The second subunit of DNA-polymerase delta is required for ...€¦ · 25/04/2016 · POLD2...

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The second subunit of DNA-polymerase delta is required for genomic stability and 1

epigenetic regulation 2

Jixiang Zhang1, Shaojun Xie2, 3, Jinkui Cheng1, Jinsheng Lai4, Jian-Kang Zhu2, 3, and 3

Zhizhong Gong 1, 5 4

1State Key Laboratory of Plant Physiology and Biochemistry, College of Biological 5

Sciences, China Agricultural University, Beijing 100193, China. 6

2Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, 7

Chinese Academy of Sciences, Shanghai 200032, China 8

3Department of Horticulture and Landscape Architecture, Purdue University, West 9

Lafayette, IN 47906, USA. 10

4 State Key Laboratory of Agrobiotechnology, China National Maize Improvement 11

Center, Department of Plant Genetics and Breeding, China Agricultural University, 12

Beijing 100193, China. 13

5Corresponding author: 14

Zhizhong Gong 15

State Key Laboratory of Plant Physiology and Biochemistry, College of Biological 16

Sciences, China Agricultural University, Beijing 100193, China. 17

Email: [email protected]; Tel: 86-10-62733733 18

Running title: POLD2, Genomic Stability and Epigenetic Regulation 19

One sentence summary 20

Plant Physiology Preview. Published on April 25, 2016, as DOI:10.1104/pp.15.01976

Copyright 2016 by the American Society of Plant Biologists

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Mutation in the subunit of DNA-polymerase delta leads to increased homologous 21

recombination and alters histone modification patterns. 22

*Address correspondence to [email protected] 23

The author responsible for distribution of materials integral to the findings presented in 24

this article in accordance with the policy described in the Instructions for Authors 25

(www.plantphysiol.org) is: Zhizhong Gong ([email protected]). 26

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This study was supported by the Natural Science Foundation of China (grants 31330041 28

and 31121002). Jixiang Zhang was supported by Chinese Universities Scientific Fund No. 29

2013YJ002. 30

J. Z. and Z. G conceived the original research plans; J. Z performed most of the 31

experiments; S. X, J. C, and J. L provided bioinformatic analysis; J. Z and Z. G designed 32

the project and wrote the article with contributions of all the authors; J-K. Z discussed the 33

data and complemented the writing. 34

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Abstract 36

DNA polymerase δ plays crucial roles in DNA repair and replication, and maintaining 37

genomic stability. However, the function of POLD2, the second small subunit of DNA 38

polymerase δ, has not been characterized yet in Arabidopsis. During a genetic screen for 39

release of transcriptional gene silencing (TGS), we identified a mutation in POLD2. 40

Whole-genome bisulfite sequencing indicated that POLD2 is not involved in the 41

regulation of DNA methylation. POLD2 genetically interacts with Ataxia Telangiectasia-42

mutated and Rad3-related (ATR) and DNA polymerase α (Pol α). The pold2-1 mutant 43

exhibits genomic instability with a high frequency of homologous recombination (HR). It 44

also exhibits hypersensitivity to DNA-damaging reagents, and short telomere length. 45

Whole-genome ChIP-seq and RNA-seq analyses suggest that pold2-1 changes 46

H3K27me3 and H3K4me3 modifications, and these changes are correlated with the gene 47

expression levels. Our study suggests that POLD2 is required for maintaining genome 48

integrity, and properly establishing the epigenetic markers during DNA replication to 49

modulate gene expression. 50

Keywords: POLD2, transcriptional gene silencing, DNA replication, homologous 51

recombination, genome stability, histone methylation, DNA methylation 52

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Introduction 54

DNA replication is a fundamental process that duplicates both genetic information (DNA 55

sequence) and epigenetic information (DNA methylation and histone modifications). 56

During DNA replication in each cell cycle, nucleosomes are reassembled onto newly 57

synthesized DNA to maintain the chromatin structures (Probst et al., 2009). Three key 58

DNA polymerases are essential for DNA replication: DNA polymerase α (Pol α), DNA 59

polymerase δ (Pol δ), and DNA polymerase ε (Pol ε). It is a well-accepted concept that, 60

after a short RNA-DNA primer extension by the Pol α-primase complex, Pol ε and Pol δ 61

replace Pol α and perform the bulk of DNA synthesis in the leading and lagging strand, 62

respectively (Burgers, 2009). 63

Pol δ is a highly accurate DNA polymerase that is essential for DNA replication, 64

repair, and recombination, and thus for genome integrity (Prindle and Loeb, 2012). 65

