Biology subjects

Lu, X.

Publications and source records attributed to Lu, X..

At least 343 records · Page 19Linked to original sources

bioRxiv2019

Jasmonate-regulated ERF109-MYB51-MYC3 ternary complexes control indolic glucosinolates biosynthesis

Jasmonates (JAs) are plant hormones which regulate biosynthesis of many secondary metabolites, such as glucosinolates (GLSs), through JAs-responsive transcription factors (TFs). The JAs-responsive CYP83B1 gene, has been shown to catalyze the conversion of indole-3-acetaldoxime (IAOx) to indolic glucosinolates (IGLSs). However, little is known about the regulatory mechanism of CYP83B1 gene expression by JAs. In yeast one-hybrid screens using the CYP83B1 promoter as bait we isolated two JAs-responsive TFs ERF109 and MYB51 that are involved in JAs-regulated IGLS biosynthesis. Furthermore, using a yeast two-hybrid assay, we identified ERF109 as an interacting partner of MYB51, and Jasmonate ZIM-domain (JAZ) proteins as interactors of MYB51, and BTB/POZ-MATH (BPM) proteins as interactors of ERF109. Both JAZ and BPM proteins are necessary for the full repression of the ERF109-MYB51-MYC3 ternary complex activity on CYP83B1 gene expression and JA-regulated IGLS biosynthesis. Biochemical analysis showed that the 26S proteasome-mediated degradation of ERF109 protein is mediated by a CRL3BPM E3 ligase independently of JA signaling. Genetic and physiological evidence shows that MYB51 acts as an adaptor and activator to bridge the interaction with the co-activators MYC3 and ERF109, for synergistically activating the CYP83B1 gene expression, and all three factors are essential and exert a coordinated control in JAs-induced IGLS biosynthesis. Overall, this study provides insights into the molecular mechanisms of JAs-responsive ERF109-MYB51-MYC3 ternary complexes in controlling JAs-regulated GLSs biosynthesis, which provides a better understanding of plant secondary metabolism. One-sentence summaryThe JA-responsive ERF109-MYB51-MYC3 ternary complex controls JAs-regulated GLSs biosynthesis.

bioengineering↗

bioRxiv2019

Inhibition of ADORA1 attenuates hepatic steatosis by gut microbiota-derived acetic acid from Astragalus polysaccharides

The authors have withdrawn this manuscript, because some data could not be replicated. During the process of subsequent revision of the manuscript, we separated the data into two parts. The majority data of the preprint draft, the anti-NAFLD effect of Astragalus polysaccharides (APS) in mice and the contribution of gut microbiota, were independently published in 2021 after substantial revision (doi: https://doi.org/10.1080/19490976.2021.1930874). However, the data on figure 6 (about ARs inhibitors DPCPX orally ameliorating NAFLD in mice, and Adora1 si-RNA data in vitro) could not be fully replicated in subsequent experiments. The most probable reason might be due to the batch differences of mice / cells, or other undetermined factors during experiment. Moreover, we have carried out in-depth studies on the exact role of hepatic A1R on NAFLD formation, which is opposite to our prior assumption. Therefore, we do not wish this work to be cited as reference for the project. We apologize for any inconvenience caused to our readers. Any questions can be addressed to first/corresponding author.

