Junli Zhou

Publications (15)136.01 Total impact

• Article: Extracellular calmodulin acceleratesrbcS-GUS expression in suspension-cultured transgenic tobacco cell

  Ligeng Ma, Junli Zhou, Suqiao Zhang, Qiang Liu, Daye Sun
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  ABSTRACT: The role of extracellular calmodulin in regulating expression ofrbcS in darkness was examined. A suspension-cultured cell line was generated from the transgenicrbcS-GUS tobacco. It was demonstrated that purified calmodulin added to the media enhancedrbcS-GUS expression. The time course of expression ofrbcS-GUS and that of the secretion of calmodulin in the suspended transgenic tobacco cells in darkness were very similar. Both showed initial increase followed by decline with maximum calmodulin secretion preceding maximumGUS expression. The addition of membrane-impermeable calmodulin antagonist W7-agarose inhibited the expression ofrbcS-GUS in darkness, but this inhibitory effect was completely reversed by adding exogenous purified calmodulin. These results provide the first evidence that extracellular calmodulin acceleratesrbcS gene expression. Keywordsextracellular calmodulin- rbcS expression-transgenic tobacco
  Chinese Science Bulletin 04/2012; 45(22):2089-2092. · 1.32 Impact Factor
• Source

  Available from: openwetware.org

  Article: Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression.

  Junli Zhou, Xiangfeng Wang, Kun He, Jean-Benoit F Charron, Axel A Elling, Xing Wang Deng
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  ABSTRACT: Lysine residue 9 of histone H3 can either be acetylated or mono-, di-, or tri-methylated. These epigenetic states have a diverse impact on regulating gene transcriptional activity and chromatin organization. H3K9ac is invariably correlated with transcriptional activation, whereas H3K9me2 has been reported to be mainly located in constitutive heterochromatin in Arabidopsis. Here, we present epigenetic landscapes for histone H3 lysine 9 acetylation (H3K9ac) and dimethylation (H3K9me2) in Arabidopsis seedlings. The results show that H3K9ac targeted 5,206 non-transposable element (non-TE) genes and 321 transposable elements (TEs), whereas H3K9me2 targeted 2,281 TEs and 1,112 non-TE genes. H3K9ac was biased towards the 5' end of genes and peaked at the ATG position, while H3K9me2 tended to span the entire gene body. H3K9ac correlated with high gene expression, while H3K9me2 correlated with low expression. Analyses of H3K9ac and H3K9me2 with the available datasets of H3K27me3 and DNA methylation revealed a correlation between the occurrence of multiple epigenetic modifications and gene expression. Genes with H3K9ac alone were actively transcribed, while genes that were also modified by either H3K27me3 or DNA methylation showed a lower expression level, suggesting that a combination of repressive marks weakened the positive regulatory effect of H3K9ac. Furthermore, we observed a significant increase of the H3K9ac modification level of selected target genes in hda19 (histone deacetylase 19) mutant seedlings, which indicated that HDA19 plays an important role in regulating the level of H3K9ac and thereby influencing the transcriptional activity in young seedlings.
  Plant Molecular Biology 04/2010; 72(6):585-95. · 4.15 Impact Factor
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  Available from: PubMed Central

  Article: NTAP: for NimbleGen tiling array ChIP-chip data analysis.

  Kun He, Xueyong Li, Junli Zhou, Xing-Wang Deng, Hongyu Zhao, Jingchu Luo
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  ABSTRACT: NTAP is designed to analyze ChIP-chip data generated by the NimbleGen tiling array platform and to accomplish various pattern recognition tasks that are useful especially for epigenetic studies. The modular design of NTAP makes the data processing highly customizable. Users can either use NTAP to perform the full process of NimbleGen tiling array data analysis, or choose post-processing modules in NTAP to analyze pre-processed epigenetic data generated by other platforms. The output of NTAP can be saved in standard GFF format files and visualized in GBrowse. Availability and Implementation:The source code of NTAP is freely available at http://ntap.cbi.pku.edu.cn/. It is implemented in Perl and R and can be used on Linux, Mac and Windows platforms.
  Bioinformatics 06/2009; 25(14):1838-40. · 5.47 Impact Factor
• Article: NTAP: for NimbleGen tiling array ChIP-chip data analysis.

