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author:("Wu, kliang")
1.  The Arabidopsis SWI2/SNF2 Chromatin Remodeler BRAHMA Regulates Polycomb Function during Vegetative Development and Directly Activates the Flowering Repressor Gene SVP 
PLoS Genetics  2015;11(1):e1004944.
The chromatin remodeler BRAHMA (BRM) is a Trithorax Group (TrxG) protein that antagonizes the functions of Polycomb Group (PcG) proteins in fly and mammals. Recent studies also implicate such a role for Arabidopsis (Arabidopsis thaliana) BRM but the molecular mechanisms underlying the antagonism are unclear. To understand the interplay between BRM and PcG during plant development, we performed a genome-wide analysis of trimethylated histone H3 lysine 27 (H3K27me3) in brm mutant seedlings by chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Increased H3K27me3 deposition at several hundred genes was observed in brm mutants and this increase was partially supressed by removal of the H3K27 methyltransferase CURLY LEAF (CLF) or SWINGER (SWN). ChIP experiments demonstrated that BRM directly binds to a subset of the genes and prevents the inappropriate association and/or activity of PcG proteins at these loci. Together, these results indicate a crucial role of BRM in restricting the inappropriate activity of PcG during plant development. The key flowering repressor gene SHORT VEGETATIVE PHASE (SVP) is such a BRM target. In brm mutants, elevated PcG occupancy at SVP accompanies a dramatic increase in H3K27me3 levels at this locus and a concomitant reduction of SVP expression. Further, our gain- and loss-of-function genetic evidence establishes that BRM controls flowering time by directly activating SVP expression. This work reveals a genome-wide functional interplay between BRM and PcG and provides new insights into the impacts of these proteins in plant growth and development.
Author Summary
In flowering plants, the proper transition from vegetative growth to flowering is critical for their reproductive success and must be controlled precisely. Multiple genes have been shown to regulate the floral transition in response to environmental and endogenous cues. Among them is SHORT VEGETATIVE PHASE (SVP), a key flowering repressor gene in Arabidopsis. SVP is highly expressed during the vegetative phase to promote growth, but the mechanism by which the high expression level of SVP is maintained remains unknown. Here, we report a genome-wide study to examine the functional interplay between the BRM chromatin remodeler and the PcG proteins that catalyze trimethylation of lysine 27 on histone H3 (H3K27me3), a histone mark normally associated with transcriptionally repressed genes. We identify BRM as a direct upstream activator of SVP. BRM acts to keep the levels of H3K27me3 low at the SVP locus by inhibiting the binding and activities of the PcG proteins. Thus, our work identifies a previously unknown mechanism in regulation of flowering time and demonstrates the power of genome-wide approaches in dissecting regulatory networks controlling plant development.
doi:10.1371/journal.pgen.1004944
PMCID: PMC4304717  PMID: 25615622
2.  Histone Acetylation Accompanied with Promoter Sequences Displaying Differential Expression Profiles of B-Class MADS-Box Genes for Phalaenopsis Floral Morphogenesis 
PLoS ONE  2014;9(12):e106033.
Five B-class MADS-box genes, including four APETALA3 (AP3)-like PeMADS2∼5 and one PISTILLATA (PI)-like PeMADS6, specify the spectacular flower morphology in orchids. The PI-like PeMADS6 ubiquitously expresses in all floral organs. The four AP3-like genes, resulted from two duplication events, express ubiquitously at floral primordia and early floral organ stages, but show distinct expression profiles at late floral organ primordia and floral bud stages. Here, we isolated the upstream sequences of PeMADS2∼6 and studied the regulatory mechanism for their distinct gene expression. Phylogenetic footprinting analysis of the 1.3-kb upstream sequences of AP3-like PeMADS2∼5 showed that their promoter regions have sufficiently diverged and contributed to their subfunctionalization. The amplified promoter sequences of PeMADS2∼6 could drive beta-glucuronidase (GUS) gene expression in all floral organs, similar to their expression at the floral primordia stage. The promoter sequence of PeMADS4, exclusively expressed in lip and column, showed a 1.6∼3-fold higher expression in lip/column than in sepal/petal. Furthermore, we noted a 4.9-fold increase in histone acetylation (H3K9K14ac) in the translation start region of PeMADS4 in lip as compared in petal. All these results suggest that the regulation via the upstream sequences and increased H3K9K14ac level may act synergistically to display distinct expression profiles of the AP3-like genes at late floral organ primordia stage for Phalaenopsis floral morphogenesis.