Dysfunction of Pol δ results in genomic instability and cancer (Church et al., 2013; Palles 66

et al., 2013). Pol δ in mammals consists of four subunits: the catalytic subunit p125 67

(POLD1, corresponding to Pol3p in Saccharomyces cerevisiae and CDC6 in S. pombe); 68

the accessory subunit p50 (POLD2, corresponding to Pol31p in S. cerevisiae and CDC1 69

in S. pombe); p68 (POLD3, corresponding to Pol32p in S. cerevisiae and CDC27 in S. 70

pombe); and the smallest subunit p12 (POLD4, corresponding to CDM1 in S. pombe) 71

(Prindle and Loeb, 2012). The Pol31p and Pol32p subunits in yeast also interact with 72

DNA polymerase zeta (Pol ζ) to participate in DNA translesion synthesis (TLS) and 73

mutagenesis (Johnson et al., 2012). Recent studies suggest that Pol δ may replicate both 74

strands (Johnson et al., 2015; Miyabe et al., 2015). 75



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Several DNA-replication factors have been reported to help mediate transcriptional 77

gene silencing (TGS) in plants (Liu and Gong, 2011). In Arabidopsis, mutations in 78

replication factor C1 (RFC1), Pol ε, Pol α, and replication protein A2A (RPA2A) can 79

suppress gene silencing in a DNA methylation-independent manner (Elmayan et al., 2005; 80

Kapoor et al., 2005; Xia et al., 2006; Liu et al., 2010; Liu et al., 2010). These mutants are 81

hypersensitive to DNA damage and exhibit reduced telomere length and increased 82

genomic instability. BRUSHY1 (BRU1), TEBICHI, and FASCIATA1 (FAS1, chromatin 83

assembly factor 1) are also related to DNA damage and TGS (Takeda et al., 2004; 84

Ramirez-Parra and Gutierrez, 2007; Inagaki et al., 2009). Because all of these proteins are 85

involved in the DNA replication and repair pathway, we refer to this pathway as the DNA 86

replication and repair-mediated TGS pathway (DRR-TGS pathway). However, the 87

molecular mechanism of this pathway is not well known. 88

Repressor of silencing 1 (ROS1), a 5-meC DNA glycosylase/demethylase, and its 89

homologous proteins DEMETER and DEMETER-like 2-3 (DML2-3), are essential for 90

maintaining the expression of endogenous genes and transgenes through active DNA 91

demethylation (Gong et al., 2002; Zhu, 2009). In a previous study, we performed a 92

genetic screen for additional ROS genes by using a transgenic Arabidopsis line that 93

carries a T-DNA insertion expressing both the ProRD29A:LUC (firefly luciferase 94

reporter driven by the stress-responsive RD29A promoter) gene and the Pro35S:NPTII 95

(neomycin phosphotransferase II driven by the CaMV 35S promoter) gene. Using this 96

screen, we identified several genes in the RNA-directed DNA methylation (RdDM) 97



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pathway whose mutations silence Pro35S:NPTII because of the reduced expression of 98

ROS1, indicating that the RdDM pathway positively modulates ROS1 expression (Huettel 99

et al., 2006; Li et al., 2012). One of these mutants isolated from the screen was defective 100

in meristem silencing 3 (dms3-4) (Li et al., 2012). DMS3 is a silencing factor in RdDM 101

that coordinates the formation of the DDR complex by defective in RNA-directed DNA 102

methylation 1 (DRD1) and RNA-directed DNA methylation 1 (RDM1) and that 103

facilitates Pol V transcript (Law and Jacobsen, 2010). 104

In this study, we used the dms3-4 mutant to identify genes whose mutations release the 105

silencing of Pro35S:NPTII, and we cloned POLD2 from a pold2-1 mutant. Whole-106

genome bisulfite sequencing indicated that pold2-1 does not change DNA methylation. 107

Combining ChIP-seq with RNA-seq data, we found a high correlation between 108

H3K27me3 and H3K4me3 modification and gene expression caused by the pold2-1. We 109

also found that pold2-1 exhibits sensitivity to DNA-damaging reagents, short telomere 110

length, and genomic instability, including a high frequency of homologous recombination 111