  Kun He, Xueyong Li, Junli Zhou, Xingwang Deng, Hongyu Zhao, Jingchu Luo
  Bioinformatics. 01/2009; 25:1838-1840.
• Article: Histone modifications and expression of light-regulated genes in Arabidopsis are cooperatively influenced by changing light conditions.

  Lan Guo, Junli Zhou, Axel A Elling, Jean-Benoit F Charron, Xing Wang Deng
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  ABSTRACT: Here, we analyzed the effects of light regulation on four selected histone modifications (H3K4me3, H3K9ac, H3K9me2, and H3K27me3) and the relationship of these histone modifications with the expression of representative light-regulated genes. We observed that the histone modifications examined and gene transcription were cooperatively regulated in response to changing light environments. Using H3K9ac as an example, our analysis indicated that histone modification patterns are set up very early and are relatively stable during Arabidopsis (Arabidopsis thaliana) seedling development. Distinct photoreceptor systems are responsible for mediating the effects of different light qualities on histone modifications. Moreover, we found that light regulation of gene-specific histone modifications involved the known photomorphogenesis-related proteolytic system defined by the pleiotropic CONSTITUTIVE PHOTOMORPHOGENIC/DE-ETOLIATED proteins and histone modification enzymes (such as HD1). Furthermore, our data suggest that light-regulated changes in histone modifications might be an intricate part of light-controlled gene transcription. Thus, it is possible that variations in histone modifications are an important physiological component of plant responses to changing light environments.
  Plant physiology 07/2008; 147(4):2070-83. · 6.53 Impact Factor
• Article: Coordinated regulation of Arabidopsis thaliana development by light and gibberellins.

  Suhua Feng, Cristina Martinez, Giuliana Gusmaroli, Yu Wang, Junli Zhou, Feng Wang, Liying Chen, Lu Yu, Juan M Iglesias-Pedraz, Stefan Kircher, Eberhard Schäfer, Xiangdong Fu, Liu-Min Fan, Xing Wang Deng
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  ABSTRACT: Light and gibberellins (GAs) mediate many essential and partially overlapping plant developmental processes. DELLA proteins are GA-signalling repressors that block GA-induced development. GA induces degradation of DELLA proteins via the ubiquitin/proteasome pathway, but light promotes accumulation of DELLA proteins by reducing GA levels. It was proposed that DELLA proteins restrain plant growth largely through their effect on gene expression. However, the precise mechanism of their function in coordinating GA signalling and gene expression remains unknown. Here we characterize a nuclear protein interaction cascade mediating transduction of GA signals to the activity regulation of a light-responsive transcription factor. In the absence of GA, nuclear-localized DELLA proteins accumulate to higher levels, interact with phytochrome-interacting factor 3 (PIF3, a bHLH-type transcription factor) and prevent PIF3 from binding to its target gene promoters and regulating gene expression, and therefore abrogate PIF3-mediated light control of hypocotyl elongation. In the presence of GA, GID1 proteins (GA receptors) elevate their direct interaction with DELLA proteins in the nucleus, trigger DELLA protein's ubiquitination and proteasome-mediated degradation, and thus release PIF3 from the negative effect of DELLA proteins.
  Nature 02/2008; 451(7177):475-9. · 36.28 Impact Factor
• Article: Coordinated regulation of Arabidopsisthaliana development by light and gibberellins

  Suhua Feng, Cristina Martinez, Giuliana Gusmaroli, Yu Wang, Junli Zhou, Feng Wang, Liying Chen, Lu Yu, Juan M. Iglesias-Pedraz, Stefan Kircher, Eberhard Sch|[auml]|fer, Xiangdong Fu, Liu-Min Fan, Xing Wang Deng
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  ABSTRACT: Light and gibberellins (GAs) mediate many essential and partially overlapping plant developmental processes. DELLA proteins are GA-signalling repressors that block GA-induced development
  Nature 01/2008; 451(7177):475-479. · 36.28 Impact Factor
• Source

  Available from: PubMed Central

  Article: Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle.

