Biology subjects

Qi, L.

Publications and source records attributed to Qi, L..

At least 73 records · Page 4Linked to original sources

bioRxiv2021

An inactivated multivalent influenza A virus vaccine is broadly protective in mice and ferrets

Influenza A viruses (IAVs) present major public health threats from annual seasonal epidemics, from pandemics caused by novel virus subtypes, and from viruses adapted to a variety of animals including poultry, pigs and horses. Vaccines that broadly protect against all such IAVs, so-called "universal" influenza vaccines, do not currently exist, but are urgently needed. This study demonstrates that an inactivated, multivalent whole virus vaccine, delivered intramuscularly or intranasally, is broadly protective against challenges with multiple IAV HA/NA subtypes in both mice and ferrets, including challenges with IAV subtypes not contained in the vaccine. This vaccine approach indicates the feasibility of eliciting broad "universal" IAV protection, and identifies a promising candidate for influenza vaccine clinical development. One-Sentence SummaryAn inactivated, whole avian influenza virus vaccine delivered intramuscularly or intranasally provides extremely broad protection against antigenically divergent viral challenge and is a promising candidate for a "universal" influenza virus vaccine.

microbiology↗

bioRxiv2021

The rs1421085 variant within FTO promotes but not inhibits thermogenesis and is potentially associated with human migration

Disease-associated GWAS loci are predominantly scattered among noncoding regions of the human genome, which impedes causality estimation. One lead risk signal of obesity-rs1421085 T>C within the FTO gene-is reported to functional in vitro but lack of organismal evidence. Here, we established global and the brown-adipocyte specific locus-knock-in mice to recapitulate this homologous variant in humans, and discovered the minor allele (C-allele) as one candidate thermogenic locus. Mice carrying the C-alleles showed increased thermogenic capacity and a resistance to high-fat diet-induced adiposity. In terms of mechanism, the knock-in models showed enhanced FTO expression, while FTO knockdown or inhibition effectively eliminated the increased thermogenic ability of brown adipocytes. In humans, the C-allele was associated with lower birthweight, and its allele frequency increases following the environmental temperature decreases. Cumulatively, these findings demonstrated rs1421085 T>C as a functional variant regulating whole-body thermogenesis, and this variation was possibly related to early human migration from hot to cold environments.

genetics↗

bioRxiv2021

Annealing synchronizes the 70S ribosome into a minimum-energy conformation

Researchers commonly anneal metals, alloys, and semiconductors to repair defects and improve microstructures via recrystallization. Theoretical studies indicate simulated annealing on biological macromolecules helps predict the final structures with minimum free energy. Experimental validation of this homogenizing effect and further exploration of its applications are fascinating scientific questions that remain elusive. Here, we chose the apo-state 70S ribosome from Escherichia coli as a model, wherein the 30S subunit undergoes a thermally driven inter-subunit rotation and exhibits substantial structural flexibility as well as distinct free energy. We experimentally demonstrate that annealing at a fast cooling rate enhances the 70S ribosome homogeneity and improves local resolution on the 30S subunit. After annealing, the 70S ribosome is in a nonrotated state with respect to corresponding intermediate structures in unannealed or heated ribosomes, and exhibits a minimum energy in the free energy landscape. One can readily crystallize these minimum-energy ribosomes, which have great potential for synchronizing proteins on a single-molecule level. Our experimental results are consistent with theoretical analysis on the temperature-dependent Boltzmann distribution, and offer a facile yet robust approach to enhance protein stability, which is ideal for high-resolution cryogenic electron microscopy. Beyond structure determination, annealing can be extended to study protein folding and explore conformational and energy landscape. Significance statementIn metallurgy, annealing heats a metal or alloy to a predetermined temperature, holding for a certain time, and then cooling to room temperature to change the physical and sometimes also the chemical properties of the material. Researchers introduce the similar concept as simulated annealing to predict minimum-energy conformations of biological macromolecules. In this work, we experimentally verify that annealing at a fast cooling rate can synchronize the 70S ribosome into a nonrotated state with a minimum energy in the free energy landscape. Our results not only offer a facile yet robust approach to stabilize proteins for high-resolution structural analysis, but also contribute to the understanding of protein folding and temperature adaptation.