physiology↗

bioRxiv2019

Fitness barriers limit reversion of a proofreading-deficient coronavirus

The 3'-to-5' exoribonuclease in coronavirus (CoV) nonstructural protein 14 (nsp14-ExoN) mediates RNA proofreading during genome replication. ExoN catalytic residues are arranged in three motifs: I (DE), II (E), III (D). Alanine substitution of the motif I residues (AA-E-D, four nucleotide substitutions) in murine hepatitis virus (MHV) and SARS-CoV yields viable mutants with impaired replication and fitness, increased mutation rates, and attenuated virulence in vivo. Despite these impairments, MHV- and SARS-CoV ExoN motif I AA mutants (ExoN-AA) have not reverted at motif I in diverse in vitro and in vivo environments, suggesting that profound fitness barriers prevent motif I reversion. To test this hypothesis, we engineered MHV-ExoN-AA with 1, 2 or 3 nucleotide mutations along genetic pathways to AA-to-DE reversion. We show that engineered intermediate revertants were viable but had no increased replication or competitive fitness compared to MHV-ExoN-AA. In contrast, a low passage (P10) MHV-ExoN-AA showed increased replication and competitive fitness without reversion of ExoN-AA. Finally, engineered reversion of ExoN-AA to ExoN-DE in the presence of ExoN-AA passage-adaptive mutations resulted in significant fitness loss. These results demonstrate that while reversion is possible, at least one alternative adaptive pathway is more rapidly advantageous than intermediate revertants and may alter the genetic background to render reversion detrimental to fitness. Our results provide an evolutionary rationale for lack of ExoN-AA reversion, illuminate potential multi-protein replicase interactions and coevolution, and support future studies aimed at stabilizing attenuated CoV ExoN-AA mutants.\n\nIMPORTANCECoronaviruses encode an exoribonuclease (ExoN) that is important for viral replication, fitness, and virulence, yet coronaviruses with a defective ExoN (ExoN-AA) have not reverted under diverse experimental conditions. In this study, we identify multiple impediments to MHV-ExoN-AA reversion. We show that ExoN-AA reversion is possible but evolutionarily unfavorable. Instead, compensatory mutations outside of ExoN-AA motif I are more accessible and beneficial than partial reversion. We also show that coevolution between replicase proteins over long-term passage partially compensates for ExoN-AA motif I but renders the virus inhospitable to a reverted ExoN. Our results reveal the evolutionary basis for the genetic stability of ExoN-inactivating mutations, illuminate complex functional and evolutionary relationships between coronavirus replicase proteins, and identify potential mechanisms for stabilization of ExoN-AA coronavirus mutants.

microbiology↗

bioRxiv2019

TCR repertoire analysis reveals effector memory T cells differentiation into Th17 cells in rheumatoid arthritis

The pathogenesis of rheumatoid arthritis (RA), a systemic autoimmune disease characterized by autoreactive T-cell accumulation and pro-inflammatory cytokine overproduction, is unclear. Systematically addressing T-cell receptor (TCR) repertoires of different CD4+ T-cell subsets could help understand RA pathogenesis. Here, peripheral CD4+ T cells from treatment-naive RA patients and healthy controls were sorted into seven subsets including naive, effector, central memory, effector memory (EMT), Th1, Th17, and regulatory T cells. T-cell receptor {beta} chain repertoires were then analyzed by next-generation sequencing. We identified T-cell clonal expansion in EMT and Th17 cells, with highly similar TCR repertoires between them. Ex vivo experiments demonstrated the preferred differentiation from EMT to Th17 cells in RA. Moreover, TCR diversity in subsets including Th17 was negatively correlated with RA disease activity indices such as C-reactive protein and erythrocyte sedimentation rate. Thus, shared and abnormally expanded EMT and Th17 TCR repertoires might be pivotal for RA pathogenesis.

immunology↗

bioRxiv2019

Phenological matching drives wheat pest range shift under climate change

Shifting geographical ranges of crop pests and pathogens in response to climate change pose a threat to food security (1, 2). The orange wheat blossom midge (Sitodiplosis mosellana Gehin) is responsible for significant yield losses in China (3), the worlds largest wheat producer. Here we report that rising temperatures in the North China Plain have resulted in a mean northward range shift of 3.3{degrees} (58.8 km per decade) from the 1950s to 2010s, which accelerated to 91.3 km per decade after 1985 when the highly toxic pesticide hexachlorocyclohexane (HCH) was banned (4). Phenological matching between wheat midge adult emergence and wheat heading in this new expanded range has resulted in greater damage to wheat production. Around $286.5 million worth of insecticides were applied to around 19 million hectares in an attempt to minimize wheat midge damage to crops between 1985 and 2016. Despite use of these pesticides, wheat midge caused losses of greater than 0.95 million metric tons of grain during this period. Our results demonstrate the potential for indirect negative impacts of climate change on crop production and food security, and constitute the first large scale example of plant pest range shift due to global warming.