(HR). These results suggest that POLD2 is a new component in DRR-TGS pathway, 112

which does not affect the DNA methylation and H3K9me2, but H3K27me3 and 113

H3K4me3 modification with changing the expression of specific genes. 114

Results 115

Isolation of a new component in the DRR-TGS pathway 116

dms3-4 was identified during a genetic screen for mutants that silence Pro35S:NPTII in a 117

transgenic Arabidopsis line carrying expressed ProRD29A:LUC and Pro35S:NPTII (C24 118

accession, which was used as the wild type in this study) (Li et al., 2012). We performed 119



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a forward genetic screen using an ethyl methanesulfonate (EMS)-mutagenized dms3-4 120

population to isolate the mutants that release the silenced Pro35S:NPTII in dms3-4. We 121

isolated several mutants including pold2-1, rfc1-4, ubiquitin-specific protease26 (ubp26-122

5), and histone deacetylase 6 (hda6-11) in this screen (Figure 1A and Supplementary 123

Figure S1). The dms3-4 mutant was kanamycin-sensitive because of the silencing of 124

Pro35S:NPTII caused by the reduced expression of ROS1, while pold2-1, rfc1-4, and 125

ubp26-5 partially rescued the expression of NPTII in the dms3-4 background (Figure 1B) 126

and hda6-11 fully recovered the expression of NPTII. UBP26 is a H2B deubiquitination 127

enzyme that is identified in a genetic screening for releasing silencing of ProRD29A:LUC 128

and Pro35S:NPTII in ros1-1 (Sridhar et al., 2007). HDA6 is a histone deacetylase that is 129

involved in mediating DNA methylation and TGS (Murfett et al., 2001; Aufsatz et al., 130

2002; Probst et al., 2004). However, the expression level of ROS1 was not greatly 131

restored in these mutants (Figure 1C). TSIs are endogenous TGS loci (Steimer et al., 132

2000), the expression of which is altered in some mutants involved in DNA methylation, 133

histone modification, or DNA replication (Steimer et al., 2000; Xia et al., 2006; Yin et al., 134

2009; Liu et al., 2010; Liu et al., 2010). The expression of TSIs was increased in these 135

isolated mutants (Figure 1D). Interestingly, although pold2-1 suppresses the silenced 136

Pro35S:NPTII in the dms3-4 mutant, the expression of NPTII in the pold2-1 single 137

mutant was lower than in the wild type (Figure 1B). To confirm the role of POLD2 in 138

controlling the TGS of Pro35S:NPTII, we crossed pold2-1 with other TGS-related 139

mutants. ROS1 and ROS4 (IDM1) are DNA demethylation factors, and ros1 and ros4 140

exhibited kanamycin sensitivity due to the silencing of Pro35S:NPTII (Li et al., 2012). 141



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The double mutants pold2-1 ros1-1 and pold2-1 ros4-1 were resistant to kanamycin 142

(Figure 1E). pold2-1 also suppressed the kanamycin-sensitive phenotype in nrpd1-8 and 143

nrpe1-14 (Figure 1E). However, pold2-1 had little effect on the ProRD29A:LUC locus in 144

dms3-4. Like mutants of DNA replication-related proteins (Elmayan et al., 2005; Xia et 145

al., 2006; Yin et al., 2009; Liu et al., 2010; Liu et al., 2010), pold2-1 failed to suppress 146

the silenced ProRD29A:LUC in the ros1-1 mutant (Figure 1F). These results indicate that 147

pold2-1 suppresses the TGS of Pro35S:NPTII and that POLD2 is a newly identified 148

component in the DRR-TGS pathway. 149

Map-based cloning of POLD2 150

The F1 progeny of pold2-1 dms3-4 backcrossed with dms3-4 had a kanamycin-sensitive 151

phenotype like that of dms3-4 (Figure 2A), and the F2 progeny showed a kanamycin-152

sensitive to kanamycin-resistant ratio of about 3:1 (177:56) (Figure 2B), indicating that 153

the pold2-1 allele is recessive and caused by a single nuclear gene mutation. pold2-1 154

mutant plants were much smaller and flowered earlier than the wild type (Figure S2B). 155

To clone POLD2, we crossed pold2-1 dms3-4 (C24) with the dms3-1 mutant (Columbia-156

0). The mutants with a kanamycin-resistant phenotype were isolated from the F2 progeny. 157

