Biology subjects

Yue, L.

Publications and source records attributed to Yue, L..

32 records · Page 2Linked to original sources

bioRxiv2022

Phospholipase Cβ2 Promotes Vascular Endothelial Growth Factor Induced Vascular Permeability

BackgroundRegulation of vascular permeability (VP) is critical to maintaining tissue metabolic homeostasis. Vascular endothelial growth factor (VEGF) is a key stimulus of VP in acute and chronic diseases including ischemia reperfusion injury, sepsis and cancer. Identification of novel regulators of VP would allow for the development of effective targeted therapeutics for patients with unmet medical need. MethodsIn vitro and in vivo models of VEGFA-induced vascular permeability, pathological permeability, quantitation of intracellular calcium release and cell entry, and PIP2 levels were evaluated with and without modulation of PLC{beta}2. ResultsGlobal knock-out of PLC{beta}2 in mice resulted in blockade of VEGFA-induced vascular permeability in vivo and trans-endothelial permeability in primary lung endothelial cells. Further work in an immortalized human microvascular cell line modulated with stable knock-down of PLC{beta}2 recapitulated the observations in the mouse model and primary cell assays. Additionally, loss of PLC{beta}2 limited both intracellular release and extracellular entry of calcium following VEGF stimulation as well as reduced basal and VEGFA-stimulated levels of PIP2 compared to control cells. Finally, loss of PLC{beta}2 in both a hyperoxia induced lung permeability model and a cardiac ischemia:reperfusion model resulted in improved animal outcomes when compared to WT controls. ConclusionsThe results implicate PLC{beta}2 as a key positive regulator of VEGF-induced VP through regulation of both calcium flux and PIP2 levels at the cellular level. Targeting of PLC{beta}2 in a therapeutic setting may provide a novel approach to regulating vascular permeability in patients. Graphic Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY HighlightsO_LIPLC{beta}2 promotes VEGFA induced vascular permeability. C_LIO_LILoss of PLC{beta}2 prevents VEGFA vascular permeability via repression of cellular calcium flux and membrane PIP2 levels. C_LIO_LILoss of PLC{beta}2 reduces vascular permeability and improves outcomes in a hyperoxic lung damage model and a cardiac ischemia:reperfusion model in vivo. C_LIO_LITargeting PLC{beta}2 inhibition may lead to a novel therapeutic for diseases such as stroke and myocardial infarction. C_LI