ecology↗

bioRxiv2019

A Pandas complex adapted for piRNA-guided transposon silencing

The repression of transposons by the Piwi-interacting RNA (piRNA) pathway is essential to protect animal germ cells. In Drosophila ovaries, Panoramix (Panx) enforces transcriptional silencing by binding to the target-engaged Piwi-piRNA complex, although the precise mechanisms by which this occurs remain elusive. Here, we show that Panx functions together with a germline specific paralogue of a nuclear export factor, dNxf2, and its cofactor dNxt1 (p15), as a ternary complex to suppress transposon expression. Structural and functional analyses demonstrate that dNxf2 binds Panx via its UBA domain, which plays an important role in transposon silencing. Unexpectedly, dNxf2 interacts directly with dNxf1 (TAP), a general nuclear export factor. As a result, dNxf2 prevents dNxf1 from binding to the FG repeats of the nuclear pore complex, a process required for proper RNA export. Transient tethering of dNxf2 to nascent transcripts leads to their nuclear retention. Therefore, we propose that dNxf2 may function as a Pandas (Panoramix-dNxf2 dependent TAP/p15 silencing) complex, which counteracts the canonical RNA exporting machinery and restricts transposons to the nuclear peripheries. Our findings may have broader implications for understanding how RNA metabolism modulates epigenetic gene silencing and heterochromatin formation.

molecular biology↗

bioRxiv2019

CD4 T-cell transcriptome expression reversal of the lncRNA-mRNA co-expression network in elite controller vs. normal-process HIV patients

Elite controller refers to a patient with human imunodeficienvcy virus infection with an undetected viral load without anti-viral treatment. Studies on gene expression and regulation in these individuals are limited but significant. We enrolled 196 patients and collected CD4 T-cell samples from two elite controllers, two normal-process infected patients, and two healthy controls to perform second-generation transcriptome sequencing. Using the Cuffdiff model, we identified differentially expressed mRNAs and long non-coding RNAs with corrected P value < 0.05, and constructed a protein-protein interaction network as well a long non-coding RNA-mRNA co-expression network based on the Pearson correlation coefficient. Interestingly, some interactions within the networks were identified as associated with viral infections and immune responses. This was the first study to examine gene transcription in elite controllers and to study their functional relationships. Our results provide a reference for subsequent functional verification at the molecular or cellular level.\n\nAuthor SummarySome individuals can spontaneously inhibit HIV replication after infection with HIV, and thus lack any symptoms. Studies on these patients, termed elite controllers (ECs) will help researchers and clinicians to understand the interrelationship between HIV and the host. In the present study, we focused on the interactions and functional relationships between significantly differentially expressed long non-coding RNAs (lncRNAs) and mRNAs in ECs vs. normal-process patients (NPs). RNA-sequencing was performed for six representative samples of CD4 T-cells. Using the Pearson correlation test, an lncRNA-mRNA co-expression network was constructed. Several new regulatory relationships between transcripts were revealed that might be closely related to the ability of ECs to maintain a low viral load for long periods without anti-viral treatment. For example, lncRNA C3orf35 was upregulated in ECs vs. NPs and was positively related to downregulation of GNG2 mRNA (encoding G protein subunit gamma 2), which functions in chemokine signaling pathways and HIV-1 infection. Overall, we identified certain interesting genetic interactions that will provide information about the mechanism of host suppression of viral replication.

bioinformatics↗

bioRxiv2019

Is microbial activity in tropical forests limited by phosphorus availability? Evidence from a tropical forest in China

The prevailing paradigm for soil microbial activity in tropical forests is that microbial activity is limited by phosphorus (P) availability. Thus, exogenous P addition should increase rates of organic matter decomposition. Studies have also confirmed that soil respiration is accelerated when P is added experimentally. However, we hypothesize that the increased rates of soil microbial respiration could be due to the release of organic material from the surface of soil minerals when P is added, because P is more successful at binding to soil particles than organic compounds. In this study, we demonstrate that P addition to soil is associated with significantly higher dissolved organic carbon (DOC) content in a tropical evergreen forest in southern China. Our results indicate that P fertilization stimulated soil respiration but suppressed litter decomposition. Results from a second sorption experiment revealed that the recovery ratio of added DOC in the soil of a plot fertilized with P for 9 years was larger than the ratio in the soil of a non-fertilized plot, although the difference was small. We also conducted a literature review on the effects of P fertilization on the decomposition rates of litter and soil organic matter at our study site. Previous studies have consistently reported that P addition led to higher response ratios of soil microbial respiration than litter decomposition. Therefore, experiments based on P addition cannot be used to test whether microbial activity is P-limited in tropical forest soils, because organic carbon desorption occurs when P is added. Our findings suggest that the prevailing paradigm on the relationship between P and microbial activity in tropical forest soils should be re-evaluated.