doi:10.1371/journal.pone.0106033
PMCID: PMC4263434  PMID: 25501842
3.  Identification and characterization of histone deacetylases in tomato (Solanum lycopersicum) 
Histone acetylation and deacetylation at the N-terminus of histone tails play crucial roles in the regulation of eukaryotic gene activity. Histone acetylation and deacetylation are catalyzed by histone acetyltransferases and histone deacetylases (HDACs), respectively. A growing number of studies have demonstrated the importance of histone deacetylation/acetylation on genome stability, transcriptional regulation, development and response to stress in Arabidopsis. However, the biological functions of HDACs in tomato have not been investigated previously. Fifteen HDACs identified from tomato (Solanum lycopersicum) can be grouped into RPD3/HDA1, SIR2 and HD2 families based on phylogenetic analysis. Meanwhile, 10 members of the RPD3/HDA1 family can be further subdivided into four groups, namely Class I, Class II, Class III, and Class IV. High similarities of protein sequences and conserved domains were identified among SlHDACs and their homologs in Arabidopsis. Most SlHDACs were expressed in all tissues examined with different transcript abundance. Transient expression in Arabidopsis protoplasts showed that SlHDA8, SlHDA1, SlHDA5, SlSRT1 and members of the HD2 family were localized to the nucleus, whereas SlHDA3 and SlHDA4 were localized in both the cytoplasm and nucleus. The difference in the expression patterns and subcellular localization of SlHDACs suggest that they may play distinct functions in tomato. Furthermore, we found that three members of the RPD3/HDA1 family, SlHDA1, SIHDA3 and SlHDA4, interacted with TAG1 (TOMATO AGAMOUS1) and TM29 (TOMATO MADS BOX29), two MADS-box proteins associated with tomato reproductive development, indicating that these HDACs may be involved in gene regulation in reproductive development.
doi:10.3389/fpls.2014.00760
PMCID: PMC4285013  PMID: 25610445
histone deacetylases; subcellular localization; gene expression; MADS-box proteins; tomato
4.  Histone Deacetylase HDA6 Is Functionally Associated with AS1 in Repression of KNOX Genes in Arabidopsis 
PLoS Genetics  2012;8(12):e1003114.
ASYMMETRIC LEAVES 1 (AS1) is a MYB-type transcription repressor that controls leaf development by regulating KNOX gene expression, but the underlying molecular mechanism is still unclear. In this study, we demonstrated that AS1 can interact with the histone deacetylase HDA6 in vitro and in vivo. The KNOX genes were up-regulated and hyperacetylated in the hda6 mutant, axe1-5, indicating that HDA6 may regulate KNOX expression through histone deacetylation. Compared with the single mutants, the as1-1/axe1-5 and as2-1/axe1-5 double mutants displayed more severe serrated leaf and short petiole phenotypes. In addition, the frequencies of leaf lobes and leaflet-like structures were also increased in as1-1/axe1-5 and as2-1/axe1-5 double mutants, suggesting that HDA6 acts together with AS1 and AS2 in regulating leaf development. Chromatin immunoprecipitation assays revealed that HDA6 and AS1 bound directly to KNAT1, KNAT2, and KNATM chromatin. Taken together, these data indicate that HDA6 is a part of the AS1 repressor complex to regulate the KNOX expression in leaf development.
Author Summary
AS1 is a MYB-type transcription repressor that controls leaf patterning by repressing class-1 KNOX gene expression. The molecular mechanism by which AS1 represses KNOX gene expression is still unclear. In this study, we found that AS1 interacted with the histone deacetylase HDA6. Furthermore, HDA6 repressed KNOX gene expression by histone deacetylation. hda6 mutants displayed serrated leaf and short petiole phenotypes. Additionally, hda6/as1-1 double-mutant plants showed a more severe phenotype compared to the single mutants, indicating that HDA6 may act together with AS1 in controlling leaf development. Taken together, our data indicated that HDA6 is an important component of the AS1 repressor complex in regulating the KNOX gene expression.
doi:10.1371/journal.pgen.1003114
PMCID: PMC3521718  PMID: 23271976
5.  HD2 proteins interact with RPD3-type histone deacetylases 
Plant Signaling & Behavior  2012;7(6):608-610.
