Xia Cui

Publications of Xia Cui

• Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development.

  Authors: Xianwei Song, Dekai Wang, Lijia Ma, Zhiyu Chen, Pingchuan Li, Xia Cui, Chunyan Liu, Shouyun Cao, Chengcai Chu, Yuezhi Tao, Xiaofeng Cao

  The Plant journal : for cell and molecular biology. 03/2012;

  Higher plants have evolved multiple RNA-dependent RNA polymerases (RDRs), which work with Dicer-like (DCL) proteins to produce different classes of small RNAs with specialized molecular functions.Higher plants have evolved multiple RNA-dependent RNA polymerases (RDRs), which work with Dicer-like (DCL) proteins to produce different classes of small RNAs with specialized molecular functions. Here we report that OsRDR6, the rice homolog of Arabidopsis RDR6, acts in the biogenesis of various types and sizes of small RNAs. We isolated a rice osrdr6-1 mutant, which was temperature sensitive and showed spikelet defects. This mutant displays reduced accumulation of tasiR-ARFs, the conserved trans-acting siRNAs (tasiRNAs) derived from the TAS3 locus, and ectopic expression of tasiR-ARF target genes, the Auxin Response Factors (including ARF2 and ARF3/ETTIN). The loss of tasiR-mediated repression of ARFs in osrdr6-1 can explain its morphological defects, as expression of two non-targeted ARF3 gene constructs (ARF3muts) in a wild-type background mimics the osrdr6 and osdcl4-1 mutant phenotypes. Small RNA high-throughput sequencing also reveals that besides tasiRNAs, 21-nucleotide (nt) phased small RNAs are also largely dependent on OsRDR6. Unexpectedly, we found that osrdr6-1 has a strong impact on accumulation of 24-nt phased small RNAs but not on unphased ones. Our work uncovers the key roles of OsRDR6 in small RNA biogenesis and directly illustrates the crucial functions of tasiR-ARFs in rice development. Published 2012. This article is a US Government work and is in the public domain in the USA.

• ARGONAUTE10 and ARGONAUTE1 regulate the termination of floral stem cells through two microRNAs in Arabidopsis.

  Authors: Lijuan Ji, Xigang Liu, Jun Yan, Wenming Wang, Rae Eden Yumul, Yun Ju Kim, Thanh Theresa Dinh, Jun Liu, Xia Cui, Binglian Zheng, Manu Agarwal, Chunyan Liu, Xiaofeng Cao, Guiliang Tang, Xuemei Chen

  PLoS genetics. 03/2011; 7(3):e1001358.

  Stem cells are crucial in morphogenesis in plants and animals. Much is known about the mechanisms that maintain stem cell fates or trigger their terminal differentiation. However, little is knownStem cells are crucial in morphogenesis in plants and animals. Much is known about the mechanisms that maintain stem cell fates or trigger their terminal differentiation. However, little is known about how developmental time impacts stem cell fates. Using Arabidopsis floral stem cells as a model, we show that stem cells can undergo precise temporal regulation governed by mechanisms that are distinct from, but integrated with, those that specify cell fates. We show that two microRNAs, miR172 and miR165/166, through targeting APETALA2 and type III homeodomain-leucine zipper (HD-Zip) genes, respectively, regulate the temporal program of floral stem cells. In particular, we reveal a role of the type III HD-Zip genes, previously known to specify lateral organ polarity, in stem cell termination. Both reduction in HD-Zip expression by over-expression of miR165/166 and mis-expression of HD-Zip genes by rendering them resistant to miR165/166 lead to prolonged floral stem cell activity, indicating that the expression of HD-Zip genes needs to be precisely controlled to achieve floral stem cell termination. We also show that both the ubiquitously expressed ARGONAUTE1 (AGO1) gene and its homolog AGO10, which exhibits highly restricted spatial expression patterns, are required to maintain the correct temporal program of floral stem cells. We provide evidence that AGO10, like AGO1, associates with miR172 and miR165/166 in vivo and exhibits "slicer" activity in vitro. Despite the common biological functions and similar biochemical activities, AGO1 and AGO10 exert different effects on miR165/166 in vivo. This work establishes a network of microRNAs and transcription factors governing the temporal program of floral stem cells and sheds light on the relationships among different AGO genes, which tend to exist in gene families in multicellular organisms.

