Publications by authors named "Xuncheng Wang"

18 Publications

  • Page 1 of 1

Natural variation in the transcription factor REPLUMLESS contributes to both disease resistance and plant growth in Arabidopsis.

Plant Commun 2022 Jun 26:100351. Epub 2022 Jun 26.

School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address:

When attacked by pathogens, plants need to reallocate energy from growth to defense to fend off the invaders, frequently incurring growth penalties. This phenomenon is known as the growth-defense tradeoff and is orchestrated by a hardwired transcriptional network. Altering key factors involved in this network has the potential to increase disease resistance without growth or yield loss, but the mechanisms underlying such changes require further investigation. By conducting a genome-wide association study (GWAS) of leaves infected by the hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000, we discovered that the Arabidopsis transcription factor REPLUMLESS (RPL) is necessary for bacterial resistance. More importantly, RPL functions in promoting both disease resistance and growth. Transcriptome analysis revealed a cluster of genes in the GRETCHEN HAGEN 3 (GH3) family that were significantly upregulated in rpl mutants, leading to the accumulation of indole-3-acetic acid-aspartic acid (IAA-Asp). Consistent with this observation, transcripts of virulence effector genes were activated by IAA-Asp accumulated in the rpl mutants. We found that RPL protein could directly bind to GH3 promoters and repress their expression. RPL also repressed flavonol synthesis by directly repressing CHI expression and thus activated the auxin transport pathway, which promotes plant growth. Therefore, RPL plays an important role in plant immunity and functions in the auxin pathway to optimize Arabidopsis growth and defense.
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http://dx.doi.org/10.1016/j.xplc.2022.100351DOI Listing
June 2022

The photomorphogenic repressors BBX28 and BBX29 integrate light and brassinosteroid signaling to inhibit seedling development in Arabidopsis.

Plant Cell 2022 05;34(6):2266-2285

Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.

B-box containing proteins (BBXs) integrate light and various hormonal signals to regulate plant growth and development. Here, we demonstrate that the photomorphogenic repressors BBX28 and BBX29 positively regulate brassinosteroid (BR) signaling in Arabidopsis thaliana seedlings. Treatment with the BR brassinolide stabilized BBX28 and BBX29, which partially depended on BR INSENSITIVE1 (BRI1) and BIN2. bbx28 bbx29 seedlings exhibited larger cotyledon aperture than the wild-type when treated with brassinazole in the dark, which partially suppressed the closed cotyledons of brassinazole resistant 1-1D (bzr1-1D). Consistently, overexpressing BBX28 and BBX29 partially rescued the short hypocotyls of bri1-5 and bin2-1 in both the dark and light, while the loss-of-function of BBX28 and BBX29 partially suppressed the long hypocotyls of bzr1-1D in the light. BBX28 and BBX29 physically interacted with BR-ENHANCED EXPRESSION1 (BEE1), BEE2, and BEE3 and enhanced their binding to and activation of their target genes. Moreover, BBX28 and BBX29 as well as BEE1, BEE2, and BEE3 increased BZR1 accumulation to promote the BR signaling pathway. Therefore, both BBX28 and BBX29 interact with BEE1, BEE2, and BEE3 to orchestrate light and BR signaling by facilitating the transcriptional activity of BEE target genes. Our study provides insights into the pivotal roles of BBX28 and BBX29 as signal integrators in ensuring normal seedling development.
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http://dx.doi.org/10.1093/plcell/koac092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9134050PMC
May 2022

Systemic Identification and Functional Characterization of Common in Fungal Extracellular Membrane Proteins in .

Front Plant Sci 2021 20;12:804696. Epub 2021 Dec 20.

Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.

