Jian Xu

Jian Xu
National University of Singapore | NUS · Department of Biological Sciences

36.67
 · 
Ph.D. Utrecht University

About

56
Publications
21,491
Reads
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6,366
Citations
Introduction
Jian currently works as Professor of Plant Systems Physiology at the Institute for Water and Wetland Research, Radboud University, the Netherlands.
Research Experience
July 2018 - present
National University of Singapore
Position
  • Associate Professor
January 2009 - June 2018
National University of Singapore
Position
  • Assistant Professor
January 2009 - present
National University of Singapore
Position
  • Principal Investigator

Publications

Publications (56)
Article
Full-text available
Root angle has a major impact on acquisition of nutrients like phosphate that accumulate in topsoil and in many species; low phosphate induces shallower root growth as an adaptive response. Identifying genes and mechanisms controlling root angle is therefore of paramount importance to plant breeding. Here we show that the actin-binding protein Rice...
Article
Temperature has a profound influence on plant and animal development, but its effects on stem cell behavior and activity remain poorly understood. Here, we characterize the responses of the Arabidopsis root to chilling (low but above-freezing) temperature. Chilling stress at 4°C leads to DNA damage predominantly in root stem cells and their early d...
Article
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Topoisomerase 1 (TOP1), which releases DNA torsional stress generated during replication through its DNA relaxation activity, plays vital roles in animal and plant development. In Arabidopsis, TOP1 is encoded by two paralogous genes (TOP1α and TOP1β), of which TOP1α displays specific developmental functions that are critical for the maintenance of...
Article
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The Lugol's staining method has been widely used to detect changes in the maintenance of stem cell fate in the columella root cap of Arabidopsis roots since the late 1990s. However, various limitations of this method demand for additional or complementary new approaches. For instance, it is unable to reveal the division rate of columella root cap s...
Article
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The tip of the root is covered by a thimble-shaped root cap that is the site of perception and transduction for many environmental stimuli. Until now, however, little was known about how the root cap of rice develops and functions to regulate the adaptive behavior of the root. To address this we examined the formation of rice root cap during embryo...
Article
Joint profiling of transcriptome and chromatin accessibility within single cells allows for the deconstruction of the complex relationship between transcriptional states and upstream regulatory programs determining different cell fates. Here, we developed an automated method with high sensitivity, assay for single-cell transcriptome and accessibili...
Article
Plants are known for their outstanding capacity to recover from various wounds and injuries. However, it remains largely unknown how plants sense diverse forms of injury and canalize existing developmental processes into the execution of a correct regenerative response. Auxin, a cardinal plant hormone with morphogen-like properties, has been previo...
Preprint
Full-text available
Cis Regulatory Elements (CREs) regulate the expression of the genes in their genomic neighborhoods and influence cellular processes such as cell-fate maintenance and differentiation. To date, there remain major gaps in the functional characterization of CREs and the identification of its target genes in the cellular native environment. In this stud...
Preprint
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We developed ASTAR-Seq (Assay for Single-cell Transcriptome and Accessibility Regions) integrated with automated microfluidic chips, which allows for parallel sequencing of transcriptome and chromatin accessibility within the same single-cell. Using ASTAR-Seq, we profiled 192 mESCs cultured in serum+LIF and 2i medium, 424 human cell lines including...
Preprint
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To unravel the mechanism of human cellular reprogramming process at single-cell resolution, we performed parallel scRNA-Seq and scATAC-Seq analysis. Our analysis reveals that the cells undergoing reprogramming proceed in an asynchronous trajectory and diversify into heterogeneous sub-populations. BDD2-C8 fluorescent probe staining and negative stai...
Article
Blood reprogramming, in which induced pluripotent stem cells (iPSCs) are derived from hematopoietic lineages, has rapidly advanced over the past decade. Since the first report using human blood, hematopoietic cell types from various sources, such as the peripheral bone‐marrow and cord blood, have been successfully reprogrammed. The volume of blood...
Article