biophysics↗

bioRxiv2021

Notch-Induced Endoplasmic Reticulum-Associated Degradation Governs Thymocyte β-Selection

Signals from the pre-T cell receptor and Notch coordinately instruct {beta}-selection of CD4-CD8- double negative (DN) thymocytes to generate {beta} T cells in the thymus. However, how these signals ensure a high-fidelity proteome and safeguard the clonal diversification of the pre- selection TCR repertoire given the considerable translational activity imposed by {beta}-selection is largely unknown. Here, we identify the endoplasmic reticulum (ER)-associated degradation (ERAD) machinery as a critical proteostasis checkpoint during {beta}-selection. Expression of the SEL1L-HRD1 complex, the most conserved branch of ERAD, is directly regulated by the transcriptional activity of the Notch intracellular domain. Deletion of Sel1l impaired DN3 to DN4 thymocyte transition and severely impaired {beta} T cell development. Mechanistically, Sel1l deficiency induced unresolved ER stress that triggered thymocyte apoptosis through the PERK pathway. Accordingly, genetically inactivating PERK rescued T cell development from Sel1l- deficient thymocytes. Our study reveals a critical developmental signal controlled proteostasis mechanism that enforces T cell development to ensure a healthy adaptive immunity.

immunology↗

bioRxiv2021

In vivo co-registered hybrid-contrast imaging by successive photoacoustic tomography and magnetic resonance imaging

Magnetic resonance imaging (MRI) and photoacoustic tomography (PAT) are two advanced imaging modalities that offer two distinct image contrasts: MRI has a multi-parameter contrast mechanism that provides excellent anatomical soft tissue contrast, whereas PAT is capable of mapping tissue physiological metabolism and exogenous contrast agents with optical specificity. Attempts have been made to integrate these two modalities, but rigid and reliable registration of the images for in vivo imaging is still challenging. In this paper, we present a complete hardware-software solution for the successive acquisition and co-registration of PAT and MRI images in in vivo animal studies. Based on commercial PAT and MRI scanners, our solution includes a 3D-printed dual-modality animal imaging bed, a 3-D spatial image co-registration algorithm with bi-model markers, and a robust modality switching protocol for in vivo imaging studies. Using the proposed solution, we successfully demonstrated co-registered hybrid-contrast PAT-MRI imaging that simultaneously display multi-scale anatomical, functional and molecular characteristics on healthy and cancerous living mice. Week-long longitudinal dual-modality imaging of tumor development reveals information on size, border, vascular pattern, blood oxygenation, and molecular probe metabolism of the tumor micro-environment at the same time. Additionally, by incorporating soft-tissue information in the co-registered MRI image, we further show that PAT image quality could be enhanced by MRI-guided light fluence correction. The proposed methodology holds the promise for a wide range of pre-clinical research applications that benefit from the PAT-MRI dual-modality image contrast.

bioengineering↗

bioRxiv2020

Genome-Wide Mapping of Cisplatin Damaged Gene Loci

Cisplatin is a DNA targeting anticancer drug, yet its damaged gene loci have remained unclear. In the present work, combining affinity isolation and high throughput sequencing, we genome-widely mapped 17729 gene loci containing platination lesions, which mainly function as enzymes, transcription regulators, transporters and kinases, and of which 445 genes account for 71% of potential gene targets for cancer therapy reported in the literature. The most related core signaling pathway, disease and tissue toxicity of 7578 genes with an enrichment fold (EFG) of >12, where EFG refers to the ratio of total read counts of a gene detected in cells with and without cisplatin treatment, are sperm motility, cancer and hepatotoxicity with association P values of < 1x10-22. Among 616 kinase genes damaged by cisplatin, 427 are protein kinases which account for 82% of putative protein kinases, suggesting that cisplatin may act as broad-spectrum protein kinase inhibitor. Western Blot assays verified that expression of 8 important protein kinase genes was significantly reduced due to cisplatin damage. SPAG9 is closely related to 147 of 361 cancer diseases which the cisplatin damaged genes are associated with and was severely damaged by cisplatin. Given SPAG9 abundantly expresses JIP-4, a upstream mediator of protein kinase signaling, in testis, it may be responsible for the high sensitivity of testicular cancer to cisplatin, thus being a potential therapeutic target for precise treatment of testicular cancer. These findings provide novel insights into better understanding in molecular mechanism of anticancer activity and toxicity of cisplatin, more importantly inspire further studies in prioritizing gene targets for precise treatment of cancers.