• Arabidopsis REF6 is a histone H3 lysine 27 demethylase.

  Authors: Falong Lu, Xia Cui, Shuaibin Zhang, Thomas Jenuwein, Xiaofeng Cao

  Nature genetics. 01/2011; 43(7):715-9.

  Polycomb group (PcG)-mediated histone H3 lysine 27 trimethylation (H3K27me3) has a key role in gene repression and developmental regulation. There is evidence that H3K27me3 is actively removed inPolycomb group (PcG)-mediated histone H3 lysine 27 trimethylation (H3K27me3) has a key role in gene repression and developmental regulation. There is evidence that H3K27me3 is actively removed in plants, but it is not known how this occurs. Here we show that RELATIVE OF EARLY FLOWERING 6 (REF6), also known as Jumonji domain-containing protein 12 (JMJ12), specifically demethylates H3K27me3 and H3K27me2, whereas its metazoan counterparts, the KDM4 proteins, are H3K9 and H3K36 demethylases. Plants overexpressing REF6 resembled mutants defective in H3K27me3-mediated gene silencing. Genetic interaction tests indicated that REF6 acts downstream of H3K27me3 methyltransferases. Mutations in REF6 caused ectopic and increased H3K27me3 level and decreased mRNA expression of hundreds of genes involved in regulating developmental patterning and responses to various stimuli. Our work shows that plants and metazoans use conserved mechanisms to regulate H3K27me3 dynamics but use distinct subfamilies of enzymes.

• Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome.

  Authors: Soichi Inagaki, Asuka Miura-Kamio, Yasukazu Nakamura, Falong Lu, Xia Cui, Xiaofeng Cao, Hiroshi Kimura, Hidetoshi Saze, Tetsuji Kakutani

  The EMBO journal. 10/2010; 29(20):3496-506.

  In diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Although selective H3K9me is critical forIn diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Although selective H3K9me is critical for maintaining genome integrity, mechanisms to exclude H3K9me from active genes remain largely unexplored. Here, we show in Arabidopsis that the exclusion depends on a histone demethylase gene, IBM1 (increase in BONSAI methylation). Loss-of-function ibm1 mutation results in ectopic H3K9me and non-CG methylation in thousands of genes. The ibm1-induced genic H3K9me depends on both histone methylase KYP/SUVH4 and DNA methylase CMT3, suggesting interdependence of two epigenetic marks--H3K9me and non-CG methylation. Notably, IBM1 enhances loss of H3K9me in transcriptionally de-repressed sequences. Furthermore, disruption of transcription in genes induces ectopic non-CG methylation, which mimics the loss of IBM1 function. We propose that active chromatin is stabilized by an autocatalytic loop of transcription and H3K9 demethylation. This process counteracts a similarly autocatalytic accumulation of silent epigenetic marks, H3K9me and non-CG methylation.

• The BUD2 mutation affects plant architecture through altering cytokinin and auxin responses in Arabidopsis.

  Authors: Xia Cui, Chunmin Ge, Renxiao Wang, Huanzhong Wang, Weiqi Chen, Zhiming Fu, Xiangning Jiang, Jiayang Li, Yonghong Wang

  Cell research. 04/2010; 20(5):576-86.

  The ratio of auxin and cytokinin plays a crucial role in regulating aerial architecture by promoting or repressing axillary bud outgrowth. We have previously identified an Arabidopsis mutant bud2The ratio of auxin and cytokinin plays a crucial role in regulating aerial architecture by promoting or repressing axillary bud outgrowth. We have previously identified an Arabidopsis mutant bud2 that displays altered root and shoot architecture, which results from the loss-of-function of S-adenosylmethionine decarboxylase 4 (SAMDC4). In this study, we demonstrate that BUD2 could be induced by auxin, and the induction is dependent on auxin signaling. The mutation of BUD2 results in hyposensitivity to auxin and hypersensitivity to cytokinin, which is confirmed by callus induction assays. Our study suggests that polyamines may play their roles in regulating the plant architecture through affecting the homeostasis of cytokinins and sensitivities to auxin and cytokinin.

• JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis.

  Authors: Falong Lu, Xia Cui, Shuaibin Zhang, Chunyan Liu, Xiaofeng Cao

  Cell research. 02/2010; 20(3):387-90.

• Judgment Number Reduction: an Issue in the Analytic Hierarchy Process.

  Authors: Long-Ting Wu, Xia Cui, Ruwei Dai

  International Journal of Information Technology and Decision Making. 01/2010; 9:175-189.

• Histone methylation in higher plants.

  Authors: Chunyan Liu, Falong Lu, Xia Cui, Xiaofeng Cao

  Annual review of plant biology. 01/2010; 61:395-420.

  Histone methylation plays a fundamental role in regulating diverse developmental processes and is also involved in silencing repetitive sequences in order to maintain genome stability. TheHistone methylation plays a fundamental role in regulating diverse developmental processes and is also involved in silencing repetitive sequences in order to maintain genome stability. The methylation marks are written on lysine or arginine by distinct enzymes, namely, histone lysine methyltransferases (HKMTs) or protein arginine methyltransferases (PRMTs). Once established, the methylation marks are specifically recognized by the proteins that act as readers and are interpreted into specific biological outcomes. Histone methylation status is dynamic; methylation marks can be removed by eraser enzymes, the histone demethylases (HDMs). The proteins responsible for writing, reading, and erasing the methylation marks are known mostly in animals. During the past several years, a growing body of literature has demonstrated the impact of histone methylation on genome management, transcriptional regulation, and development in plants. The aim of this review is to summarize the biochemical, genetic, and molecular action of histone methylation in two plants, the dicot Arabidopsis and the monocot rice.

• Sixty-eight cases of child chronic cough treated by moxibustion.

  Authors: Xia Cui, Su-mei Wang, Li-qun Wu

  Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan / sponsored by All-China Association of Traditional Chinese Medicine, Academy of Traditional Chinese Medicine. 04/2009; 29(1):9-10.

  OBJECTIVE: To observe the therapeutic effects of moxibustion for chronic cough in children. METHODS: 68 child cases of chronic cough were treated by moxibustion. RESULTS: 54 cases were cured, 13OBJECTIVE: To observe the therapeutic effects of moxibustion for chronic cough in children. METHODS: 68 child cases of chronic cough were treated by moxibustion. RESULTS: 54 cases were cured, 13 cases improved, and one case failed. The cure rate was 79.2%, with a total effective rate of 98.5%. CONCLUSION: The moxibustion therapy has definite therapeutic effect for children chronic cough.

• Meta-synthetic Computing Formula of Situation Assessment in Social Interactions

  Authors: Xia Cui, Ruwei Dai

  Computer Software and Applications, 2008. COMPSAC '08. 32nd Annual IEEE International; 09/2008

  Situation assessment in interactions needs to make an explicit evaluation of the social interactions. When there is more than one agent or ldquoplayerrdquo, the logic of knowledge and belief play anSituation assessment in interactions needs to make an explicit evaluation of the social interactions. When there is more than one agent or ldquoplayerrdquo, the logic of knowledge and belief play an important role. One is interested not only in each personpsilas knowledge and beliefs about substantive matters, but also in his knowledge and beliefs about the others. This paper explored the meta-synthetic computing formula of situation assessment in social interactions. First, each personpsilas knowledge and belief determines the interactive structure, which can be computer-aided calculation. Second, the process of interactions is dynamic, the assessment needs an open interactive environment to analyze and understand the situation, which is human-computer symbiotic. Third, these interactions are supported by the data and information processing algorithm and models. Interactive structure aided by computer, human-computer symbiotic open interactive environment, data and information processing algorithm and models constitute meta-synthetic computing formula of situation assessment.

• Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice.