cell biology↗

bioRxiv2021

Replication Study: RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth

As part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Bhargava et al., 2016) that described how we intended to replicate selected experiments from the paper "RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth" (Hatzivassiliou et al., 2010). Here we report the results. We found two unrelated RAF inhibitors, PLX4720 or GDC-0879, selectively inhibited BRAF(V600E) cell proliferation, while the MEK inhibitor, PD0325901, inhibited BRAF(V600E), wild-type RAF/RAS, and mutant RAS cancer cell proliferation, similar to the original study (Figure 1A; Hatzivassiliou et al., 2010). We found knockdown of CRAF, but not BRAF, in mutant RAS cells attenuated the phospho-MEK induction observed after PLX4720 treatment, similar to the original study (Figure 2B; Hatzivassiliou et al., 2010). The original study reported analogous results with GDC-0879, which was not observed in this replication, although unexpected control results confound the interpretation. We also attempted a replication of an assay with recombinant proteins to test the differential effect of RAF inhibitors on BRAF-CRAF heterodimerization (Figure 4A; Hatzivassiliou et al., 2010). Although we were unable to conduct the experiment as planned, we observed differential binding of BRAF by RAF inhibitors; however, it was between BRAF and beads, independent of CRAF. While these data were unable to address whether, under the conditions of the original study, the same observations could be observed, we discuss key differences between the original study and this replication that are important to consider for further experiments. Finally, where possible, we report meta-analyses for each result. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=62 SRC="FIGDIR/small/470372v2_fig1.gif" ALT="Figure 1"> View larger version (7K): org.highwire.dtl.DTLVardef@1f77d0eorg.highwire.dtl.DTLVardef@1333494org.highwire.dtl.DTLVardef@c10824org.highwire.dtl.DTLVardef@fda30f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Cellular dose response curves for RAF and MEK inhibitors in BRAF(V600E), mutant RAS, and wild-type RAF/RAS cell lines Cell viability assays were performed for RAF inhibitors (PLX4720 and GDC-0879) and MEK inhibitor (PD0325901) against A375, (BRAF(V600E)), HCT116 (mutant RAS), and MeWo (wild-type RAF/RAS) cells. Absolute half-maximum effective concentration (EC50) values ({micro}M) were determined for each biological repeat. EC50 values unable to be accurately estimated are reported as either >20 {micro}M or <0.078 {micro}M, which are the largest and smallest doses tested, respectively. Absolute EC50 values for each biological repeat for A375, HCT116, and MeWo cells treated with (A) PLX4720, (B) GDC-0879, or (C) PD0325901 for this replication attempt are plotted with the EC50 value reported in Hatzivassiliou et al. (2010) displayed as a single point (red triangle) for comparison. Where possible the mean and 95% confidence interval of the replication data are shown. Additional details for this experiment can be found at https://osf.io/52zp9/. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/470372v2_fig2.gif" ALT="Figure 2"> View larger version (34K): org.highwire.dtl.DTLVardef@1dc3058org.highwire.dtl.DTLVardef@e9f5d9org.highwire.dtl.DTLVardef@baf5eorg.highwire.dtl.DTLVardef@126717a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO Cellular dose response curves for each biological repeat This is the same experiment as in Figure 1. The dose response curve of each biological repeat [n=4] for A375, HCT116, and MeWo cells treated with (A) PLX4720, (B) GDC-0879, or (C) PD0325901 for this replication attempt are plotted. Additional details for this experiment can be found at https://osf.io/52zp9/. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/470372v2_fig4.gif" ALT="Figure 4"> View larger version (33K): org.highwire.dtl.DTLVardef@e4357eorg.highwire.dtl.DTLVardef@73e9ceorg.highwire.dtl.DTLVardef@1fb01c6org.highwire.dtl.DTLVardef@31a799_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 4.C_FLOATNO Testing of BRAF and CRAF antibodies used in original study The BRAF and CRAF antibodies reported in the original study (Hatzivassiliou et al., 2010) were tested for suitability by Western blot. (A) Representative Western blots and Ponceau-stained membrane (experiment performed independently 3 times) of 0.5 {micro}g of purified recombinant BRAF kinase domain (KD). Membranes were probed with the BRAF antibody used in the original study (RRID:AB_1840330) or with a different BRAF antibody used in this replication attempt (RRID:AB_2721113). (B) Representative Western blots and Ponceau-stained membrane (experiment performed independently 3 times) of 0.5 {micro}g of purified recombinant GST tagged CRAF KD. Membranes were probed with the CRAF antibody used in the original study (RRID:AB_397552) or with a different CRAF antibody used in this replication attempt (RRID:AB_10989977). (C) Representative Western blots (experiment performed once) of 16 {micro}g of whole cell lysates from the indicated human cell lines. Membranes were probed with the BRAF (RRID:AB_1840330) or CRAF (RRID:AB_397552) antibodies used in the original study. (D) Screenshot from the Constraint-based Multiple Alignment Tool (COBALT) (Papadopoulos and Agarwala, 2007) showing the alignment of full-length BRAF (NCBI Reference Sequence: NP_004324.2), the region of BRAF used as the immunogenic peptide used to generate the BRAF antibody used in the original study (RRID:AB_1840330), the BRAF KD used in this replication attempt, and the BRAF KD used in the original study. (E) Screenshot from COBALT showing the alignment of full-length CRAF (NCBI Reference Sequence: NP_002871.1), the region of CRAF used as the immunogenic peptide used to generate the CRAF antibody used in the original study (RRID:AB_397552), and the CRAF KD used in the original study and this replication attempt. Additional details for this experiment can be found at https://osf.io/6f3sk/. C_FIG

cancer biology↗

bioRxiv2021

Oxalic acid binds to gustatory receptor Gr23a and inhibits feeding in the brown planthopper