  Junli Zhou, Xiangfeng Wang, Yuling Jiao, Yonghua Qin, Xigang Liu, Kun He, Chen Chen, Ligeng Ma, Jian Wang, Lizhong Xiong, Qifa Zhang, Liumin Fan, Xing Wang Deng
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  ABSTRACT: To elucidate genome-level responses to drought and high-salinity stress in rice, a 70 mer oligomer microarray covering 36,926 unique genes or gene models was used to profile genome expression changes in rice shoot, flag leaf and panicle under drought or high-salinity conditions. While patterns of gene expression in response to drought or high-salinity stress within a particular organ type showed significant overlap, comparison of expression profiles among different organs showed largely organ-specific patterns of regulation. Moreover, both stresses appear to alter the expression patterns of a significant number of genes involved in transcription and cell signaling in a largely organ-specific manner. The promoter regions of genes induced by both stresses or induced by one stress in more than one organ types possess relative enrichment of two cis-elements (ABRE core and DRE core) known to be associated with water stress. An initial computational analysis indicated that novel promoter motifs are present in the promoters of genes involved in rehydration after drought. This analysis suggested that rice might possess a mechanism that actively detects rehydration and facilitates rapid recovery. Overall, our data supports a notion that organ-specific gene regulation in response to the two abiotic stresses may primarily be mediated by organ-specific transcription responses.
  Plant Molecular Biology 04/2007; 63(5):591-608. · 4.15 Impact Factor
• Source

  Available from: Sulan Bai

  Article: Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice.

  Ning Su, Kun He, Yuling Jiao, Chen Chen, Junli Zhou, Lei Li, Sulan Bai, Xueyong Li, Xing Wang Deng
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  ABSTRACT: Most plant cells retain the capacity to differentiate into all the other cell and organ types that constitute a plant. However, genome-wide transcriptional activities underlying the process of cell differentiation are poorly understood, especially in monocot plants. Here we used a rice (Oryza sativa) cell culture system to generate somatic embryos, which were further induced into shoots and roots. The global transcriptional reorganization during the development of somatic embryos, shoots, and roots from cultured cells was studied using a rice whole genome microarray and verified by RNA blotting analysis of representative genes. Overall, only 1-3% of expressed genes were differentially regulated during each organogenesis process at the examined time point. Also metabolic pathways were minimally regulated. Thus the genes that dictating organ formation should be relatively small in number. Comparison of these three transcriptomes revealed little overlap during these three organogenesis processes. These results indicate that each organogenesis involves specific reorganization of genome expression.
  Plant Molecular Biology 03/2007; 63(3):337-49. · 4.15 Impact Factor
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  Available from: yale.edu

  Article: Development of rabbit monoclonal and polyclonal antibodies for detection of site-specific histone modifications and their application in analyzing overall modification levels.

  Lan Guo, Benliang Yin, Junli Zhou, Xueyong Li, Xing Wang Deng
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  ABSTRACT: In addition to DNA sequence information, site-specific histone modifications are another important determinant of gene expression in a eukaryotic organism. We selected four modification sites in common histones that are known to significantly impact chromatin function and generated monoclonal or polyclonal antibodies that recognize each of those site-specific modifications. We used these antibodies to demonstrate that the site-specific histone modification levels remain relatively constant in different organs of the same organism. We also compared the levels of selected histone modifications among several representative organisms and found that site-specific modifications are highly variable among different organisms, providing new insight into the evolutionary divergence of specific histone modifications.
  Cell Research 06/2006; 16(5):519-27. · 8.19 Impact Factor
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  Available from: Yongbiao Xue

  Article: Evolution in action: following function in duplicated floral homeotic genes.

  Barry Causier, Rosa Castillo, Junli Zhou, Richard Ingram, Yongbiao Xue, Zsuzsanna Schwarz-Sommer, Brendan Davies
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  ABSTRACT: Gene duplication plays a fundamental role in evolution by providing the genetic material from which novel functions can arise. Newly duplicated genes can be maintained by subfunctionalization (the duplicated genes perform different aspects of the original gene's function) and/or neofunctionalization (one of the genes acquires a novel function). PLENA in Antirrhinum and AGAMOUS in Arabidopsis are the canonical C-function genes that are essential for the specification of reproductive organs. These functionally equivalent genes encode closely related homeotic MADS-box transcription factors. Using genome synteny, we confirm phylogenetic analyses showing that PLENA and AGAMOUS are nonorthologous genes derived from a duplication in a common ancestor. Their respective orthologs, SHATTERPROOF in Arabidopsis and FARINELLI in Antirrhinum, have undergone independent subfunctionalization via changes in regulation and protein function. Surprisingly, the functional divergence between PLENA and FARINELLI, is morphologically manifest in both transgenic Antirrhinum and Arabidopsis. This provides a clear illustration of a random evolutionary trajectory for gene functions after a duplication event. Different members of a duplicated gene pair have retained the primary homeotic functions in different lineages, illustrating the role of chance in evolution. The differential ability of the Antirrhinum genes to promote male or female development provides a striking example of subfunctionalization at the protein level.
  Current Biology 09/2005; 15(16):1508-12. · 9.65 Impact Factor
• Article: The F-box protein AhSLF-S2 controls the pollen function of S-RNase-based self-incompatibility.