HD2 proteins were previously identified as plant specific histone deacetylases (HDACs). The molecular mechanism of the function of HD2 proteins is still unclear. Using Bimolecular fluorescence complementation assay, we demonstrated that Arabidopsis HD2 proteins, HD2A, HD2C and HD2D, can interact with RPD3-type HDACs, HDA6 and HDA19, suggesting that that these proteins may act in the same protein complex. Our study indicates that HD2 proteins may functionally associate with RPD3-type HDACs to regulate gene expression in plants.
doi:10.4161/psb.20044
PMCID: PMC3442851  PMID: 22580696
Abiotic stress; HD2 proteins; HDA19; HDA6; histone deacetylases
6.  Epigenetic interplay of histone modifications and DNA methylation mediated by HDA6 
Plant Signaling & Behavior  2012;7(6):633-635.
One of the most fundamental questions in the control of gene expression is how epigenetic patterns of DNA methylation and histone modifications are established. Our recent studies demonstrate that histone deacetylase HDA6 integrates DNA methylation and histone modifications in gene silencing by interacting with DNA methyltransferase MET1 and histone demethylase FLD, suggesting that regulatory crosstalk between histone modifications and DNA methylation could be mediated by the interaction of various epigenetic modification proteins.
doi:10.4161/psb.19994
PMCID: PMC3442857  PMID: 22580702
DNA Methylation; FLD; HDA6; MET1; histone deacetylation; histone demethylation
7.  Histone acetyltransferases in rice (Oryza sativa L.): phylogenetic analysis, subcellular localization and expression 
BMC Plant Biology  2012;12:145.
Background
Histone acetyltransferases (HATs) play an important role in eukaryotic transcription. Eight HATs identified in rice (OsHATs) can be organized into four families, namely the CBP (OsHAC701, OsHAC703, and OsHAC704), TAFII250 (OsHAF701), GNAT (OsHAG702, OsHAG703, and OsHAG704), and MYST (OsHAM701) families. The biological functions of HATs in rice remain unknown, so a comprehensive protein sequence analysis of the HAT families was conducted to investigate their potential functions. In addition, the subcellular localization and expression patterns of the eight OsHATs were analyzed.
Results
On the basis of a phylogenetic and domain analysis, monocotyledonous CBP family proteins can be subdivided into two groups, namely Group I and Group II. Similarly, dicotyledonous CBP family proteins can be divided into two groups, namely Group A and Group B. High similarities of protein sequences, conserved domains and three-dimensional models were identified among OsHATs and their homologs in Arabidopsis thaliana and maize. Subcellular localization predictions indicated that all OsHATs might localize in both the nucleus and cytosol. Transient expression in Arabidopsis protoplasts confirmed the nuclear and cytosolic localization of OsHAC701, OsHAG702, and OsHAG704. Real-time quantitative polymerase chain reaction analysis demonstrated that the eight OsHATs were expressed in all tissues examined with significant differences in transcript abundance, and their expression was modulated by abscisic acid and salicylic acid as well as abiotic factors such as salt, cold, and heat stresses.
Conclusions
Both monocotyledonous and dicotyledonous CBP family proteins can be divided into two distinct groups, which suggest the possibility of functional diversification. The high similarities of protein sequences, conserved domains and three-dimensional models among OsHATs and their homologs in Arabidopsis and maize suggested that OsHATs have multiple functions. OsHAC701, OsHAG702, and OsHAG704 were localized in both the nucleus and cytosol in transient expression analyses with Arabidopsis protoplasts. OsHATs were expressed constitutively in rice, and their expression was regulated by exogenous hormones and abiotic stresses, which suggested that OsHATs may play important roles in plant defense responses.