Plants produce diverse secondary compounds as natural protection against microbial and insect attack. Most of these compounds, including bitters and acids, are sensed by insect gustatory receptors (Grs). Acids are potentially toxic to insects, but there are few reports on sour compounds as ligands of insect Grs. Here, using two different heterologous expression systems, the insect Sf9 cell line and the mammalian HEK293T cell line, we started from crude extracts of rice (Oryza sativa) and successfully identified oxalic acid (OA) as a ligand of NlGr23a, a Gr in the brown planthopper Nilaparvata lugens. The antifeedant effect of OA on the brown planthopper was dose dependent, and NlGr23a is essential for OAs antifeedant activity in both artificial diets and rice plants. NlGr23a is also indispensable for tarsal OA sensing. To our knowledge, OA is the first identified ligand starting from plant crude extracts and the first known strong acid for insect Grs. These findings on rice-planthopper interactions will be of broad interest for pest control in agriculture and also for better understanding of how insects select host plants. Research organismNilaparvata lugens

ecology↗

bioRxiv2021

TRPM2 deficiency protects against atherosclerosis by inhibiting TRPM2-CD36 inflammatory axis in macrophages

Atherosclerosis is the major cause of ischemic heart diseases and ischemic brain stroke, which are the leading causes of mortality worldwide. The central pathological features of atherosclerosis include macrophage infiltration and foam cell formation. However, the detailed mechanisms regulating these two processes remain unclear. Here we show that oxidative stress-activated Ca2+-permeable TRPM2 plays a key role in the pathogenesis of atherosclerosis. Trpm2 deletion produces a potent protective effect against atherosclerosis in ApoE-/- mice fed with a high-fat diet (HFD), as evidenced by reduced atherosclerotic plaque burden, decreased macrophage load and suppressed inflammasome activation in the vessel wall. Moreover, we show that Trpm2 deletion or inhibition reduces oxidized low-density lipoprotein (oxLDL) uptake by macrophages, suppresses macrophage infiltration induced by monocyte chemoattractant protein-1 (MCP1), and prevents the impairment of macrophage emigration caused by oxLDL. Intriguingly, we uncover that activation of CD36, an oxLDL receptor, can promote the activation of TRPM2, and vice versa, the CD36-mediated inflammatory cascade in atherosclerosis is dependent on TRPM2. In transfected HEK293T cells, CD36 ligands oxLDL and TSP1 induce TRPM2 activation in a CD36-dependent manner. Deleting Trpm2 or inhibiting TRPM2 activity in cultured macrophages suppresses the CD36 signaling cascade induced by oxLDL and TSP1. Our studies establish TRPM2-CD36 axis as a new mechanism underlying atherogenesis, and suggest TRPM2 as an effective therapeutic target for atherosclerosis. HIGHLIGHTSO_LITrpm2 deletion protects against atherosclerosis in ApoE-/- mice fed with a high-fat diet (HFD) C_LIO_LITrpm2 deficiency reduces atherosclerotic lesions by minimizing foam cell formation, inhibiting macrophage infiltration and preserving macrophage emigration C_LIO_LITRPM2 activation is required for CD36-induced oxLDL uptake and subsequent inflammatory responses C_LIO_LIThe ligands of CD36, oxLDL and TSP1, activate TRPM2, thereby perpetuating TRPM2-CD36 inflammatory cycle in atherogenesis cascade C_LIO_LIOur data establish TRPM2-CD36 axis as a new atherogenesis mechanism and TRPM2 as a novel therapeutic target for atherosclerosis C_LI O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY TRPM2-mediated Ca2+ signal is essential for CD36 induced oxLDL uptake and atherosclerosis in ApoE-/- mice fed with a high-fat diet (HFD). The activation of CD36 and TRPM2 form a positive feedback loop in atherogenesis. C_FIG_DISPLAY

physiology↗

bioRxiv2021

Functional coupling of TRPM2 and NMDARs exacerbates excitotoxicity in ischemic brain injury