pharmacology and toxicology↗

bioRxiv2020

Morphologic Classification and Automatic Nugent Scoring of Bacterial Vaginosis by Deep Neural Networks

BackgroundBacterial vaginosis (BV) was the most common condition for womens health caused by the disruption of normal vaginal flora and an overgrowth of certain disease-causing bacteria, affecting 30-50% of women at some time in their lives. Gram stain followed by Nugent scoring (NS) based on bacterial morphotypes under the microscope was long considered golden standard for BV diagnosis. This conventional manual method was often considered labor intensive, time consuming, and variable results from person to person. MethodsWe developed four convolutional neural networks (CNN) models, and evaluated their ability to automatic identify vaginal bacteria and classify Nugent scores from microscope images. All the CNN models were first trained with 23280 microscopic images labeled with Nugent scores from top experts. A separate set of 5815 images were evaluated by the CNN models. The best CNN model was selected to generalize its application on an independent sets of 1082 images collecting from three teaching hospitals. Different hardwares were used to take images in hospitals. ResultsOur model could classify three Nugent Scores from images with high three classification accuracy of 89.3% (with 82.4% sensitivity and 96.6% specificity) on the 5815 test images, which was better diagnostic yield than the top-level technologists and obstetricians in China. The ability of generalization for our model was strong that it obtained 75.1%, which was 6.6% higher than the average of technologists. ConclusionThe CNN model over performed human healthcare practitioners on accuracy, efficiency and stability for BV diagnosis using microscopic image-based Nugent scores. The deep learning model may offer translational application in automating diagnosis of bacterial vaginosis with proper supporting hardware.

microbiology↗

bioRxiv2020

Comparative secretome of Magnaporthe oryzae identified proteins involved in virulence and cell wall integrity

Plant fungal pathogens secrete numerous proteins into the apoplast at the plant-fungus contact sites to facilitate colonization. Only a few secreted proteins were functionally characterized in Magnaporthe oryzae, the fungal pathogen causing rice blast disease worldwide. ALG3 is an -1, 3-mannosyltransferase function in N-glycan synthesis for secreted N-glycosylated proteins, and the {Delta}alg3 mutants show strong defects in cell wall integrity and fungal virulence, indicating a potential effect on the secretion of multiple proteins. In this study, we compared the secretome of wild type and {Delta}alg3 mutants, and identified 51 proteins that require ALG3 for proper secretion. These are predicted to be involved in metabolic processes, interspecies interactions, cell wall organization, and response to chemicals. The tested secreted proteins localized at the apoplast region surrounding the fungal infection hyphae. Moreover, the N-glycosylation of candidate proteins was significantly changed in the {Delta}alg3 mutant, leading to the reduction of protein secretion and abnormal protein localization. Furthermore, we tested the function of two genes, one is a previously reported M. oryzae gene Invertase 1 (INV1) encoding a secreted invertase, and the other one is a gene encoding an Acid mammalian chinitase (AMCase). The fungal virulence was significantly reduced and the cell wall integrity was altered in the {Delta}inv1 and {Delta}amcase mutant strains. Elucidation of the comparative secretome of M. oryzae improves our understanding of the proteins that require ALG3 for secretion, and of their function in fungal virulence and cell wall integrity.

plant biology↗

bioRxiv2020

Mesophasic organization of GABAA receptors in hippocampal inhibitory synapse

Information processing in the brain depends on synaptic transmission and plasticity, which in turn require specialized organization of neurotransmitter receptors and scaffolding proteins within the postsynaptic density (PSD). However, how these molecules are organized in situ remains largely elusive, limiting our mechanistic understanding of synaptic formation and functions. Here, we have developed template-free classification of over-sampled sub-tomograms to analyze cryo-electron tomograms of hippocampal synapses, enabling us to identify type-A {gamma}-aminobutyric acid receptor (GABAAR) in inhibitory synapses and determine its in situ structure at 19 [A] resolution. We found that these receptors are organized hierarchically: from GABAAR super-complexes with a fixed 11-nm inter-receptor distance but variable relative angles, through semi-ordered two-dimensional receptor networks with reduced Voronoi entropy, to mesophasic assembly with a sharp phase boundary. This assembly aligns with condensates of postsynaptic scaffolding proteins and putative presynaptic vesicle release sites. Such mesophasic self-organization may allow synapses to achieve a "Goldilocks" state with a delicate balance between stability and flexibility, enabling both reliability and plasticity in information processing.