doi:10.1186/1471-2229-12-145
PMCID: PMC3502346  PMID: 22894565
Histone acetyltransferase; Hormone; Phylogenetic tree; Subcellular localization; Rice; Stress
8.  Comparative Analysis of SWIRM Domain-Containing Proteins in Plants 
Chromatin-remodeling complexes affect gene expression by using the energy of ATP hydrolysis to locally disrupt or alter the association of histones with DNA. SWIRM (Swi3p, Rsc8p, and Moira) domain is an alpha-helical domain of about 85 residues in chromosomal proteins. SWIRM domain-containing proteins make up large multisubunit complexes by interacting with other chromatin modification factors and may have an important function in plants. However, little is known about SWIRM domain-containing proteins in plants. In this study, 67 SWIRM domain-containing proteins from 6 plant species were identified and analyzed. Plant SWIRM domain proteins can be divided into three distinct types: Swi-type, LSD1-type, and Ada2-type. Generally, the SWIRM domain forms a helix-turn-helix motif commonly found in DNA-binding proteins. The genes encoding SWIRM domain proteins in Oryza sativa are widely expressed, especially in pistils. In addition, OsCHB701 and OsHDMA701 were downregulated by cold stress, whereas OsHDMA701 and OsHDMA702 were significantly induced by heat stress. These observations indicate that SWIRM domain proteins may play an essential role in plant development and plant responses to environmental stress.
doi:10.1155/2012/310402
PMCID: PMC3424641  PMID: 22924025
9.  HD2C interacts with HDA6 and is involved in ABA and salt stress response in Arabidopsis 
Journal of Experimental Botany  2012;63(8):3297-3306.
HD2 proteins are plant specific histone deacetylases. Four HD2 proteins, HD2A, HD2B, HD2C, and HD2D, have been identified in Arabidopsis. It was found that the expression of HD2A, HD2B, HD2C, and HD2D was repressed by ABA and NaCl. To investigate the function of HD2 proteins further, two HD2C T-DNA insertion lines of Arabidopsis, hd2c-1 and hd2c-3 were identified. Compared with wild-type plants, hd2c-1 and hd2c-3 plants displayed increased sensitivity to ABA and NaCl during germination and decreased tolerance to salt stress. These observations support a role of HD2C in the ABA and salt-stress response in Arabidopsis. Moreover, it was demonstrated that HD2C interacted physically with a RPD3-type histone deacetylase, HDA6, and bound to histone H3. The expression of ABA-responsive genes, ABI1 and ABI2, was increased in hda6, hd2c, and hda6/hd2c-1 double mutant plants, which was associated with increased histone H3K9K14 acetylation and decreased histone H3K9 dimethylation. Taken together, our results suggested that HD2C functionally associates with HDA6 and regulates gene expression through histone modifications.
doi:10.1093/jxb/ers059
PMCID: PMC3350937  PMID: 22368268
ABA; Arabidopsis; HD2C; HDA6; histone deacetylases
10.  Subcellular Localization of Class II HDAs in Arabidopsis thaliana: Nucleocytoplasmic Shuttling of HDA15 Is Driven by Light 
PLoS ONE  2012;7(2):e30846.
Class II histone deacetylases in humans and other model organisms undergo nucleocytoplasmic shuttling. This unique functional regulatory mechanism has been well elucidated in eukaryotic organisms except in plant systems. In this study, we have paved the baseline evidence for the cytoplasmic and nuclear localization of Class II HDAs as well as their mRNA expression patterns. RT-PCR analysis on the different vegetative parts and developmental stages reveal that Class II HDAs are ubiquitously expressed in all tissues with minimal developmental specificity. Moreover, stable and transient expression assays using HDA-YFP/GFP fusion constructs indicate cytoplasmic localization of HDA5, HDA8, and HDA14 further suggesting their potential for nuclear transport and deacetylating organellar and cytoplasmic proteins. Organelle markers and stains confirm HDA14 to abound in the mitochondria and chloroplasts while HDA5 localizes in the ER. HDA15, on the other hand, shuttles in and out of the nucleus upon light exposure. In the absence of light, it is exported out of the nucleus where further re-exposition to light treatments signals its nuclear import. Unlike HDA5 which binds with 14-3-3 proteins, HDA15 fails to interact with these chaperones. Instead, HDA15 relies on its own nuclear localization and export signals to navigate its subcellular compartmentalization classifying it as a Class IIb HDA. Our study indicates that nucleocytoplasmic shuttling is indeed a hallmark for all eukaryotic Class II histone deacetylases.
doi:10.1371/journal.pone.0030846
PMCID: PMC3281883  PMID: 22363501
11.  Absolute Quantitation of DNA Methylation of 28 Candidate Genes in Prostate Cancer Using Pyrosequencing 
Disease markers  2011;30(4):151-161.