Excitotoxicity caused by NMDA receptors (NMDARs) is a major cause of neuronal death in ischemic stroke. However, past efforts of directly targeting NMDARs have unfortunately failed in clinical ischemic stroke trials. Here we reveal an unexpected mechanism underlying NMDARs-mediated neurotoxicity, which leads to identification of a novel target and development of an effective therapeutic peptide for ischemic stroke. We show that NMDARs excitotoxicity upon ischemic insults is mediated by physical and functional coupling to TRPM2. The physical interaction of TRPM2 with NMDARs results in markedly increase in the surface expression of NMDARs, leading to enhanced NMDAR function and increased neuronal death. We identified a specific NMDAR-interacting domain on TRPM2, and developed a cell-permeable peptide to uncouple TRPM2-NMDARs. The disrupting-peptide protects neurons against ischemic injury in vitro and protects mice against ischemic stroke in vivo. These findings provide an unconventional strategy to eliminate excitotoxic neuronal death without directly targeting NMDARs. HIGHLIGHTSO_LITRPM2 physically and functionally interacts with NMDARs C_LIO_LIInteraction of TRPM2 with NMDARs exacerbates NMDARs extrasynaptic excitotoxicity by increasing NMDARs surface expression during ischemic injury C_LIO_LITRPM2 recruits PKC{gamma} to the interacting complexes to increase NMDARs surface expression C_LIO_LIUncoupling the interaction between TRPM2 and NMDARs with a disrupting peptide (TAT-EE3) protects neurons against ischemic stroke in vitro and in vivo C_LI GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=175 HEIGHT=200 SRC="FIGDIR/small/454247v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@e618c5org.highwire.dtl.DTLVardef@646350org.highwire.dtl.DTLVardef@b4478corg.highwire.dtl.DTLVardef@1c5742f_HPS_FORMAT_FIGEXP M_FIG C_FIG TRPM2 excerbates NMDARs excitotoxicity by physically and functionally interacting with NMDARs. The disrupting pipette TAT-EE3 protects neurons against ischemic injury in vitro and in vivo.

neuroscience↗

bioRxiv2021

aCPSF1 in synergy with terminator U-tract dictates archaeal transcription termination efficiency via the KH domains recognizing U-tract

Recently, aCPSF1 was reported to function as the long-sought global transcription termination factor of archaea, while the working mechanism remains elusive. This work, through analyzing transcript-3'end-sequencing data of Methanococcus maripaludis, found positive correlations of both the terminator uridine(U)-tract and aCPSF1 with hierarchical transcription termination efficiencies (TTEs) at the genome-wide level. In vitro assays determined that aCPSF1 specifically binds to the terminator U-tract with U-tract number-related binding abilities, and in vivo assays demonstrated the two are indispensable in dictating high TTEs, revealing that aCPSF1 and the terminator U-tract in synergy determine high TTEs. The N-terminal KH domains equip aCPSF1 of specific binding to terminator U-tract and the in vivo aCPSF1-terminator U-tract synergism; aCPSF1s nuclease activity was also required for TTEs. aCPSF1 also functioned as back-up termination for transcripts with weak intrinsic terminator signals. aCPSF1 orthologs from Lokiarchaeota and Thaumarchaeota exhibited similar U-tract synergy in dictating TTEs. Therefore, aCPSF1 and the intrinsic U-rich terminator could work in a noteworthy two-in-one termination mode in Archaea, which could be widely employed by archaeal phyla; using one factor recognizing U-rich terminator signal and cleaving transcript 3'-end, the archaeal aCPSF1-dependent transcription termination could display a simplified archetypal mode of the eukaryotic RNA polymerase II termination machinery.