Plant pathogenic fungi deploy secreted proteins into apoplastic space or intracellular lumen to promote successful infections during plant-pathogen interactions. In the present study, fourteen CFEM domain-containing proteins were systemically identified in and eight of them were functionally characterized. All eight proteins were confirmed to be secreted into extracellular space by a yeast signal peptide trapping system. The transcriptional levels of most CFEM genes, except for and , were significantly elevated during infection. In addition, almost all genes, apart from , , and , were transcriptionally up-regulated at 35°C in contrast to that at 25°C and 30°C. As two elicitors, LtCFEM1 induced local yellowish phenotype and LtCFEM4 triggered cell death in leaves. Furthermore, these proteins displayed distinct subcellular localizations when expressed transiently in . Moreover, two genes, and , were found to be spliced alternatively by RT-PCR and sequencing. Therefore, our data suggest that LtCFEM proteins play important roles in multiple aspects, including pathogenicity and plant immune response, which will enhance our understanding of the sophisticated pathogenic mechanisms of plant opportunistic pathogen .
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http://dx.doi.org/10.3389/fpls.2021.804696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8721227PMC
December 2021

A missense mutation in WRKY32 converts its function from a positive regulator to a repressor of photomorphogenesis.

New Phytol 2022 07 7;235(1):111-125. Epub 2022 Jan 7.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.

CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) mediates various cellular and physiological processes in plants by targeting a large number of substrates for ubiquitination and degradation. In this study, we reveal that a substitution of Pro for Leu at amino acid position 409 in WRKY32 largely suppresses the short hypocotyls and expanded cotyledon phenotypes of cop1-6. WRKY32 promotes hypocotyl growth and inhibits the opening of cotyledons in Arabidopsis. Loss of WRKY32 function mutant seedlings display elongated hypocotyls, whereas overexpression of WRKY32 leads to shortened hypocotyls. WRKY32 directly associates with the promoter regions of HY5 to activate its transcription. COP1 interacts with and targets WRKY32 for ubiquitination and degradation in darkness. WRKY32 exhibits enhanced DNA binding ability and affects the expression of more genes compared with WRKY32 in Arabidopsis. Our results not only reveal the basic role for WRKY32 in promoting photomorphogenesis, but also provide insights into manipulating plant growth by engineering key components of light signaling.
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http://dx.doi.org/10.1111/nph.17932DOI Listing
July 2022

A central circadian oscillator confers defense heterosis in hybrids without growth vigor costs.

Nat Commun 2021 04 19;12(1):2317. Epub 2021 Apr 19.

School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.

Plant immunity frequently incurs growth penalties, which known as the trade-off between immunity and growth. Heterosis, the phenotypic superiority of a hybrid over its parents, has been demonstrated for many traits but rarely for disease resistance. Here, we report that the central circadian oscillator, CCA1, confers heterosis for bacterial defense in hybrids without growth vigor costs, and it even significantly enhances the growth heterosis of hybrids under pathogen infection. The genetic perturbation of CCA1 abrogated heterosis for both defense and growth in hybrids. Upon pathogen attack, the expression of CCA1 in F hybrids is precisely modulated at different time points during the day by its rhythmic histone modifications. Before dawn of the first infection day, epigenetic activation of CCA1 promotes an elevation of salicylic acid accumulation in hybrids, enabling heterosis for defense. During the middle of every infection day, diurnal epigenetic repression of CCA1 leads to rhythmically increased chlorophyll synthesis and starch metabolism in hybrids, effectively eliminating the immunity-growth heterosis trade-offs in hybrids.
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http://dx.doi.org/10.1038/s41467-021-22268-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8055661PMC
April 2021

A Positive Feedback Loop of BBX11-BBX21-HY5 Promotes Photomorphogenic Development in .

Plant Commun 2020 09 16;1(5):100045. Epub 2020 Apr 16.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.