The mutated position in pold2-1 was mapped at the end of chromosome 2, between BAC 158

clones T28M21 and F18O19. A G-A mutation located at 1170 nucleotides from the 159

putative start codon was identified in AT2G42120 (Figure 2C). Because the mutated 160

nucleotide is located at a splicing site between the fifth intron and the sixth exon, we 161

sequenced the various transcripts using OligodT reverse-transcribed cDNAs. Unlike 162

POLD2 in the wild type, the mis-spliced allele in pold2-1 produced several forms of 163



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transcripts (a total of five transcripts were identified from 23 clones). Among them, four 164

transcripts produced premature stop codons, and one transcript missing 6-bp caused 165

deletion of two amino acids and mutation of one amino acid, which might result in the 166

translation of a protein with reduced function (Figure 2D). To confirm that the 167

kanamycin-resistant and retarded-growth phenotype was caused by the POLD2 mutation, 168

we complemented the pold2-1 dms3-4 double mutant with the full-length POLD2 169

genomic sequence. The transgenic progeny showed kanamycin sensitivity on MS plates 170

containing 50 mg/L kanamycin, and grew normally in the absence of kanamycin (Figure 171

2E). The other two constructs, Pro35S:FLAG-HA-POLD2 and ProPOLD2: POLD2-GFP, 172

could also complement the pold2-1 phenotypes (Figure 2E). The T-DNA insertion mutant 173

pold2-2 (762B02) was embryo lethal (Supplementary Figure S2A), indicating that 174

POLD2 is an essential gene in Arabidopsis. We crossed pold2-1 with pold2-2-/+, and 175

about half of the F1 progeny showed more severe dwarf phenotypes than the pold2-1 176

mutant, indicating that pold2-1 protein dosage influences the plant growth phenotype 177

(Supplementary Figure S2B). To determine whether the transcript missing 6 bp in pold2-178

1 is functional in plants, we transferred this transcript driven by the 35S promoter 179

(Pro35S:pold2-1) into heterozygous pold2-2-/+ plants. Like the pold2-1 mutant, the 180

transgenic plants carrying Pro35S:pold2-1 with homozygous T-DNA insertion were 181

small (Supplementary Figure S2C). These results suggest that this transcript from pold2-1 182

is partially functional in plants. ProPOLD2:GUS expression indicated that POLD2 is 183

highly expressed in the shoot meristem, cotyledons, and older true leaves (Supplementary 184



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Figure S3A). POLD2-GFP localization in transgenic plants indicated that POLD2 is a 185

nuclear protein (Supplementary Figure S3B). 186

Genetic analysis of POLD2 with other DNA-replication proteins 187

To better characterize the genetic interactions between POLD2 and other DNA-188

replication proteins, we crossed pold2-1 with some DNA replication-related mutants and 189

analyzed the phenotypes of the double mutants (Figure 3). pold2-1 mutant plants were 190

much smaller and flowered earlier than the wild type (Figure 3A). pold2-1 polα double 191

mutants were smaller and exhibited more severe growth phenotypes than polα or pold2-1 192

single mutants (Figure 3A), suggesting that the two genes have additive effects on plant 193

growth and development. In contrast, polε polα double mutants exhibited phenotypes 194

similar to polα mutants (Figure 3B), suggesting that Polα and Pol ε do not have additive 195

effect on plant growth and work in the same pathway. The phenotypes of the pold2-1 196

ror1-2 (rpa2a) and polε ror1-2 double mutant were very similar to those of the ror1-2 197

single mutant (Figure 3C, 3D), suggesting that RPA2A is a limiting factor for leading- 198

and lagging-strand DNA replication. The pold2-1 pol ε double mutant was similar to 199

pold2-1 (Figure 3E), indicating that POLD2 acts at or has an epistasis effect on Pol ε for 200

controlling plant development. Furthermore, polα ror1-2 double mutants exhibited more 201

severe growth phenotypes than polα or ror1-2 single mutants (Figure 3F), suggesting that 202

Polα and RPA2A interact genetically in controlling plant growth (Figure 3F). 203

ATR (Ataxia Telangiectasia-mutated and Rad3-related) is a DNA damage-activated 204

protein kinase that is involved in the progression of DNA replication forks, and ATM 205

(Ataxia Telangiectasia-Mutated) is a double-strand break-activated protein kinase. The 206



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atr mutant did not show a clear growth phenotype, and the atm mutant had a partially 207

sterile phenotype relative to the wild type under normal growing conditions (Garcia et al., 208