ecology↗

bioRxiv2019

De novo assembly of the Mongolian gerbil genome and transcriptome

BACKGROUNDThe Mongolian gerbil (Meriones unguiculatus) has historically been used as a model organism for the auditory and visual systems, stroke/ischemia, epilepsy and aging related research since 1935 when laboratory gerbils were separated from their wild counterparts. In this study we report genome sequencing, assembly, and annotation further supported by transcriptome data from 27 different tissues samples. FINDINGSThe genome was assembled using Illumina HiSeq 2000 and resulted in a final genome size of 2.54 Gbp with contig and scaffold N50 values of 31.4 Kbp and 500.0 Kbp, respectively. Based on the k-mer estimated genome size of 2.48 Gbp, the assembly appears to be complete. The genome annotation was supported by transcriptome data that identified 36 019 predicted protein-coding genes across 27 tissue samples. A BUSCO search of 3023 mammalian groups resulted in 86% of curated single copy orthologs present among predicted genes, indicating a high level of completeness of the genome. CONCLUSIONSWe report a de novo assembly of the Mongolian gerbil genome that was further enhanced by annotation of transcriptome data from several tissues. Sequencing of this genome increases the utility of the gerbil as a model organism, opening the availability of now widely used genetic tools. The data sets supporting the results of this article are available in the China National GeneBank CNSA repository, Accession id: CNP0000340.

genomics↗

bioRxiv2018

A Strategy Study on Risk Communication of Pandemic Influenza ----A Mental Model Study of College Students in Beijing

Understanding the risk perception of pandemic influenza can improve the risk communication efficiency of the government and ultimately reduce losses caused by the disaster. A mental model interview of 28 individuals who discussed pandemic influenza was analyzed in this paper. The interviewees were college students in Beijing, China who were evaluated to understand their views on the risk perception of pandemic influenza. Referring to the mental model theory, the researchers using Delphi method to identify the key risk factors and concepts to examine the public understanding of these contents; then, the researchers identify the deviations in their understanding so that suggestions and countermeasures have been put forward to enhance the effectiveness of risk communication. Most of the conceptual content was mentioned by most interviewees. However, some interviewees showed misunderstanding including excessive optimism about the consequences of pandemic influenza, a lack of detailed mitigation measures, and negative attitudes toward health education and vaccination. Once faced with threats, this may lead to the failure of risk communication. In Beijing City, the center of domestic and international education, the historical SARS epidemic and this years seasonal flu peak are all hints of the potential risk of a pandemic outbreak. Beijings college students one-sided understanding and misunderstanding of the relevant risk information may increase the risk during an influenza pandemic. The results highlight the necessity for the government to clearly focus on the communication content of the student group, provide an official reference plan for the public and update health education on this topic.

scientific communication and education↗

bioRxiv2018

Beyond a ribosomal RNA methyltransferase, the wider role of MraW in DNA methylation, motility and colonization in Escherichia coli O157:H7

MraW (RsmH) is an AdoMet-dependent 16S rRNA methyltransferase conserved in bacteria and plays a role in the fine-tuning of the ribosomal decoding center. It was recently found to contribute to the virulence of Staphylococcus aureus in host animals. In this study, we examined the function of MraW in Escherichia coli O157:H7 and found that deletion of mraW led to decreased motility and flagellar production. Whole-genome bisulfite sequencing showed genome wide decrease of methylation of 336 genes and 219 promoters in the mraW mutant. The methylation level of 4 flagellar gene sequences were further confirmed by bisulfite PCR sequencing. Quantitative reverse transcription PCR results indicated the transcription of these genes was also affected. MraW was observed to directly bind to the four flagellar gene sequences by electrophoretic mobility shift assay (EMSA). A common motif in differentially methylated regions of promoters and coding regions of the 4 flagellar genes was identified. Reduced methylation was correlated with altered expression of 21 of the 24 genes tested. DNA methylation activity of MraW was confirmed by DNA methyltransferase (DNMT) activity assay in vitro. The mraW mutant colonized poorer than wild type in mice. we further found that the expression of mraZ in the mraW mutant was increased confirming the antagonistic effect of mraW on mraZ. In conclusion, mraW was found to be a DNA methylase and has a wide-ranging effect on E. coli O157:H7 including motility and virulence in vivo via genome wide methylation and mraZ antagonism.\n\nIMPORTANCEMraW is a well-studied 16S rRNA methyltransferase and was recently found have an impact on bacterial virulence. Here we demonstrated its new function as a DNA methylase and effect on motility, colonization in mice, DNA methylation in genome wide and contribution to virulence. Its direct binding of differentially methylated flagellar-encoding DNA sequences was observed, indicating a correlation between DNA methylation and regulation of flagellar genes. In addition, the expression of mraZ which function as an antagonist of mraW was increased in the mraW mutant. mraW plays an important role in gene regulation likely through DNA methylation. Clearly it plays a role in virulence in E. coli O157:H7. It also opens a new research field for virulence study in bacteria.