Light is the most important environmental factor affecting many aspects of plant development. In this study, we report that B-box protein 11 (BBX11) acts as a positive regulator of red light signaling. BBX11 loss-of-function mutant seedlings display significantly elongated hypocotyls under conditions of both red light and long day, whereas overexpression causes markedly shortened hypocotyls under various light states. BBX11 binds to the promoter to activate its transcription, while both BBX21 and HY5 associate with the promoter of to positively regulate its expression. Taken together, our results reveal positive feedback regulation of photomorphogenesis consisting of BBX11, BBX21, and HY5, thus substantiating a transcriptional regulatory mechanism in the response of plants to light during normal development.
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http://dx.doi.org/10.1016/j.xplc.2020.100045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7747993PMC
September 2020

BBX4, a phyB-interacting and modulated regulator, directly interacts with PIF3 to fine tune red light-mediated photomorphogenesis.

Proc Natl Acad Sci U S A 2019 12 27;116(51):26049-26056. Epub 2019 Nov 27.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, 210095 Nanjing, China;

Phytochrome B (phyB) absorbs red light signals and subsequently initiates a set of molecular events in plant cells to promote photomorphogenesis. Here we show that phyB directly interacts with B-BOX CONTAINING PROTEIN 4 (BBX4), a positive regulator of red light signaling, and positively controls its abundance in red light. BBX4 associates with PHYTOCHROME INTERACTING FACTOR 3 (PIF3) and represses PIF3 transcriptional activation activity and PIF3-controlled gene expression. The degradation of BBX4 in darkness is dependent on CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and the 26S proteasome system. Collectively, BBX4 acts as a key component of the phyB-PIF3-mediated signaling module and fine tunes the red light action. phyB promotes the accumulation of BBX4, which in turn serves to repress PIF3 action through direct physical interaction to promote photomorphogenic development in red light.
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http://dx.doi.org/10.1073/pnas.1915149116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6925995PMC
December 2019

A new regulator of seed size control in Arabidopsis identified by a genome-wide association study.

New Phytol 2019 04 2;222(2):895-906. Epub 2019 Feb 2.

School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.

Organ size in plants is controlled by the interaction between genotype and the environment. Seed size, an important agronomic trait, largely determines yield and is an important focus of research. However, the genetic components underpinning natural variation of seed size in undomesticated species remain largely unidentified. Here we report a genome-wide association study (GWAS) of seed size in Arabidopsis thaliana, which identified 38 significantly associated loci, including one locus associated with CYCB1;4. Natural variations in CYCB1;4, which encodes a cyclin protein involved in the cell cycle, significantly influence seed size in A. thaliana. Transgenic plants with enhanced CYCB1;4 expression show normal development, exhibit increased seed size as a result of an accelerated cell cycle progression, and tend to produce higher yields. By contrast, cycb1;4 mutants have smaller seeds, and the effect is especially pronounced in a large-seed accession. The temporal and spatial expression pattern of CYCB1;4 suggests that this gene may function in both maternal tissues and zygotic tissues to coordinate the final size of seeds. Taken together, our results provide genetic insights into natural variation in seed size in Arabidopsis. Moreover, CYCB1;4 homologs in other crops could have great potential as targets for efforts aimed at yield improvement.
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http://dx.doi.org/10.1111/nph.15642DOI Listing
April 2019

Cis-regulated alternative splicing divergence and its potential contribution to environmental responses in Arabidopsis.

Plant J 2019 02 14;97(3):555-570. Epub 2018 Dec 14.

State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China.

Alternative splicing (AS) plays key roles in plant development and the responses of plants to environmental changes. However, the mechanisms underlying AS divergence (differential expression of transcript isoforms resulting from AS) in plant accessions and its contribution to responses to environmental stimuli remain unclear. In this study, we investigated genome-wide variation of AS in Arabidopsis thaliana accessions Col-0, Bur-0, C24, Kro-0 and Ler-1, as well as their F hybrids, and characterized the regulatory mechanisms for AS divergence by RNA sequencing. We found that most of the divergent AS events in Arabidopsis accessions were cis-regulated by sequence variation, including those in core splice site and splicing motifs. Many genes that differed in AS between Col-0 and Bur-0 were involved in stimulus responses. Further genome-wide association analyses of 22 environmental variables showed that single nucleotide polymorphisms influencing known splice site strength were also associated with environmental stress responses. These results demonstrate that cis-variation in genomic sequences among Arabidopsis accessions was the dominant contributor to AS divergence, and it may contribute to differences in environmental responses among Arabidopsis accessions.
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http://dx.doi.org/10.1111/tpj.14142DOI Listing
February 2019

Transcriptomic analyses reveal molecular mechanisms underlying growth heterosis and weakness of rubber tree seedlings.