microbiology↗

bioRxiv2021

Three bacterium-plasmid golden combinations facilitate the spread of ST11/CG258 carbapenemase-producing Klebsiella pneumoniae in China

Carbapenemase-producing Klebsiella pneumoniae (cpKP) poses serious threats to public health. Previous studies showed that only ST11/CG258-cpKP successfully disseminated in China, however, the underlying genetic bases are still unknown. We conducted a comprehensive genomic-epidemiology analysis on 420 cpKP isolates from 70 hospitals in 24 Chinese provinces during 2009-2017 based on short-/long-reads sequencing. Three golden combinations of host--blaKPC-carrying plasmids (Clade 3.1+3.2--IncFIIpHN7A8, Clade 3.1+3.2--IncFIIpHN7A8:IncR, Clade 3.3--IncFIIpHN7A8:IncpA1763-KPC) endowed cpKP with advantages both in genotypes (strong-correlation/co-evolution) and phenotypes (resistance/growth/competition), thereby facilitating nationwide spread of ST11/CG258-cpKP. Intriguingly, Bayesian skyline illustrated that the three golden combinations might directly lead to the strong population expansion during 2007-2008 and subsequent maintenance of the dissemination of ST11/CG258-cpKP after 2008. We tested drug-resistance profiles and proposed combination treatment regimens for CG258/non-CG258 cpKP. Our findings systematically revealed the molecular-epidemiology and genetic-basis for dissemination of Chinese ST11/CG258 cpKP and reminded us to monitor the golden combinations of cpKP- plasmid closely.

microbiology↗

bioRxiv2020

Precision methylome and in vivo methylation kinetics characterization of Klebsiella pneumoniae

Klebsiella pneumoniae (K. pneumonia) is an important pathogen that can cause severe hospital-/community-acquired infections. To panoramically analyze K. pneumoniaes methylation features, we completed the whole genome sequences of 14 K. pneumoniae strains covering various serotypes, multilocus-sequence typings (MLSTs), clonal groups (CG), viscosity/virulence and drug-resistances, and further characterized their methylomes using PacBio-SMRT and bisulfite technologies. We identified 15 methylation motifs (13 6mA and two 5mC motifs), among which eight were novel ones. Their corresponding MTases were further validated. Additionally, we analyzed the genomic distribution of GATC and CCWGG methylation motifs shared by all strains, and identified differential distributive patterns of some hemi/un-methylated GATC motifs tending to locate in the intergenic regions (IGRs). Specifically, we characterized the in vivo methylation kinetics at single-base resolution on a genome-wide scale by simulating the dynamic processes of replication-mediated passive demethylation and MTase-catalyzed re-methylation. The slower methylation-rates of the GATC motifs in the replication origins (oriC) and IGRs suggest an epigenetic mechanism implicated in the regulation of replication-initiation and transcription. Our findings illustrate the first comprehensive dynamic methylome map of K. pneumonia at single base resolution, and provide an efficient means and important reference for a better understanding of epigenetic regulation in bacteria.

genomics↗

bioRxiv2020

The oriental fruit moth genome provides insights into evolutionary adaptation of tortricid pests