  Hong Qiao, Fei Wang, Lan Zhao, Junli Zhou, Zhao Lai, Yansheng Zhang, Timothy P Robbins, Yongbiao Xue
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  ABSTRACT: Recently, we have provided evidence that the polymorphic self-incompatibility (S) locus-encoded F-box (SLF) protein AhSLF-S(2) plays a role in mediating a selective S-RNase destruction during the self-incompatible response in Antirrhinum hispanicum. To investigate its role further, we first transformed a transformation-competent artificial chromosome clone (TAC26) containing both AhSLF-S(2) and AhS(2)-RNase into a self-incompatible (SI) line of Petunia hybrida. Molecular analyses showed that both genes are correctly expressed in pollen and pistil in four independent transgenic lines of petunia. Pollination tests indicated that all four lines became self-compatible because of the specific loss of the pollen function of SI. This alteration was transmitted stably into the T1 progeny. We then transformed AhSLF-S(2) cDNA under the control of a tomato (Lycopersicon esculentum) pollen-specific promoter LAT52 into the self-incompatible petunia line. Molecular studies revealed that AhSLF-S(2) is specifically expressed in pollen of five independent transgenic plants. Pollination tests showed that they also had lost the pollen function of SI. Importantly, expression of endogenous SLF or SLF-like genes was not altered in these transgenic plants. These results phenocopy a well-known phenomenon called competitive interaction whereby the presence of two different pollen S alleles within pollen leads to the breakdown of the pollen function of SI in several solanaceaous species. Furthermore, we demonstrated that AhSLF-S(2) physically interacts with PhS(3)-RNase from the P. hybrida line used for transformation. Together with the recent demonstration of PiSLF as the pollen determinant in P. inflata, these results provide direct evidence that the polymorphic SLF including AhSLF-S(2) controls the pollen function of S-RNase-based self-incompatibility.
  The Plant Cell 10/2004; 16(9):2307-22. · 8.99 Impact Factor
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  Available from: Yongbiao Xue

  Article: The F-box protein AhSLF-S2 physically interacts with S-RNases that may be inhibited by the ubiquitin/26S proteasome pathway of protein degradation during compatible pollination in Antirrhinum.

  Hong Qiao, Hongyun Wang, Lan Zhao, Junli Zhou, Jian Huang, Yansheng Zhang, Yongbiao Xue
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  ABSTRACT: Self-incompatibility S-locus-encoded F-box (SLF) proteins have been identified in Antirrhinum and several Prunus species. Although they appear to play an important role in self-incompatible reaction, functional evidence is lacking. Here, we provide several lines of evidence directly implicating a role of AhSLF-S(2) in self-incompatibility in Antirrhinum. First, a nonallelic physical interaction between AhSLF-S(2) and S-RNases was demonstrated by both coimmunoprecipitation and yeast two-hybrid assays. Second, AhSLF-S(2) interacts with ASK1- and CULLIN1-like proteins in Antirrhinum, and together, they likely form an Skp1/Cullin or CDC53/F-box (SCF) complex. Third, compatible pollination was specifically blocked after the treatment of the proteasomal inhibitors MG115 and MG132, but they had little effect on incompatible pollination both in vitro and in vivo, indicating that the ubiquitin/26S proteasome activity is involved in compatible pollination. Fourth, the ubiquitination level of style proteins was increased substantially after compatible pollination compared with incompatible pollination, and coimmunoprecipitation revealed that S-RNases were ubiquitinated after incubating pollen proteins with compatible but not with incompatible style proteins, suggesting that non-self S-RNases are possibly degraded by the ubiquitin/26S proteasome pathway. Fifth, the S-RNase level appeared to be reduced after 36 h of compatible pollination. Taken together, these results show that AhSLF-S(2) interacts with S-RNases likely through a proposed SCF(AhSLF-S2) complex that targets S-RNase destruction during compatible rather than incompatible pollination, thus providing a biochemical basis for the inhibition of pollen tube growth as observed in self-incompatible response in Antirrhinum.
  The Plant Cell 04/2004; 16(3):582-95. · 8.99 Impact Factor
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  Available from: Yongbiao Xue