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Many plants have a high regenerative capacity, which can be used to induce de novo organogenesis and produce various valuable plant species and products. In the classic 2-step protocol for de novo shoot organogenesis, small pieces of plant parts or tissues known as explants are initially cultured on an auxin-rich medium to produce a cell mass calle...
Article
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Salinity affects growth and development of plants, but mangroves exhibit exceptional salt tolerance. With direct exposure to salinity, mangrove roots possess specific adaptations to tolerate salt stress. Therefore, studying the early effects of salt on mangrove roots can help us better understand the tolerance mechanisms. Using two-month-old greenh...
Article
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Phototropism is the process by which plants grow towards the light in order to maximize the capture of light for photosynthesis, which is particularly important for germinating seedlings. In Arabidopsis, hypocotyl phototropism is predominantly triggered by blue light (BL), which has a profound effect on the establishment of asymmetric auxin distrib...
Article
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Abstract Plants are sessile organisms that must deal with various threats resulting in tissue damage, such as herbivore feeding, and physical wounding by wind, snow or crushing by animals. During wound healing, phytohormone crosstalk orchestrates cellular regeneration through the establishment of tissue-specific asymmetries. In turn, hormone-regula...
Article
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Background Plants have the remarkable property to elaborate entire body plan from any tissue part. The conversion of lateral root primordium (LRP) to shoot is an ideal method for plant propagation and for plant researchers to understand the mechanism underlying trans-differentiation. Until now, however, a robust method that allows the efficient con...
Article
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A decade of studies on middle cortex (MC) formation in the root endodermis of Arabidopsis have revealed a complex regulatory network that is orchestrated by several GRAS family transcription factors, including SHORT-ROOT (SHR), SCARECROW (SCR) and SCARECROW-LIKE 3 (SCL3). However, how their functions are regulated remains obscure. Here we show that...
Article
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Embryonic stem cells (ESCs) are chiefly characterized by their ability to self-renew and to differentiate into any cell type derived from the three main germ layers. It was demonstrated that somatic cells could be reprogrammed to form induced pluripotent stem cells (iPSCs) via various strategies. Gene editing is a technique that can be used to make...
Article
The establishment of auxin maxima by PIN-FORMED 3 (PIN3)- and AUXIN RESISTANT 1/LIKE AUX1 (LAX) 3 (AUX1/LAX3)-mediated auxin transport is essential for hook formation in Arabidopsis hypocotyls. Until now, however, the underlying regulatory mechanism remains poorly understood. Here, we show that loss of clathrin light chain CLC2 and CLC3 enhanced au...
Article
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Author Summary Little is known concerning the identity of regulatory components and signaling pathways that control the growth of meristem cells in plants. Here, we report that rice plants deficient in the AP2/ERF family gene SHOEBOX (SHB) exhibited a severe reduction in the root meristem size. These plants had shorter cells in the root meristems f...
Article
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Rice production faces the challenge to be enhanced by 50% by year 2030 to meet the growth of the population in rice-eating countries. Whereas yield of cereal crops tend to reach plateaus and a yield is likely to be deeply affected by climate instability and resource scarcity in the coming decades, building rice cultivars harboring root systems that...
Article
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ROP GTPases are crucial for the establishment of cell polarity and for controlling responses to hormones and environmental signals in plants. In this work, we show that ROP3 plays important roles in embryo development and auxin-dependent plant growth. Loss-of-function and dominant-negative (DN) mutations in ROP3 induced a spectrum of similar defect...
Article
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Abiotic stress conditions adversely affect plant growth, resulting in significant decline in crop productivity. To mitigate and recover from the damaging effects of such adverse environmental conditions, plants have evolved various adaptive strategies at cellular and metabolic levels. Most of these strategies involve dynamic changes in protein abun...
Article
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In plants, active transport of auxin plays an essential role in root development. Localization of the PIN1 auxin transporters to the basal membrane of cells directs auxin flow and depends on the trafficking mediator GNOM. GNOM-dependent auxin transport is vital for root development and thus offers a useful tool for the investigation of a possible t...
Article