Moths of the family Tortricidae (Insecta: Lepidoptera) usually distribute in temperate and tropical high upland regions. The oriental fruit moth (OFM) Grapholita molesta is a globally important pest of stone and pome fruit from this family. In this study, we assembled a chromosome-level genome for the OFM and conducted a comparative genomic analysis with other lepidopterans. This genome was assembled to 28 chromosomes with a size of 517.71 Mb, an N50 of 19.5 Mb, and a BUSCO completeness of 97.1%. In total, 19968 protein-coding genes were predicted, among which 15269 were functionally annotated. We manually annotated ten gene families for 13 representative genomes from the Lepidopteran. In general, two tortricid moths have a moderate number of detoxification and receptor genes and the lowest number of HSP genes, congruent with their polyphagous dietary and pattern of distribution. However, the OFM has the highest number of P450, I Rs and ORs among all species. Compared to the other tortricid species of the codling moth Cydia pomonella, the OFM has more genes in all gene families. Our results indicate that the high number of some detoxification and receptor genes may be related to the strong adaptation of OFM as a global pest. The high-quality genome of OFM provides an invaluable resource for understanding the ecology, genetics, and evolution of tortricid moths.

genomics↗

bioRxiv2020

Fertility-LightGBM: A fertility-related protein prediction model by multi-information fusion and light gradient boosting machine

The identification of fertility-related proteins plays an essential part in understanding the embryogenesis of germ cell development. Since the traditional experimental methods are expensive and time-consuming to identify fertility-related proteins, the purposes of predicting protein functions from amino acid sequences appeared. In this paper, we propose a fertility-related protein prediction model. Firstly, the model combines protein physicochemical property information, evolutionary information and sequence information to construct the initial feature space ALL. Then, the least absolute shrinkage and selection operator (LASSO) is used to remove redundant features. Finally, light gradient boosting machine (LightGBM) is used as a classifier to predict. The 5-fold cross-validation accuracy of the training dataset is 88.5%, and the independent accuracy of the training dataset is 91.5%. The results show that our model is more competitive for the prediction of fertility-related proteins, which is helpful for the study of fertility diseases and related drug targets.

bioinformatics↗

bioRxiv2020

Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth in the Context of a CD8 T-Cell Mediated HIV Response

Predictive models are becoming more and more commonplace as tools for candidate antigen discovery to meet the challenges of enabling epitope mapping of cohorts with diverse HLA properties. Here we build on the concept of using two key parameters, diversity metric of the HLA profile of individuals within a population and consideration of sequence diversity in the context of an individuals CD8 T-cell immune repertoire to assess the HIV proteome for defined regions of immunogenicity. Using this approach, Analysis of HLA adaptation and functional immunogenicity data enabled the identification of regions within the proteome that offer significant conservation, HLA recognition within a population, low prevalence of HLA adaptation and demonstrated immunogenicity. We believe this unique and novel approach to vaccine design that, in combination with in vitro functional assays, offers a bespoke pipeline for expedited and rational CD8 T-cell vaccine design for HIV and potentially other pathogens with the potential for both global and local coverage.

immunology↗

bioRxiv2020

DPHL: A pan-human protein mass spectrometry library for robust biomarker discovery using Data-Independent Acquisition and Parallel Reaction Monitoring

To answer the increasing need for detecting and validating protein biomarkers in clinical specimens, proteomic techniques are required that support the fast, reproducible and quantitative analysis of large clinical sample cohorts. Targeted mass spectrometry techniques, specifically SRM, PRM and the massively parallel SWATH/DIA technique have emerged as a powerful method for biomarker research. For optimal performance, they require prior knowledge about the fragment ion spectra of targeted peptides. In this report, we describe a mass spectrometric (MS) pipeline and spectral resource to support data-independent acquisition (DIA) and parallel reaction monitoring (PRM) based biomarker studies. To build the spectral resource we integrated common open-source MS computational tools to assemble an open source computational workflow based on Docker. It was then applied to generate a comprehensive DIA pan-human library (DPHL) from 1,096 data dependent acquisition (DDA) MS raw files, and it comprises 242,476 unique peptide sequences from 14,782 protein groups and 10,943 SwissProt-annotated proteins expressed in 16 types of cancer samples. In particular, tissue specimens from patients with prostate cancer, cervical cancer, colorectal cancer, hepatocellular carcinoma, gastric cancer, lung adenocarcinoma, squamous cell lung carcinoma, diseased thyroid, glioblastoma multiforme, sarcoma and diffuse large B-cell lymphoma (DLBCL), as well as plasma samples from a range of hematologic malignancies were collected from multiple clinics in China, the Netherlands and Singapore and included in the resource. This extensive spectral resource was then applied to a prostate cancer cohort of 17 patients, consisting of 8 patients with prostate cancer (PCa) and 9 with benign prostate hyperplasia (BPH), respectively. Data analysis of DIA data from these samples identified differential expressions of FASN, TPP1 and SPON2 in prostate tumors. Thereafter, PRM validation was applied to a larger PCa cohort of 57 patients and the differential expressions of FASN, TPP1 and SPON2 in prostate tumors were validated. As a second application, the DPHL spectral resource was applied to a patient cohort consisting of samples from 19 DLBCL patients and 18 healthy individuals. Differential expressions of CRP, CD44 and SAA1 between DLBCL cases and healthy controls were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supported that DIA-PRM MS pipeline enables robust protein biomarker discoveries.