2003; Culligan et al., 2004). The pold2-1 atr double mutant showed severe defects in leaf 209

development and fertility (Figure 3G), and the pold2 atm double mutant showed growth 210

phenotypes similar to those of pold2-1 (Figure 3H). These results suggest that POLD2 211

and ATR have additive roles in controlling plant development. 212

The pold2-1 mutant exhibits sensitivity to DNA damage, a delayed cell cycle, 213

increased homologous recombination, and a reduced telomere length 214

Previous studies indicated that DNA replication-related proteins have roles in controlling 215

the cell cycle, homologous recombination, and genomic stability (Liu and Gong, 2011). 216

In evaluating the effects of POLD2 on these processes, we found that the pold2-1 mutant 217

was more sensitive to alkylating agent methyl methanesulfonate (MMS) than to the 218

DNA-replication inhibitor hydroxyurea (HU) or to the DNA-interstrand crosslink-reagent 219

cisplatin (Figure 4A, 4B). QRT-PCR assessment of the expression of several genes that 220

are responsible for DNA repair including breast cancer susceptibility 1 (BRCA1), RAD51, 221

poly(ADP-ribose) polymerase 1 (PARP1), and PARP2. These genes were expressed at 222

higher levels in pold2-1 or pold2-1 dms3-4 than in the wild type or dms3-4 (Figure 4C). 223

To investigate cell cycle progression in the pold2-1 mutant, we crossed pold2-1 with the 224

ProCYCB1;1:GUS reporter line (CYCB1;1 is expressed during the G2/M transition and 225

serves as a marker for cell cycle regulation). GUS activity in both the root and the shoot 226

apical meristem was much stronger in pold2-1 than in the wild type (Figure 4Da-d). RT-227



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PCR confirmed that expression of the mitotic cyclin CYCB1;1 was higher in pold2-1 than 228

in the wild type (Figure 4De). This result indicates that pold2-1 delays the cell cycle. 229

We evaluated the frequency of HR in pold2-1 by introducing the reporter line 651 (in 230

C24 accession) into the pold2-1. Reporter line 651 carries an inverted orientation of the 231

inactive GUS gene (Lucht et al., 2002). A blue sector indicates that an intrachromosomal 232

recombination event has reconstituted a functional GUS gene. As shown in Figure 4E, 233

many more GUS staining sectors were observed in the cotyledons in pold2-1 than in the 234

wild type, suggesting that HR is negatively modulated by POLD2. A previous study 235

indicated that mutations in the catalytic subunit of Pol δ (POLD1) result in genome 236

instability and enhance the frequency of somatic intramolecular HR (Schuermann et al., 237

2009). We also found that the telomere was shorter in pold2-1 or pold2-1 dms3-4 than in 238

the wild type or dms3-4 (Figure 4F and 4G), suggesting that POLD2 is involved in 239

modulating telomere length. 240

pold2-1-released NPTII silencing in dms3-4 is independent of DNA methylation 241

We used whole-genome bisulfite sequencing (BS-seq) to determine whether DNA 242

methylation is altered by pold2-1. Consistent with a previous study (Zhao et al., 2014), 243

the 35S promoter region had a high level of DNA methylation (Figure 5A). The level of 244

DNA methylation in 35S was similar among pold2-1, pold2-1 dms3-4, dms3-4, and the 245

wild type (Figure 5B). Researchers have reported that, in ros1 and some other related 246

mutants, the DNA methylation level at the NOS region is increased (Zhao et al., 2014), 247

which leads to the silencing of NPTII. Indeed, we found that DNA methylation and 248

especially CG methylation is increased in the dms3-4 mutant because of the reduced 249



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expression of ROS1 (Li et al., 2012). The methylation level, however, is similar in dms3-250

4 and pold2-1 dms3-4 (Figure 5C). Interestingly, DNA methylation pattern in pold2-1 is 251

much more similar to that in the pold2-1 dms3-4 or dms3-4 mutant than to that in the wild 252

type (Figure 5C). This is probably because the pold2-1 single mutant was obtained from 253

the progeny of pold2-1 dms3-4 crossed with the wild type, and the hyper DNA 254

methylation pattern was maintained after dms3-4 was recovered. These results suggest 255

that DNA methylation is not responsible for the release of the silencing of NPTII in the 256

dms3-4 mutant background. 257

We next checked DNA methylation on a genome-wide scale using the BS-seq. 258

pold2-1 mutant did not show a significantly altered DNA methylation level at the whole-259

genome scale (Figure 5D-E). In agreement with a previous study showing that the DNA 260

single-stranded binding protein RPA2A does not affect DNA methylation (Elmayan et al., 261