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CLAVATA3 (CLV3)/ENDOSPERM SURROUNDING REGION (ESR)-related (CLE) proteins belong to a small peptide family conserved in plants. Recent studies in Arabidopsis and rice have revealed a key role for CLEs in mediating cell–cell communication and stem cell maintenance during plant development, but how CLE signalling controls root development in the rice...
Chapter
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Unlike the dicotyledonous model plant Arabidopsis, which has a taproot system dominated by the primary root, rice has a fibrous root system that is developed postembryonically (Fig. 20.1). The root system architecture of rice is typical of monocotyledons in which the primary root, often termed as seminal root, is known to be ephemeral and short liv...
Article
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The growth and development of plants are influenced by the integration of diverse endogenous and environmental signals. Acting as a mediator of extrinsic signals, the stress hormone, abscisic acid (ABA), has been shown to regulate many aspects of plant development in response to unfavourable environmental stresses, allowing the plant to cope and su...
Article
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By being sessile, plants have evolved a remarkable capacity to perceive and respond to changes in environmental conditions throughout their life cycle. Light represents probably the most important environmental factor that impinge on plant development because, other than supplying the energy source for photosynthesis, it also provides seasonal and...
Article
Full-text available
When a plant germinates in the soil, elongation of stem-like organs is enhanced whereas leaf and root growth is inhibited. How these differential growth responses are orchestrated by light and integrated at the organismal level to shape the plant remains to be elucidated. Here, we show that light signals through the master photomorphogenesis repres...
Article
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In plants, where cells cannot migrate, asymmetric cell divisions (ACDs) must be confined to the appropriate spatial context. We investigate tissue-generating asymmetric divisions in a stem cell daughter within the Arabidopsis root. Spatial restriction of these divisions requires physical binding of the stem cell regulator SCARECROW (SCR) by the RET...
Article
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The directional transport of the phytohormone auxin depends on the phosphorylation status and polar localization of PIN-FORMED (PIN) auxin efflux proteins. While PINIOD (PID) kinase is directly involved in the phosphorylation of PIN proteins, the phosphatase holoenzyme complexes that dephosphorylate PIN proteins remain elusive. Here, we demonstrate...
Article
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Heading date and grain weight are two determining agronomic traits of crop yield. To date, molecular factors controlling both heading date and grain weight have not been identified. Here we report the isolation of a hemizygous mutation, heading and grain weight (hgw), which delays heading and reduces grain weight in rice. Analysis of hgw mutant phe...
Article
Full-text available
To develop a growing root, cell division in the root meristem has to be properly regulated in order to generate or propagate new cells. How cell division is regulated in the root meristem remains largely unknown. Here, we report the identification and characterization of the Arabidopsis (Arabidopsis thaliana) RETARDED ROOT GROWTH (RRG) gene that pl...
Article
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Recent identification of the Arabidopsis thaliana tyrosylprotein sulfotransferase (TPST) and a group of Tyr-sulfated peptides known as root meristem growth factors (RGFs) highlights the importance of protein Tyr sulfation in plant growth and development. Here, we report the action mechanism of TPST in maintenance of the root stem cell niche, which...
Article
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Polar membrane cargo delivery is crucial for establishing cell polarity and for directional transport processes. In plants, polar trafficking mediates the dynamic asymmetric distribution of PIN FORMED (PIN) carriers, which drive polar cell-to-cell transport of the hormone auxin, thereby generating auxin maxima and minima that control development. T...
Article
Because plant cells do not migrate, cell division planes are crucial determinants of plant cellular architecture. In Arabidopsis roots, stringent control of cell divisions leads to a virtually invariant division pattern, including those that create new tissue layers. However, the mechanisms that control oriented cell divisions are hitherto poorly u...
Article
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Dynamically polarized membrane proteins define different cell boundaries and have an important role in intercellular communication-a vital feature of multicellular development. Efflux carriers for the signalling molecule auxin from the PIN family are landmarks of cell polarity in plants and have a crucial involvement in auxin distribution-dependent...
Article