bioinformatics↗

bioRxiv2019

aCPSF1 controlled archaeal transcription termination: a prototypical eukaryotic model

Transcription termination defines RNA 3'-ends and guarantees programmed transcriptomes, thus is an essential biological process for life. However, transcription termination mechanisms remain almost unknown in Archaea. Here reported the first general transcription termination factor of Archaea, the conserved ribonuclease aCPSF1, and elucidated its 3'-end cleavage dependent termination mechanism. Depletion of Mmp-aCPSF1 in a methanoarchaeon Methanococcus maripaludis caused a genome-wide transcription termination defect and overall transcriptome chaos, and cold-sensitive growth. Transcript-3'end-sequencing (Term-seq) revealed transcriptions mostly terminated downstream of a uridine-rich terminator motif, where Mmp-aCPSF1 performed cleavage. The endoribonuclease activity was determined essential to terminate transcription in vivo as well. Through super-resolution photoactivated localization microscopy imaging, co-immunoprecipitation, and chromatin immunoprecipitation, we demonstrated that Mmp-aCPSF1 localizes within nucleoid and associates with RNAP and chromosomes. aCPSF1 appears to co-evolve with archaeal RNAPs, and two distant orthologs each from Lokiarchaeota and Thaumarchaeota could replace Mmp-aCPSF1 to termination transcription. Thus, aCPSF1 dependent termination mechanism could be universally employed in Archaea, including Lokiarchaeota, one supposed archaeal ancestor of Eukaryotes. Therefore, the reported aCPSF1 cleavage-dependent termination mode not only hints an archetype of Eukaryotic 3'-end processing/cleavage triggered RNAP II termination, but also would shed lights on understanding the complex eukaryotic termination based on the simplified archaeal model.

microbiology↗

bioRxiv2017

The depletion of MARVELD1 leads to placenta accreta via integrin β4-dependent trophoblast cell invasion

AstractThe mammalian placenta is a remarkable organ. It serves as the interface between the mother and the fetus. Proper invasion of trophoblast cells into the maternal decidua is required for a successful pregnancy. Previous studies have found that the adhesion molecule integrin {beta}4 plays important roles during trophoblast cell invasion. Here, we found that the overall birth rate of the MARVELD1 knockout mouse is much lower than that of the wild-type mouse (P<0.001). In E18.5 MARVELD1 knockout mice, we observed an over-invasion of trophoblast cells, and indeed, the pregnant mice had a partial placenta accreta phenotype. The HTR8/SVneo cell line was used as an in vitro model to elucidate the underlying mechanisms of MARVELD1-mediated trophoblast invasion. We detected a diminished expression of integrin {beta}4 upon the downregulation of MARVELD1 and enhanced migration and invasive abilities of trophoblast cells both in vivo and in vitro. The integrin {beta}4 rescue assay also supported the results. In conclusion, this study found that MARVELD1 mediated the invasion of trophoblast cells via regulating the expression of integrin {beta}4.

developmental biology↗