puccinellia tenuiflora) under Na2CO3 stress were conducted. In addition, Western blot, real-time PCR, and transgenic techniques were applied to validate the proteomic results and test the functions of the Na2CO3-responsive proteins. A total of 104 and 102 Na2CO3-responsive proteins were identified in leaves and chloroplasts, respectively. In addition, 84 Na2CO3-responsive phosphoproteins were identified, including 56 new phosphorylation sites in 56 phosphoproteins from chloroplasts, which are crucial for the regulation of photosynthesis, ion transport, signal transduction and energy homeostasis. A full-length PtFBA encoding an alkaligrass chloroplastic fructose-bisphosphate aldolase (FBA) was overexpressed in wild-type cells of cyanobacterium Synechocystis sp. Strain PCC 6803, leading to enhanced Na2CO3 tolerance. All these results indicate that thermal dissipation, state transition, cyclic electron transport, photorespiration, repair of photosystem (PS) II, PSI activity, and ROS homeostasis were altered in response to Na2CO3 stress, and they have improved our understanding of the Na2CO3-responsive mechanisms in halophytes.

plant biology↗

bioRxiv2019

Modularized Transcriptional Regulatory Networks of Fusarium graminearum

The filamentous fungus Fusarium graminearum causes devastating crop disease and produces harmful mycotoxins worldwide. Understanding the complex F. graminearum transcriptional regulatory networks (TRNs) is vital for effective disease management. Reconstructing F. graminearum dynamic TRNs, an NP-hard problem, remains unsolved using commonly adopted reductionist or co-expression based approaches. Multi-omic data such as fungal genomic, transcriptomic data and phenomic data are vital to but so far have been largely isolated and untapped for unraveling phenotype-specific TRNs. Here for the first time, we harnessed these resources to infer global TRNs for F. graminearum using a Bayesian network based algorithm, "module networks". The inferred TRNs contain 49 regulatory modules that show condition-specific gene regulation. Through a robust validation based on prior biological knowledge including functional annotations and TF binding site enrichment, our network prediction displayed high accuracy and concordance with existing knowledge, highlighted by its accurate capture of the well-known trichothecene gene cluster. In addition, we developed a new computational method to calculate the associations between modules and phenotypes, and discovered subnetworks responsible for fungal virulence, sexual reproduction and mycotoxin production. Finally, we found a clear compartmentalization of TRN modules in core and lineage-specific genomic regions in F. graminearum, reflecting the evolution of the TRNs in fungal speciation. This system-level reconstruction of filamentous fungal TRNs provides novel insights into the intricate networks of gene regulation that underlie key processes in F. graminearum pathobiology and offers promise for the development of improved disease control strategies.

microbiology↗