microbiology↗

bioRxiv2018

Production of very-high-amylose cassava by post-transcriptional silencing of branching enzyme genes

High amylose starch, a desired raw material in the starch industry, can be produced by plants deficient in the function of branching enzymes (BEs). Here we report the production of transgenic cassava plants with starches containing up to 50% amylose due to the constitutive expression of hair-pin dsRNAs targeting the BE1 or BE2 genes. A significant decrease in BE transcripts was confirmed in these transgenic plants by quantitative real-time RT-PCR. The absence of BE1 protein in the BE1-RNAi plant lines (BE1i) and a dramatically lower level of BE2 protein in the BE2-RNAi plant lines (BE2i) were further confirmed by Western blot assays. All transgenic plant lines were grown up in the field, but with reduced biomass production of the above-ground parts and storage roots compared to wild type (WT). Considerably high amylose content in the storage roots of BE2i plant lines was achieved, though not in BE1i plant lines. Storage starch granules of BE1i and BE2i plants had similar morphology as WT, however, the size of BE1i starch granules were bigger than that of WT. Comparisons of amylograms and thermograms of all three sources of storage starches revealed dramatic changes to the pasting properties and a higher melting temperature for BE2i starches. Glucan chain length distribution analysis showed a slight increase in chains of DP>36 in BE1i lines and a dramatic increase in glucan chains between DP 10-20 and DP>40 in BE2i lines, compared to that of WT starch. Furthermore, BE2i starches displayed a B-type X-ray diffraction pattern instead of the A-type pattern found in BE1i and WT starches. Therefore, cassava BE1 and BE2 function differently in storage root starch biosynthesis; silencing of cassava BE1 or BE2 caused various changes to starch physico-chemical properties and amylopectin structure. We also report that remarkably high amylose content in cassava starch has been first obtained in transgenic cassava by silencing of BE2 expression, thus showing a high potential for future industrial utilization.

bioengineering↗

bioRxiv2018

Oxytocin effects on the resting-state mentalizing brain network

Oxytocin(OT) has effects in both human behavior and in the brain, which is not limited in the specific brain area but also with the potential effect on connectivity with other brain regions. Evidence indicate that the effects of OT on human behavior are multifaceted, such as trust behavior, decrease anxiety, empathy and bonding behavior. Since the vital role of mentalizing in understanding others, here we proposed and tested that whether OT has a general effect on theory of mind brain network which is associated to the effect of related social behavioral and personality traits. Used a randomized, double-blind placebo-controlled group design, we investigated the resting-state functional magnetic resonance imaging after intranasal OT or placebo. The functional connectivity (FC) maps with seed in left temporoparietal junction (lTPJ) and right TPJ showed that OT significantly increased connectivity between rTPJ and default attention network (DAN), while decreased the FC between lTPJ and medial prefrontal network (MPN). With implementing machine learning approach, we further reported satisfactory classification accuracy that Identified altered FCs of TPJ can classify OT and PL group. Moreover, individuals empathy trait can modulate the FC between left TPJ and right RECT, which was positively correlated with empathic concern in PL group whereas lTPJ-rRECT negatively correlated in OT group. These results demonstrate that OT has significant effect on FC with lTPJ and rTPJ, brain regions critical for mentalizing, and the empathy concern can modulate the FC. These findings add to our understanding of the neural mechanisms by which OT modulates social behaviors, especially in social interaction involving mentalizing.

neuroscience↗

bioRxiv2018

ICTD: Inference of cell types and deconvolution -- a next-generation deconvolution method for accurate assess cell population and activities in tumor microenvironment.