  Article: Structural and transcriptional analysis of S-locus F-box genes in Antirrhinum

  Junli Zhou, Fei Wang, Wenshi Ma, Yansheng Zhang, Bin Han, Yongbiao Xue
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  ABSTRACT: A class of ribonucleases termed S-RNases, which control the pistil expression of self-incompatibility, represents the only known functional products encoded by the S locus in species from the Solanaceae, Scrophulariaceae and Rosaceae. Previously, we identified a pollen-specific F-box gene, AhSLF (S locus F-box)-S2, very similar to S2-RNase in Antirrhinum, a member of the Scrophulariaceae. In addition, AhSLF-S2 also detected the presence of its homologous DNA fragments. To identify these fragments, we constructed two genomic DNA libraries from Antirrhinum self-incompatible lines carrying alleles S1S5 and S2S4, respectively, using a transformation-competent artificial chromosome (TAC) vector. With AhSLF-S2-specific primers, TAC clones containing both AhSLF-S2 and its homologs were subsequently identified (S2TAC, S5TACa, S4TAC, and S1TACa). DNA blot hybridization, sequencing and segregation analyses revealed that they are organized as single allelic copies (AhSLF-S2, -S1, -S4 and -S5) tightly linked to the S-RNases. Furthermore, clusters of F-box genes similar to AhSLF-S2 were identified. In total, three F-box genes (AhSLF-S2, -S2A and -S2C) in S2TAC (51kb), three (AhSLF-S4, -S4A and -S4D) in S4TAC (75kb), two (AhSLF-S5 and -S5A) in S5TACa (55kb), and two (AhSLF-S1 and -S1E) in S1TACa (71kb), respectively, were identified. Paralogous copies of these genes show 38–54% identity, with allelic copies sharing 90% amino acid identity. Among these genes, three (AhSLF-S2C, -S4D and -S1E) were specifically expressed in pollen, similar to AhSLF-S2, implying that they likely play important roles in pollen, whereas three AhSLF-SA alleles showed no detectable expression. In addition, several types of retroelements and transposons were identified in the sequenced regions, revealing some detailed information on the structural diversity of the S locus region. Taken together, these results indicate that both single allelic and tandemly duplicated genes are associated with the S locus in Antirrhinum. The implications of these findings in evolution and possible roles of allelic AhSLF-S genes in the self-incompatible reaction are discussed in species like Antirrhinum.
  Sexual Plant Reproduction 10/2003; 16(4):165-177. · 1.87 Impact Factor
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  Available from: amet.mnsu.edu

  Article: Coupling of thermal mass and natural ventilation in buildings

  Junli Zhou, Guoqiang Zhang, Yaolin Lin, Yuguo Li
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  ABSTRACT: The coupling of thermal mass and natural ventilation is important to passive building design. Thermal mass can be classified as external thermal mass and internal thermal mass. Due to great diurnal variation of ambient air temperature and solar radiation intensity, heat transfer through building envelopes, which is called external thermal mass, is a complex and unsteady process. Indoor furniture are internal thermal mass, affecting the indoor air temperature through the process of absorbing and releasing heat. In this paper, a heat balance model coupling the external and internal thermal mass, natural ventilation rate and indoor air temperature for naturally ventilated building is developed. In this model, the inner surface temperature of building envelopes is obtained based on the harmonic response method. The effect of external and internal thermal mass on indoor air temperature for six external walls is discussed of different configurations including lightweight and heavy structures with and without external/internal insulation. Based on this model, a simple tool is developed to estimate the indoor air temperature for certain external and internal thermal mass and to determine the internal thermal mass needed to maintain required indoor air temperature for certain external wall for naturally ventilated building.
  Energy and Buildings.