BMC Plant Biol 2018 01 9;18(1):10. Epub 2018 Jan 9.

Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan, 571737, China.

Background: Breeding rubber tree seedling with growth heterosis is vital for natural rubber production. It is the prerequisites for effectively utilizing growth heterosis to elucidate its molecular mechanisms, but the molecular mechanisms remain poorly understood in rubber tree. To elucidate seedling growth heterosis, we conducted comparative transcriptomic analyses between the two hybrids and their parents.

Results: By identifying and comparing differently expressed genes (DEGs), we found that the hybrids (BT 3410 and WC 11) show significantly differential expression profiles from their parents (PR 107 and RRIM 600). In BT 3410-parent triad, 1092 (49.95%) and 1094 (50.05%) DEGs indicated clear underdominance or overdominance, respectively. Whereas in WC 11-parent triad, most DEGs (78.2%, 721) showed low- or high-parent dominance; 160 (17.35%) exhibited expression patterns that are not statistically distinguishable from additivity, and 8 (0.87%) and 33 (3.58%) DEGs exhibited underdominance and overdominance, respectively. Furthermore, some biological processes are differentially regulated between two hybrids. Interestingly, the pathway in response to stimulus is significantly downregulated and metabolic pathways are more highly regulated in BT 3410.

Conclusions: Taken together, the genotypes, transcriptomes and biological pathways (especially, carbohydrate metabolism) are highly divergent between two hybrids, which may be associated with growth heterosis and weakness. Analyzing gene action models in hybrid-parent triads, we propose that overdominance may play important roles on growth heterosis, whereas dominance on hybrid weakness in rubber tree seedlings. These findings bring new insights into our understanding of growth heterosis of rubber tree seedling.
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http://dx.doi.org/10.1186/s12870-017-1203-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5759766PMC
January 2018

Genomic architecture of biomass heterosis in .

Proc Natl Acad Sci U S A 2017 07 10;114(30):8101-8106. Epub 2017 Jul 10.

State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China

Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200 hybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an obvious overdominance effect in hybrids. However, the accumulation of significant genetic loci identified in genome-wide association studies (GWAS) in hybrids strongly correlates with better-parent heterosis (BPH). Candidate genes for biomass BPH fall into diverse biological functions, including cellular, metabolic, and developmental processes and stimulus-responsive pathways. Important heterosis candidates include , , and some genes that encode key factors involved in cell cycle regulation. Interestingly, transcriptomic analyses in representative hybrid combinations reveal that heterosis candidate genes are functionally enriched in stimulus-responsive pathways, including responses to biotic and abiotic stimuli and immune responses. In addition, stimulus-responsive genes are repressed to low-parent levels in hybrids with high BPH, whereas middle-parent expression patterns are exhibited in hybrids with no BPH. Our study reveals a genomic architecture for understanding the molecular mechanisms of biomass heterosis in , in which the accumulation of the superior alleles of genes involved in metabolic and cellular processes improve the development and growth of hybrids, whereas the overall repressed expression of stimulus-responsive genes prioritizes growth over responding to environmental stimuli in hybrids under normal conditions.
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http://dx.doi.org/10.1073/pnas.1705423114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5544317PMC
July 2017

Transcriptome analyses reveal molecular mechanism underlying tapping panel dryness of rubber tree (Hevea brasiliensis).

Sci Rep 2016 Mar 23;6:23540. Epub 2016 Mar 23.

State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China.