  Authors: Falong Lu, Guanglin Li, Xia Cui, Chunyan Liu, Xiu-Jie Wang, Xiaofeng Cao

  Journal of integrative plant biology. 08/2008; 50(7):886-96.

  Histone methylation homeostasis is achieved by controlling the balance between methylation and demethylation to maintain chromatin function and developmental regulation. In animals, a conservedHistone methylation homeostasis is achieved by controlling the balance between methylation and demethylation to maintain chromatin function and developmental regulation. In animals, a conserved Jumonji C (JmjC) domain was found in a large group of histone demethylases. However, it is still unclear whether plants also contain the JmjC domain-containing active histone demethylases. Here we performed genome-wide screen and phylogenetic analysis of JmjC domain-containing proteins in the dicot plant, Arabidopsis, and monocot plant rice, and found 21 and 20 JmjC domain-containing, respectively. We also examined the expression of JmjC domain-containing proteins and compared them to human JmjC counterparts for potential enzymatic activity. The spatial expression patterns of the Arabidopsis JmjC domain-containing genes revealed that they are all actively transcribed genes. These active plant JmjC domain-containing genes could possibly function in epigenetic regulation to antagonize the activity of the large number of putative SET domain-containing histone methyltransferase activity to dynamically regulate histone methylation homeostasis.

• Meta-synthetic Computing Formula of Situation Assessment in Social Interactions.

  Authors: Xia Cui, Ruwei Dai

  Proceedings of the 32nd Annual IEEE International Computer Software and Applications Conference, COMPSAC 2008, 28 July - 1 August 2008, Turku, Finland; 01/2008

• Extracting Social Network among Various Entities from Chinese News Stories by Content Analysis.

  Authors: Weijie Yang, Ruwei Dai, Xia Cui

  Proceedings of the 32nd Annual IEEE International Computer Software and Applications Conference, COMPSAC 2008, 28 July - 1 August 2008, Turku, Finland; 01/2008

• A Novel Chinese Text Summarization Approach Using Sentence Extraction Based on Kernel Words Recognition.

  Authors: Weijie Yang, Ruwei Dai, Xia Cui

  Fifth International Conference on Fuzzy Systems and Knowledge Discovery, FSKD 2008, 18-20 October 2008, Jinan, Shandong, China, Proceedings, Volume 4; 01/2008

• Paradigms of Meta-synthetic Computing.

  Authors: Yaodong Li, Xia Cui, Ruwei Dai

  Proceedings of the 32nd Annual IEEE International Computer Software and Applications Conference, COMPSAC 2008, 28 July - 1 August 2008, Turku, Finland; 01/2008

• Similarity classifier in diagnosis of bladder cancer.

  Authors: Xia Cui, Ruwei Dai

  IJIIDS. 01/2008; 2:43-49.

• Oryza sativa dicer-like4 reveals a key role for small interfering RNA silencing in plant development.

  Authors: Bin Liu, Zhiyu Chen, Xianwei Song, Chunyan Liu, Xia Cui, Xianfeng Zhao, Jun Fang, Wenying Xu, Huiyong Zhang, Xiujie Wang, Chengcai Chu, Xingwang Deng, Yongbiao Xue, Xiaofeng Cao

  The Plant cell. 10/2007; 19(9):2705-18.