Aberrant DNA methylation plays a pivotal role in carcinogenesis and its mapping is likely to provide biomarkers for improved diagnostic and risk assessment in prostate cancer (PCa). We quantified and compared absolute methylation levels among 28 candidate genes in 48 PCa and 29 benign prostate hyperplasia (BPH) samples using the pyrosequencing (PSQ) method to identify genes with diagnostic and prognostic potential.
RARB, HIN1, BCL2, GSTP1, CCND2, EGFR5, APC, RASSF1A, MDR1, NKX2-5, CDH13, DPYS, PTGS2, EDNRB, MAL, PDLIM4, HLAa, ESR1 and TIG1 were highly methylated in PCa compared to BPH (p < 0.001), while SERPINB5, CDH1, TWIST1, DAPK1, THRB, MCAM, SLIT2, CDKN2a and SFN were not. RARB methylation above 21% completely distinguished PCa from BPH. Separation based on methylation level of SFN, SLIT2 and SERPINB5 distinguished low and high Gleason score cancers, e.g. SFN and SERPINB5 together correctly classified 81% and 77% of high and low Gleason score cancers respectively. Several genes including CDH1 previously reported as methylation markers in PCa were not confirmed in our study. Increasing age was positively associated with gene methylation (p < 0.0001).
Accurate quantitative measurement of gene methylation in PCa appears promising and further validation of genes like RARB, HIN1, BCL2, APC and GSTP1 is warranted for diagnostic potential and SFN, SLIT2 and SERPINB5 for prognostic potential.
doi:10.3233/DMA-2011-0790
PMCID: PMC3825083  PMID: 21694441
Prostate cancer; BPH; DNA Methylation; pyrosequencing; biomarker
12.  Role of histone deacetylases HDA6 and HDA19 in ABA and abiotic stress response 
Plant Signaling & Behavior  2010;5(10):1318-1320.
Our recent study revealed the involvement of the Arabidopsis histone deacetylase HDA6 in modulating ABA and salt stress responses. In this report, we further investigated the role of HDA19 in ABA and salt stress responses. The Arabidopsis HDA19 T-DNA insertion mutant, hda19-1, displayed a phenotype that was hypersensitive to ABA and salt stress. Compared with wild-type plants, the expression of ABA responsive genes, ABI1, ABI2, KAT1, KAT2 and RD29B, was decreased in hda19-1 plants when treated with ABA. Our study indicates that HDA6 and HDA19 may play a redundant role in modulating seed germination and salt stress response, as well as ABA- and salt stress-induced gene expression in Arabidopsis.
doi:10.4161/psb.5.10.13168
PMCID: PMC3115378  PMID: 20930557
histone deacetylases; HDA6; HDA19; abscisic acid; salt stress
13.  Involvement of Arabidopsis histone deacetylase HDA6 in ABA and salt stress response 
Journal of Experimental Botany  2010;61(12):3345-3353.
Histone modifications play an important role in the epigenetic regulation of gene expression. All histone modifications are reversible, which may therefore provide a flexible way for regulating gene expression during the plant's development and during the plant response to environmental stimuli. The reversible acetylation and deacetylation of specific lysine residues on core histones are catalysed by histone acetyltransferases and histone deacetylases (HDAs). HDA6 is an RPD3-type histone deacetylase in Arabidopsis. The Arabidopsis HDA6 mutant, axe1-5, and HDA6 RNA-interfering plants displayed a phenotype that was hypersensitive to ABA and salt stress. Compared with wild-type plants, the expression of the ABA and abiotic stress-responsive genes, ABI1, ABI2, KAT1, KAT2, DREB2A, RD29A, and RD29B, was decreased in axe1-5 and HDA6 RNA-interfering plants when treated with ABA or salt stress. It was found that both ABA and salt stress could enrich the gene activation markers, histone H3K9K14 acetylation, and H3K4 trimethylation, but decrease the gene repression marker, H3K9 dimethylation, of the ABA and abiotic stress-responsive genes. Our study indicates that HDA6-involved histone modifications modulate seed germination and the salt stress response, as well as ABA- and salt stress-induced gene expression in Arabidopsis.