Tapping panel dryness (TPD) is a serious threat to natural rubber yields from rubber trees, but the molecular mechanisms underlying TPD remain poorly understood. To identify TPD-related genes and reveal these molecular mechanisms, we sequenced and compared the transcriptomes of bark between healthy and TPD trees. In total, 57,760 assembled genes were obtained and analyzed in details. In contrast to healthy rubber trees, 5652 and 2485 genes were up- or downregulated, respectively, in TPD trees. The TPD-related genes were significantly enriched in eight GO terms and five KEGG pathways and were closely associated with ROS metabolism, programmed cell death and rubber biosynthesis. Our results suggest that rubber tree TPD is a complex process involving many genes. The observed lower rubber yield from TPD trees might result from lower isopentenyl diphosphate (IPP) available for rubber biosynthesis and from downregulation of the genes in post-IPP steps of rubber biosynthesis pathway. Our results not only extend our understanding of the complex molecular events involved in TPD but also will be useful for developing effective measures to control TPD of rubber trees.
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http://dx.doi.org/10.1038/srep23540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804210PMC
March 2016

Natural variation of H3K27me3 modification in two Arabidopsis accessions and their hybrid.

J Integr Plant Biol 2016 May 24;58(5):466-74. Epub 2015 Dec 24.

State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China.

Histone modifications affect gene expression, but the mechanism and biological consequence of natural variation in histone modifications remain unclear. Here, we generated genome-wide integrated maps of H3K27me3 modification and transcriptome for Col, C24 and their F1 hybrid. A total of 1,828 genomic regions showing variation in H3K27me3 modification between Col and C24 were identified, most of which were associated with genic regions. Natural variation of H3K27me3 modification between parents could result in allelic bias of H3K27me3 in hybrids. Furthermore, we found that H3K27me3 variation between Col and C24 was negatively correlated with gene expression differences between two accessions, especially with those arising from the cis-effect. Importantly, mutation of CLF, an Arabidopsis methyltransferase for H3K27, altered gene expression patterns between the parents. Together, these data provide insights into natural variation of histone modifications and their association with gene expression differences between Arabidopsis ecotypes.
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http://dx.doi.org/10.1111/jipb.12443DOI Listing
May 2016

Genomic features and regulatory roles of intermediate-sized non-coding RNAs in Arabidopsis.

Mol Plant 2014 Mar 7;7(3):514-27. Epub 2014 Jan 7.

College of Life Sciences, Beijing Normal University, Beijing 100875, China.

Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biological processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs (im-ncRNAs) (50~300 nt) have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. More than half (58%) are new ncRNA species, mostly evolutionary divergent. Interestingly, annotated protein-coding genes with 5'-UTR-derived novel im-ncRNAs tend to be highly expressed. For intergenic im-ncRNAs, their average abundances were comparable to mRNAs in seedlings, but subsets exhibited significantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epigenetic mechanisms to those of protein-coding genes, and some showed developmentally regulated expression patterns. Large-scale reverse genetic screening showed that the down-regulation of a number of im-ncRNAs resulted in either obvious molecular changes or abnormal developmental phenotypes in vivo, indicating the functional importance of im-ncRNAs in plant growth and development. Together, our results demonstrate that novel Arabidopsis im-ncRNAs are developmentally regulated and functional components discovered in the transcriptome.
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http://dx.doi.org/10.1093/mp/sst177DOI Listing
March 2014

Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids.

Genome Biol 2013 Jun 12;14(6):R57. Epub 2013 Jun 12.

Background: Recent genome-wide studies suggested that in addition to genetic variations, epigenetic variations may also be associated with differential gene expression and growth vigor in plant hybrids. Maize is an ideal model system for the study of epigenetic variations in hybrids given the significant heterotic performance, the well-known complexity of the genome, and the rich history in epigenetic studies. However, integrated comparative transcriptomic and epigenomic analyses in different organs of maize hybrids remain largely unexplored.