  MicroRNAs and small interfering RNAs (siRNAs) are two classes of small regulatory RNAs derived from different types of precursors and processed by distinct Dicer or Dicer-like (DCL) proteins. DuringMicroRNAs and small interfering RNAs (siRNAs) are two classes of small regulatory RNAs derived from different types of precursors and processed by distinct Dicer or Dicer-like (DCL) proteins. During evolution, four Arabidopsis thaliana DCLs and six rice (Oryza sativa) DCLs (Os DCLs) appear to have acquired specialized functions. The Arabidopsis DCLs are well characterized, but those in rice remain largely unstudied. Here, we show that both knockdown and loss of function of rice DCL4, the homolog of Arabidopsis DCL4, lead to vegetative growth abnormalities and severe developmental defects in spikelet identity. These phenotypic alterations appear to be distinct from those observed in Arabidopsis dcl4 mutants, which exhibit accelerated vegetative phase change. The difference in phenotype between rice and Arabidopsis dcl4 mutants suggests that siRNA processing by DCL4 has a broader role in rice development than in Arabidopsis. Biochemical and genetic analyses indicate that Os DCL4 is the major Dicer responsible for the 21-nucleotide siRNAs associated with inverted repeat transgenes and for trans-acting siRNA (ta-siRNA) from the endogenous TRANS-ACTING siRNA3 (TAS3) gene. We show that the biogenesis mechanism of TAS3 ta-siRNA is conserved but that putative direct targets of Os DCL4 appear to be differentially regulated between monocots and dicots. Our results reveal a critical role of Os DCL4-mediated ta-siRNA biogenesis in rice development.

• BUD2, encoding an S-adenosylmethionine decarboxylase, is required for Arabidopsis growth and development.

  Authors: Chunmin Ge, Xia Cui, Yonghong Wang, Yuxin Hu, Zhiming Fu, Dongfen Zhang, Zhukuan Cheng, Jiayang Li

  Cell research. 06/2006; 16(5):446-56.

  Polyamines are implicated in regulating various developmental processes in plants, but their exact roles and how they govern these processes still remain elusive. We report here an Arabidopsis bushyPolyamines are implicated in regulating various developmental processes in plants, but their exact roles and how they govern these processes still remain elusive. We report here an Arabidopsis bushy and dwarf mutant, bud2, which results from the complete deletion of one member of the small gene family that encodes S-adenosylmethionine decarboxylases (SAMDCs) necessary for the formation of the indispensable intermediate in the polyamine biosynthetic pathway. The bud2 plant has enlarged vascular systems in inflorescences, roots, and petioles, and an altered homeostasis of polyamines. The double mutant of bud2 and samdc1, a knockdown mutant of another SAMDC member, is embryo lethal, demonstrating that SAMDCs are essential for plant embryogenesis. Our results suggest that polyamines are required for the normal growth and development of higher plants.

• Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice.

  Authors: Zhenyu Gao, Dali Zeng, Xia Cui, Yihua Zhou, Meixian Yan, Danian Huang, Jiayang Li, Qian Qian

  Science in China. Series C, Life sciences / Chinese Academy of Sciences. 01/2004; 46(6):661-8.

  Gelatinization temperature (GT) is an important parameter for evaluating the cooking and eating quality of rice besides amylose content (AC). The inheritance of the genes affecting GT has been widelyGelatinization temperature (GT) is an important parameter for evaluating the cooking and eating quality of rice besides amylose content (AC). The inheritance of the genes affecting GT has been widely studied and is considered to be controlled by a major gene. Here, we report the map-based cloning of rice ALK that encodes the soluble starch synthase II (SSSII). Comparison between the DNA sequences from different rice varieties, together with the results obtained with digestion of the rice seeds in alkali solution, indicates that the base substitutions in coding sequence of ALK may cause the alteration in GT.

• MESSIA: Combining MESSAGE with GAIA

  Authors: Yaodong Li, Xia Cui, Ruwei Dai

  Control and Automation, 2003. ICCA '03. Proceedings. 4th International Conference on; 07/2003

  This paper proposes a new Agent-Oriented Software Engineering (AOSE) method – MESSIA. MESSIA is built on two popular AOSE methodologies: GAIA and MESSAGE. While, it has its own characteristics: 1)This paper proposes a new Agent-Oriented Software Engineering (AOSE) method – MESSIA. MESSIA is built on two popular AOSE methodologies: GAIA and MESSAGE. While, it has its own characteristics: 1) MESSIA unites the analysis models of GAIA with the refinement strategy of MESSAGE, which bridges the large gap between the system requirements and the needed models; 2) The hierarchical analysis and design in MESSIA utilize the hierarchical structure of the systems to be developed, and help developers to give their attentions to only a small part of the system in one time, which makes it possible for them to decompose the system gradually and efficiently.