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The plant growth regulator auxin controls cell identity, cell division and cell expansion. Auxin efflux facilitators (PINs) are associated with auxin maxima in distal regions of both shoots and roots. Here we model diffusion and PIN-facilitated auxin transport in and across cells within a structured root layout. In our model, the stable accumulatio...
Article
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Polar flow of the phytohormone auxin requires plasma membrane-associated PIN proteins and underlies multiple developmental processes in plants. Here we address the importance of the polarity of subcellular PIN localization for the directionality of auxin transport in Arabidopsis thaliana. Expression of different PINs in the root epidermis revealed...
Article
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Particularly in the fall, plant leaves demand attention as examples of the beauty of nature. Around that time, anyone can pick them up and have a close look at the variety in venation patterns. For a considerable time, biologists and mathematicians went one step farther, trying to find regularities in these patterns and rules behind them. Vein orga...
Article
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Plants and some animals have a profound capacity to regenerate organs from adult tissues. Molecular mechanisms for regeneration have, however, been largely unexplored. Here we investigate a local regeneration response in Arabidopsis roots. Laser-induced wounding disrupts the flow of auxin—a cell-fate–instructive plant hormone—in root tips, and we d...
Article
Cell polarity plays an important role in plant development, but the mechanisms that first establish polarity cues remain obscure. By contrast, a flurry of information has recently emerged on the elaboration of cell shape from such unknown initial cell-polarity cues. Recent studies suggest that Rho-related GTPases in plants (ROPs), and their effecto...
Article
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Brassinosteroids (BRs) are important plant growth regulators in multiple developmental processes. Previous studies have indicated that BR treatment enhanced auxin-related responses, but the underlying mechanisms remain unknown. Using (14)C-labeled indole-3-acetic acid and Arabidopsis thaliana plants harboring an auxin-responsive reporter construct,...
Article
Full-text available
CLAVATA3 (CLV3), CLV3/ESR19 (CLE19), and CLE40 belong to a family of 26 genes in Arabidopsis thaliana that encode putative peptide ligands with unknown identity. It has been shown previously that ectopic expression of any of these three genes leads to a consumption of the root meristem. Here, we show that in vitro application of synthetic 14-amino...
Article
Full-text available
Vesicle trafficking is essential for the generation of asymmetries, which are central to multicellular development. Core components of the vesicle transport machinery, such as ADP-ribosylation factor (ARF) GTPases, have been studied primarily at the single-cell level. Here, we analyze developmental functions of the ARF1 subclass of the Arabidopsis...
Article
Full-text available
Local accumulation of the plant growth regulator auxin mediates pattern formation in Arabidopsis roots and influences outgrowth and development of lateral root- and shoot-derived primordia. However, it has remained unclear how auxin can simultaneously regulate patterning and organ outgrowth and how its distribution is stabilized in a primordium-spe...
Article
In contrast to the intense attention devoted to research on intracellular sterol trafficking in animal cells, knowledge about sterol transport in plant cells remains limited, and virtually nothing is known about plant endocytic sterol trafficking. Similar to animals, biosynthetic sterol transport occurs from the endoplasmic reticulum (ER) via the G...
Article
In the Arabidopsis shoot apical meristem, an organizing center signals in a non-cell-autonomous manner to specify the overlying stem cells. Stem cells express the small, secreted protein CLAVATA3 (CLV3; ) that activates the CLV1-CLV2 receptor complex, which negatively controls the size of the organizing center. Consistently, CLV3 overexpression res...
Article
Plant cell polarity is important for cellular function and multicellular development. Classical physiological and cell biological analyses identified cues that orient cell polarity and suggested molecules that translate a cue into intracellular asymmetry. A range of proteins that either mark or are involved in the establishment of a (polar) axis ar...
Article
Full-text available
The formation of haploid spores marks the initiation of the gametophytic phase of the life cycle of all vascular plants ranging from ferns to angiosperms. In angiosperms, this process is initiated by the differentiation of a subset of floral cells into sporocytes, which then undergo meiotic divisions to form microspores and megaspores. Currently, t...

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Projects (2)
Archived project
This project aims to understand why and how specific plant cells are targeted for programmed death.