Results: Here, we generated integrated maps of transcriptomes and epigenomes of shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different organs and genotypes. We observed that whereas histone modifications vary both between organs and between genotypes, DNA methylation patterns are more distinguishable between genotypes than between organs. Histone modifications were associated with transcriptomic divergence between organs and between hybrids and parents. Further, we show that genes up-regulated in both shoots and roots of hybrids were significantly enriched in the nucleosome assembly pathway. Interestingly, 22- and 24-nt siRNAs were shown to be derived from distinct transposable elements, and for different transposable elements in both shoots and roots, the differences in siRNA activity between hybrids and patents were primarily driven by different siRNA species.

Conclusions: These results suggest that despite variations in specific genes or genomic loci, similar mechanisms may account for the genome-wide epigenetic regulation of gene activity and transposon stability in different organs of maize hybrids.
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http://dx.doi.org/10.1186/gb-2013-14-6-r57DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707063PMC
June 2013

IBM1, a JmjC domain-containing histone demethylase, is involved in the regulation of RNA-directed DNA methylation through the epigenetic control of RDR2 and DCL3 expression in Arabidopsis.

Nucleic Acids Res 2012 Oct 5;40(18):8905-16. Epub 2012 Jul 5.

National Institute of Biological Sciences, No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China.

Small RNA-directed DNA methylation (RdDM) is an important epigenetic pathway in Arabidopsis that controls the expression of multiple genes and several developmental processes. RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3) are necessary factors in 24-nt small interfering RNA (siRNA) biogenesis, which is part of the RdDM pathway. Here, we found that Increase in BONSAI Methylation 1 (IBM1), a conserved JmjC family histone demethylase, is directly associated with RDR2 and DCL3 chromatin. The mutation of IBM1 induced the hypermethylation of H3K9 and DNA non-CG sites within RDR2 and DCL3, which repressed their expression. A genome-wide analysis suggested that the reduction in RDR2 and DCL3 expression affected siRNA biogenesis in a locus-specific manner and disrupted RdDM-directed gene repression. Together, our results suggest that IBM1 regulates gene expression through two distinct pathways: direct association to protect genes from silencing by preventing the coupling of histone and DNA methylation, and indirect silencing of gene expression through RdDM-directed repression.
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http://dx.doi.org/10.1093/nar/gks647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467047PMC
October 2012

Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids.

Plant Cell 2012 Mar 20;24(3):875-92. Epub 2012 Mar 20.

Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.

Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single-base-pair resolution the DNA methylomes of Arabidopsis thaliana Landsberg erecta and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs, implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to methylome remodeling were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes circadian clock associated1 and late elongated hypocotyl. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA enhancer1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in heterosis.
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http://dx.doi.org/10.1105/tpc.111.094870DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3336129PMC
March 2012

Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulation.

Plant J 2011 Feb 30;65(3):346-58. Epub 2010 Dec 30.

Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, School of Life Sciences, Peking University, Beijing 100871, China.

LONG HYPOCOTYL 5 (HY5) is a basic leucine zipper transcription factor (TF) that functions downstream of multiple families of photoreceptors. Mutations in the HY5 gene cause a myriad of aberrant phenotypes in Arabidopsis, including elongated hypocotyl, reduced accumulation of pigments, halted chloroplast development in greening hypocotyls, altered root morphology, and defective hormonal and stimulus responses. HY5 thus acts as an integrator that links various gene networks to coordinate plant development. Here we report the experimental mapping of HY5-mediated gene networks in Arabidopsis by integrating genomic loci occupied by HY5 and HY5-dependent gene expression profiles. Our results indicate that HY5 binds to over 9000 genes, detectably affecting the expression of over 1100 genes, either positively or negatively. Further, HY5 indirectly regulate many other genes through sub-networks mediated by other regulators. In particular, HY5 regulates eight miRNA genes that in turn control the transcript abundance of specific target genes. Over-expressing HY5-targeted miR408 resulted in phenotypes that are opposite to the hy5 mutants. Together, our results reveal both transcriptional and post-transcriptional components of the HY5-mediated gene networks.
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http://dx.doi.org/10.1111/j.1365-313X.2010.04426.xDOI Listing
February 2011
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