neuroscience↗

bioRxiv2019

Cryo-EM Structure of the Human Mitochondrial Translocase TIM22 Complex

Mitochondria play vital functions in cellular metabolism, homeostasis, and apoptosis1-3. Most of the mitochondrial proteins are synthesized as precursors in the cytosol and imported into mitochondria for folding or maturation4,5. The translocase TIM22 complex is responsible for the import of multiple hydrophobic carrier proteins that are then folded in the inner membrane of mitochondria6-8. In mammalian cells, the TIM22 complex consists of at least six components, Tim22, Tim29, AGK, and three Tim chaperones (Tim9, Tim10a and Tim10b)9-14. Here, we report the cryo-EM structure of the human translocase TIM22 complex at an overall resolution of 3.7 angstrom. The core subunit, Tim22, contains four transmembrane helices, forming a partial pore that is open to the lipid bilayer. Tim29 is a single transmembrane protein that provides an N-terminal helix to stabilize Tim22 and a C-terminal intermembrane space (IMS) domain to connect AGK and two TIM chaperone hexamers to maintain complex integrity. One TIM hexamer comprises Tim9 and Tim10a in a 3:3 molar ratio, and the other consists of two Tim9 units, three Tim10a units, and one Tim10b unit. The latter hexamer faces the intramembrane region of Tim22, likely providing the dock to load the precursors to the partial pore of Tim22. Our structure serves as a molecular basis for the mechanistic understanding of TIM22 complex function.

biophysics↗

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↗

bioRxiv2019

Integrin α6β4 signaling switches DNA repair from homologous recombination to non-homologous end-joining pathway to sensitize breast cancer cells to cisplatin

Integrin 6{beta}4 is highly expressed in triple negative breast cancer (TNBC) and drives aggressiveness by stimulating proliferation, angiogenesis, cell migration, invasion and metastasis. Signaling from this integrin stimulates DNA repair and apoptosis resistance, suggesting that it could contribute to therapeutic resistance. Upon testing this hypothesis, we found that integrin 6{beta}4 signaling promoted a three-fold greater sensitivity to cisplatin but exhibited no difference in response to other chemotherapies tested. Mechanistic investigations revealed that integrin 6{beta}4 stimulated quicker and higher amplitude of activation of ATM, Chk2, p53, and 53BP1, which required the integrin {beta}4 signaling domain. Genetic manipulation of gene expression demonstrated that mutant p53 cooperated with integrin 6{beta}4 for cisplatin sensitivity and was necessary for downstream phosphorylation of 53BP1 and enhanced ATM activation. Additionally, we discovered that integrin 6{beta}4 preferentially activated DNA-PKc in response to cisplatin, which led to formation of DNA-PKc-p53 complexes and 53BP1 activation. As a result, integrin 6{beta}4 shifted double strand break repair from homologous recombination (HR) to non-homologous end joining (NHEJ). In summary, we discovered a novel function of integrin 6{beta}4 in switching DSB repair from HR to NHEJ that results in cisplatin sensitivity in TNBC.

cancer biology↗

bioRxiv2019

Endoplasmic reticulum associated degradation preserves hematopoietic stem cell quiescence and self-renewal by restricting mTOR activity

Many tissue-specific stem cells require quiescence to sustain stem cell pool and maintain lifelong tissue integrity. It remains unclear whether protein quality control is required for stem cells in quiescence when RNA content, protein synthesis and metabolic activities are significantly reduced. Here, we report that endoplasmic reticulum associated degradation (ERAD) is required to preserve the function of quiescent hematopoietic stem cells (HSC). The Sel1L/Hrd1 ERAD genes are enriched in the quiescent and inactive HSCs, and conditional knockout of Sel1L in hematopoietic tissues drives HSCs to hyper-proliferation which leads to reduced self-renewal and HSC depletion. ERAD deficiency induces a non-apoptotic ER stress and activates unfolded protein response (UPR). Furthermore, Sel1L knockout leads to mTOR activation, and mTOR inhibition rescues the HSC defects in Sel1L knockout mice. Protein quality control is, therefore, tightly regulated and actively engaged in quiescent HSCs. Sel1L/Hrd1 ERAD maintains HSC quiescence and self-renewal via restricting mTOR activity.