doi:10.1093/jxb/erq154
PMCID: PMC2905197  PMID: 20519338
Abscisic acid; Arabidopsis; HDA6; histone deacetylase; salt stress
14.  Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants 
BMC Plant Biology  2009;9:37.
Background
Although histone deacetylases from model organisms have been previously identified, there is no clear basis for the classification of histone deacetylases under the RPD3/HDA1 superfamily, particularly on plants. Thus, this study aims to reconstruct a phylogenetic tree to determine evolutionary relationships between RPD3/HDA1 histone deacetylases from six different plants representing dicots with Arabidopsis thaliana, Populus trichocarpa, and Pinus taeda, monocots with Oryza sativa and Zea mays, and the lower plants with Physcomitrella patens.
Results
Sixty two histone deacetylases of RPD3/HDA1 family from the six plant species were phylogenetically analyzed to determine corresponding orthologues. Three clusters were formed separating Class I, Class II, and Class IV. We have confirmed lower and higher plant orthologues for AtHDA8 and AtHDA14, classifying both genes as Class II histone deacetylases in addition to AtHDA5, AtHDA15, and AtHDA18. Since Class II histone deacetylases in other eukaryotes have been known to undergo nucleocytoplasmic transport, it remains unknown whether such functional regulation also happens in plants. Thus, bioinformatics studies using different programs and databases were conducted to predict their corresponding localization sites, nuclear export signal, nuclear localization signal, as well as expression patterns. We also found new conserved domains in most of the RPD3/HDA1 histone deacetylases which were similarly conserved in its corresponding orthologues. Assessing gene expression patterns using Genevestigator, it appears that RPD3/HDA1 histone deacetylases are expressed all throughout the plant parts and developmental stages of the plant.
Conclusion
The RPD3/HDA1 histone deacetylase family in plants is divided into three distinct groups namely, Class I, Class II, and Class IV suggesting functional diversification. Class II comprises not only AtHDA5, AtHDA15, and AtHDA18 but also includes AtHDA8 and AtHDA14. New conserved domains have also been identified in most of the RPD3/HDA1 family indicating further versatile roles other than histone deacetylation.
doi:10.1186/1471-2229-9-37
PMCID: PMC2671507  PMID: 19327164
15.  Phenotypic analysis of genes encoding yeast zinc cluster proteins 
Nucleic Acids Research  2001;29(10):2181-2190.
Zinc cluster proteins (or binuclear cluster proteins) possess zinc fingers of the Zn(II)2Cys6-type involved in DNA recognition as exemplified by the well-characterized protein Gal4p. These fungal proteins are transcriptional regulators of genes involved in a wide variety of cellular processes including metabolism of compounds such as amino acids and sugars, as well as control of meiosis, multi-drug resistance etc. The yeast (Saccharomyces cerevisiae) sequencing project has allowed the identification of additional zinc cluster proteins for a total of 54. However, the role of many of these putative zinc cluster proteins is unknown. We have performed phenotypic analysis of 33 genes encoding (putative) zinc cluster proteins. Only two members of the GAL4 family are essential genes. Our results show that deletion of eight different zinc cluster genes impairs growth on non-fermentable carbon sources. The same strains are also hypersensitive to the antifungal calcofluor white suggesting a role for these genes in cell wall integrity. In addition, one of these strains (ΔYFL052W) is also heat sensitive on rich (but not minimal) plates. Thus, deletion of YFL052W results in sensitivity to a combination of low osmolarity and high temperature. In addition, six strains are hypersensitive to caffeine, an inhibitor of the MAP kinase pathway and phosphodiesterase of the cAMP pathway. In conclusion, our analysis assigns phenotypes to a number of genes and provides a basis to better understand the role of these transcriptional regulators.
PMCID: PMC55459  PMID: 11353088

Results 1-15 (15)