We developed a novel deconvolution method, namely Inference of Cell Types and Deconvolution (ICTD) that addresses the fundamental issue of identifiability and robustness in current tissue data deconvolution problem. ICTD provides substantially new capabilities for omics data based characterization of a tissue microenvironment, including (1) maximizing the resolution in identifying resident cell and sub types that truly exists in a tissue, (2) identifying the most reliable marker genes for each cell type, which are tissue and data set specific, (3) handling the stability problem with co-linear cell types, (4) co-deconvoluting with available matched multi-omics data, and (5) inferring functional variations specific to one or several cell types. ICTD is empowered by (i) rigorously derived mathematical conditions of identifiable cell type and cell type specific functions in tissue transcriptomics data and (ii) a semi supervised approach to maximize the knowledge transfer of cell type and functional marker genes identified in single cell or bulk cell data in the analysis of tissue data, and (iii) a novel unsupervised approach to minimize the bias brought by training data. Application of ICTD on real and single cell simulated tissue data validated that the method has consistently good performance for tissue data coming from different species, tissue microenvironments, and experimental platforms. Other than the new capabilities, ICTD outperformed other state-of-the-art devolution methods on prediction accuracy, the resolution of identifiable cell, detection of unknown sub cell types, and assessment of cell type specific functions. The premise of ICTD also lies in characterizing cell-cell interactions and discovering cell types and prognostic markers that are predictive of clinical outcomes.

bioinformatics↗

bioRxiv2018

5-Hydroxymethylcytosines from Circulating Cell-free DNA as Diagnostic and Prognostic Markers for Hepatocellular Carcinoma

The lack of highly sensitive and specific diagnostic biomarkers is a major contributor to the poor outcomes of patients with hepatocellular carcinoma (HCC), the second-most common cause of cancer deaths worldwide. We sought to develop a clinically convenient and minimally-invasive approach that can be deployed at scale for the sensitive, specific, and highly reliable diagnosis of HCC, and to evaluate the potential prognostic value of this approach. The study cohort comprised of 2,728 subjects, including HCC patients (n = 1,208), controls (n = 965) (572 healthy individuals and 393 patients with benign lesions), as well as patients with chronic hepatitis B infection (CHB) (n =291), liver cirrhosis (LC) (n = 110), and cholangiocarcinoma (CCC) (n = 154), was recruited from three major liver cancer hospitals in Shanghai, China, from July 2016 to November 2017. Circulating cell-free DNA (cfDNA) were collected from plasma samples from these individuals before surgery or any radical treatment. Applying our 5hmC-Seal technique, the summarized 5-hydroxymethylcytosine (5hmC) profiles in cfDNA were obtained. Molecular annotation analysis suggested that the profiled 5hmC loci in cfDNA were enriched with liver tissue-derived regulatory markers (e.g., H3K4me1). We showed that a weighted diagnostic score (wd-score) based on 117 genes detected using the summarized 5hmC profiles in cfDNA accurately distinguished HCC patients from controls (AUC = 95.1%; 95% CI, 93.6-96.5%) in the validation set, markedly outperformed -fetoprotein (AFP) with superior sensitivity. The wd-scores, which not only detected early BCLC stages (e.g., Stage 0: AUC = 96.2%; 95% CI,94.1-98.4%) and small tumors (e.g., < 2 cm: AUC = 95.7%; 95% CI: 93.6-97.7%), also showed high capacity for distinguishing HCC from non-cancer patients with CHB/LC (AUC = 80.2%; 95% CI, 75.8-84.6%). Moreover, the prognostic value of 5hmC markers in cfDNA was evaluated for HCC recurrence, showing that a weighted prognostic score (wp-score) based on 16 marker genes predicted the recurrence risk (HR = 6.67; 95% CI, 2.81-15.82, p < 0.0001) in 555 patients who have been followed up after surgery. In conclusion, we have developed and validated a robust 5hmC-based diagnostic model that can be applied routinely with clinically feasible amount of cfDNA (e.g., from ~2-5 mL of plasma). Applying this new approach in the clinic could significantly improve the clinical outcomes of HCC patients, for example by early detection of those patients with surgically resectable tumors or as a convenient disease surveillance tool for recurrence.

cancer biology↗

bioRxiv2018

Genome-wide identification and expression specificity analysis of the DNA methyltransferase gene family under adversity stresses in cotton