cell biology↗

bioRxiv2019

Leptin deficient rats develop nonalcoholic steatohepatitis with unique disease progression

Nonalcoholic steatohepatitis (NASH) is an aggressive liver disease threatening public health, however its natural history is poorly understood. Unlike ob/ob mice, Lep{triangleup}I14/{triangleup}I14 rats develop unique NASH phenotype with steatosis, lymphocyte infiltration and ballooning after postnatal week 16. Using Lep{triangleup}I14/{triangleup}I14 rats as NASH model, we studied the natural history of NASH progression by performing an integrated analysis of hepatic transcriptome from postnatal week 4 to 48. Leptin deficiency results in a robust increase in expression of genes encoding 9 rate-limiting enzymes in lipid metabolism such as ACC and FASN. However, genes in positive regulation of inflammatory response are highly expressed at week 16 and then remain the steady elevated expression till week 48. The high expression of cytokines and chemokines including CCL2, TNF, IL6 and IL1{beta} is correlated with the phosphorylation of several key molecules in pathways such as JNK and NF-{kappa}B. Meanwhile, we observed cell infiltration of MPO+ neutrophils, CD8+ T cells, CD68+ hepatic macrophages and CCR2+ inflammatory monocyte-derived macrophages, together with macrophage polarization from M2 to M1. Importantly, Lep{triangleup}I14/{triangleup}I14 rats share more homologous genes with NASH patients than previously established mouse models and crab eating monkeys with spontaneous hepatic steatosis. Transcriptomic analysis showed that many drug targets in clinical trials can be evaluated in Lep{triangleup}I14/{triangleup}I14 rats.\n\nConclusionWe characterize Lep{triangleup}I14/{triangleup}I14 rats as a unique NASH model by performing a long-term (i.e., 4 to 48 postnatal weeks) integrated transcriptomic analysis. This work reveal the temporal dynamics of hepatic gene expression in lipid metabolism and inflammation, and shed light on understanding the natural history of NASH in human beings.

pathology↗

bioRxiv2019

Genomic landscape of 261 childhood cancer patient-derived xenograft models

Accelerating cures for children with cancer remains an immediate challenge due to extensive oncogenic heterogeneity between and within histologies, distinct molecular mechanisms evolving between diagnosis and relapsed disease, and limited therapeutic options. To systematically prioritize and rationally test novel agents in preclinical murine models, researchers within the Pediatric Preclinical Testing Consortium are continuously developing patient-derived xenografts (PDXs) from high-risk childhood cancers, many refractory to current standard-of-care treatments. Here, we genomically characterize 261 PDX models from 29 unique pediatric cancer malignancies and demonstrate faithful recapitulation of histologies, subtypes, and refine our understanding of relapsed disease. Expression and mutational signatures are used to classify tumors for TP53 and NF1 inactivation, as well as impaired DNA repair. We anticipate that these data will serve as a resource for pediatric oncology drug development and guide rational clinical trial design for children with cancer.\n\nHighlightsO_LIMultiplatform genomic analysis defines landscape of 261 pediatric cancer patient derived xenograft (PDX) models\nC_LIO_LIPediatric patient derived xenografts faithfully recapitulate relapsed disease\nC_LIO_LIInferred TP53 pathway inactivation correlates with pediatric cancer copy number burden\nC_LIO_LISomatic mutational signatures predict impaired DNA repair across multiple histologies\nC_LI

genomics↗

bioRxiv2019

Requirement for TRanslocon-Associated Protein (TRAP) α in insulin biogenesis

The mechanistic basis for the biogenesis of peptide hormones and growth factors is poorly understood. Here we show that the conserved endoplasmic reticulum (ER) membrane translocon-associated protein (TRAP) , also known as signal sequence receptor 1 (SSR1)1, plays a critical role in the biosynthesis of insulin. A genetic screen in the nematode Caenorhabditis elegans revealed trap-1, which encodes the C. elegans TRAP ortholog, as a modifier of DAF-2 insulin receptor (InsR) signaling. Genetic analysis indicates that TRAP-1 acts upstream of DAF-2/InsR to control C. elegans development. Endogenous C. elegans TRAP-1 and mammalian TRAP both localized to the ER. In pancreatic beta cells, TRAP deletion impaired preproinsulin translocation but did not affect the synthesis of 1-antitrypsin, indicating that TRAP selectively influences the translocation of a subset of secreted proteins. Surprisingly, loss of TRAP function also resulted in disruption of distal steps in insulin biogenesis including proinsulin processing and secretion. These results show that TRAP assists in the ER translocation of preproinsulin and unveil unanticipated additional consequences of TRAP loss-of-function on the intracellular trafficking and maturation of proinsulin. The association of common intronic single nucleotide variants in the human TRAP gene with susceptibility to Type 2 diabetes and pancreatic beta cell dysfunction2 suggests that impairment of preproinsulin translocation and proinsulin trafficking may contribute to the pathogenesis of Type 2 diabetes.

genetics↗

bioRxiv2018

The homoeologous genes for the Rec8-like meiotic cohesin in wheat: structure, function, and evolutionary implication

The Rec8-like cohesin is a cohesion protein essential for orderly chromosome segregation in meiosis. Here, we cloned two Rec8-like homoeologous genes (homoeoalleles) from tetraploid wheat (TtRec8-A1 and TtRec8-B1) and one from hexaploid wheat (TaRec8-D1), and performed expression and functional analyses of the homoeoalleles. Also, we identified other two Rec8 homoeoalleles in hexaploid wheat (TaRec8-A1 and TaRec8-B1) and the one in Aegilops tauschii (AetRec8-D1) by comparative analysis. The coding DNA sequences (CDS) of these six Rec8 homoeoalleles are all 1,827 bp in length, encoding 608 amino acids. They differed from each other primarily in introns although single nucleotide polymorphisms were detected in CDS. Substantial difference was observed between the homoeoalleles from the subgenome B (TtRec8-B1 and TaRec8-B1) and those from the subgenomes A and D (TtRec8-A1, TaRec8-A1, and TaRec8-D1). TtRec8-A1 expressed dominantly over TtRec8-B1, but comparably to TaRec8-D1. Therefore, the Rec8 homoeoalleles from the subgenomes A and D may be functionally more active than the one from the subgenome B in wheat. The structural variation and differential expression of the Rec8 homoeoalleles indicate a unique cross-genome coordination of the homoeologous genes in the polyploid, and imply the distinction of the wheat subgenome B from other subgenomes in the origin and evolution.\n\nHIGHLIGHTThis work revealed the structural and expression patterns of the Rec8-like homoeologous genes in polyploid wheat, implying a unique origin and evolutionary route of the wheat B subgenome.

genetics↗

bioRxiv2018

Elongator is required for root stem cell maintenance by regulating SHORT ROOT transcription

SHORTROOT (SHR) is essential for stem cell maintenance and radial patterning in Arabidopsis thaliana roots, but how its expression is regulated is still unknown. Here, we report that Elongator regulates the transcription of SHR. The depletion of Elongator drastically reduced SHR expression and led to defective root stem cell maintenance and radial patterning. The importance of the nuclear localization of Elongator for its functioning, together with the insensitivity of the elp1 mutant to the transcription elongation inhibitor 6-azauracil and the direct interaction of the ELP4 subunit with the C-terminal domain of RNA polymerase II (RNAPII CTD), support the notion that Elongator plays important roles in transcription elongation. Indeed, we found that ELP3 associates with the pre-mRNA of SHR and that mutation of Elongator reduces the enrichment of RNAPII on the SHR gene body. Moreover, Elongator interacted in vivo with SUPPRESSOR OF Ty4 (SPT4), a well-established transcription elongation factor that was recruited to the SHR locus. Together, these results demonstrate that Elongator acts in concert with SPT4 to regulate the transcription of SHR.

plant biology↗