DNA methylation is an important epigenetic mode of genomic DNA modification that is an important part of maintaining epigenetic content and regulating gene expression. DNA methyltransferases (MTases) are the key enzymes in the process of DNA methylation. Thus far, there has been no systematic analysis the DNA MTases found in cotton. In this study, the whole genome of cotton C5-Mtase coding genes was identified and analyzed using a bioinformatics method based on information from the cotton genome. In this study, 51 DNA MTase genes were identified, of which 8 belonged to G. raimondii (group D), 9 belonged to G. arboretum L. (group A), 16 belonged to G. hirsutum L. (group AD1) and 18 belonged to G. barbadebse L. (group AD2). Systematic evolutionary analysis divided the 51 genes into four subfamilies, including 7 MET homologous proteins, 25 CMT homologous proteins, 14 DRM homologous proteins and 5 DNMT2 homologous proteins. Further studies showed that the DNA MTases in cotton were more phylogenetically conserved. The comparison of their protein domains showed that the C-terminal functional domain of the 51 proteins had six conserved motifs involved in methylation modification, indicating that the protein has a basic catalytic methylation function and the difference in the N-terminal regulatory domains of the 51 proteins divided the proteins into four classes, MET, CMT, DRM and DNMT2, in which DNMT2 lacks an N-terminal regulatory domain. Gene expression in cotton is not the same under different stress treatments. Different expression patterns of DNA MTases show the functional diversity of the cotton DNA methyltransferase gene family. VIGS silenced Gossypium hirsutum l. in the cotton seedling of DNMT2 family gene GhDMT6, after stress treatment the growth condition was better than the control. The distribution of DNA MTases varies among cotton species. Different DNA MTase family members have different genetic structures, and the expression level changes with different stresses, showing tissue specificity. Under salt and drought stress, G. hirsutum L. TM-1 increased the number of genes more than G. raimondii and G. arboreum L. Shixiya 1. The resistance of Gossypium hirsutum L.TM-1 to cold, drought and salt stress was increased after the plants were silenced with GhDMT6 gene.

genomics↗

bioRxiv2018

FRMPD2: a novel GluN2A-interacting scaffold protein in synaptic excitatory transmission

The scaffold proteins FRMPD2 is localized at the basolateral membranes of polarized epithelial cells and associated with tight junction formation. But the expression and function of FRMPD2 in vivo remain unknown. Here, we found that postsynaptic FRMPD2 effectively alters the neuronal excitability by regulating NMDARs-component excitatory synaptic transmission in adult hippocampus. FRMPD2 anchors the NMDAR subunit GluN2A at the synapses without changing the total NMDAR expression. By using of Co-IP, Pull Down and SPR, the second PDZ (PDZ2) domain of FRMPD2 direct and binds to the C-terminus of GluN2A. Our study discover that a novel scaffold protein FRMPD2 regulates synaptic excitatory in a PDZ2 domain-dependent manner in adult hippocampus.

neuroscience↗

bioRxiv2018

Molecular Mechanisms Governing Shade Responses in Maize

Light is one of the most important environmental factors affecting plant growth and development. Plants use shade avoidance and shade tolerance strategies to adjust their growth and development thus increase their success in the competition for incoming light. To investigate the mechanism of shade responses in maize (Zea mays), we examined the anatomical and transcriptional dynamics of the early shade response in seedlings of the B73 inbred line. Transcriptome analysis identified 912 differentially expressed genes, including genes involved in light signaling, auxin responses, and cell elongation pathways. Grouping transcription factor family genes and performing enrichment analysis identified multiple types of transcription factors that are differentially regulated by shade and predicted putative core genes responsible for regulating shade avoidance syndrome. For functional tests, we ectopically over-expressed ZmHB53, a type II HD-ZIP transcription factor gene significantly induced by shade, in Arabidopsis thaliana. Transgenic Arabidopsis plants overexpressing ZmHB53 exhibited narrower leaves, earlier flowering, and enhanced expression of shade-responsive genes, suggesting that ZmHB53 participates in the regulation of shade responses in maize. This study increases our understanding of the regulatory network of the shade response in maize and provides a useful resource for maize genetics and breeding.\n\nHighlightOur findings not only increase the understanding of the regulatory network of the shade avoidance in maize, and also provide a useful resource for maize genetics and breeding.

plant biology↗