2005; Stroud et al., 2013), POLD2 is dispensable for DNA methylation. These results 262

suggest that the DNA replication machinery does not influence DNA methylation. 263

POLD2 mediates H3K27me3 and H3K4me3 histone modification in NPTII 264

Given that POLD2 does not affect DNA methylation and that its mutation changes the 265

expression of NPTII, we suspected that POLD2 may affect histone modification. We 266

performed whole-genome ChIP-seq for H3K27me3, H3K4me3, H3K9me2, and H3 in the 267

wild type and pold2-1. 268

Using ChIP-seq data, we compared the histone modification profiles on the T-DNA 269

locus. The 35S promoter region harbors a slightly higher level of H3K9me2 histone 270

modification in pold2-1 than in the wild type (Figure 6A and 6B). The NPTII region had 271



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decreased H3K27me3 and H3K4me3 but increased H3K9me2 in the pold2-1 mutant 272

comparing to the wild type (Figure 6A and 6B). We next examined histone modification 273

levels among the wild type, dms3-4, pold-1 dms3-4, and pold2-1 using ChIP-PCR. We 274

found that the H3K27me3 level at the NPTII gene body region was much lower in the 275

pold2-1 or pold2-1 dms3-4 mutant than in the wild type or in the dms3-4 mutant (Figure 276

6D), which was consistent with the ChIP-seq data that pold2-1 decreased H3K27me3 277

(Figure 6A and 6B). The H3K9me2 level of both 35S and NPTII was higher in dms3-4 278

than in the wild type (Figure 6C-D), which would lead to a repression of NPTII gene 279

expression in dms3-4. The H3K9me2 level in the pold2-1 dms3-4 double mutant and in 280

the pold2-1 single mutant, however, was similar to that in the dms3-4 mutant (6C, 6D), 281

suggesting that the release of NPTII silencing in the pold2-1 mutant in the dms3-4 282

background was not due to changes in the H3K9me2 level. The H3K4me3 level in the 283

NPTII region was lower in dms3-4 than in the wild type (Figure 6D). pold2-1 mildly 284

increased the H3K4me3 level in the dms3-4 background, but the H3K4me3 level was still 285

lower in the pold2-1 background than in the wild type, which is consistent with the lower 286

expression of NPTII in the pold2-1 mutant (Figure 1B and 6D). Ubiquitin-conjugating 287

enzyme 21 (UBI) was used as a positive control for H3K4me3 and as a negative control 288

for H3K27me3 and H3K9me2, and the histone modification pattern on the UBI region 289

was similar among the four samples (Figure 6E). Together, these results suggest that the 290

release of NPTII silencing in the dms3-4 mutant by pold2-1 results from a reduced level 291

of H3K27me3. 292



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We next sought to determine whether H3K27me3 or H3K4me3 is altered in the other 293

mutants isolated from the same screen. Indeed, we found the H3K27me3 level on the 294

NPTII was decreased in the rfc1-4, ubp26-5 and hda6-11 mutants compared to that in the 295

wild type (Figure S4A). We also found that rfc1-4 and ubp26-5 could partially restore the 296

level of H3K4me3 in the dms3-4 background (Figure S4B). hda6-11 greatly increased 297

H3K4me3, and the expression level of NPTII was higher in the hda6-11 mutant than 298

other mutants (Figure S4B and Figure 1B). These results suggest that RFC1, UBP26 and 299

HDA6 are also involved in mediating H3K27me3 and H3K4me3 modification and NPTII 300

expression. 301

Correlation between changes in levels of H3K27me3 or H3K4me3 and changes in 302

gene expression in the pold2-1 mutant 303

We identified 7786 genes with H3K27me3 (Supplementary Figure S5A, Supplementary 304

table S1), and these genes largely overlap with those identified in two previous studies: 305

they overlap with 85.4% (4,346 of 5,090, Supplementary Figure S5A) of the genes 306

previously identified in a ChIP-seq study (Lu et al., 2011) and with 83.4% (4154 out of 307

4980, Supplementary Figure S5A) of those genes previously identified in another ChIP-308

chip analysis (Zhang et al., 2007). We identified 17,849 genes with H3K4me3, and these 309

genes overlap with 97.8% (13,899 of 14,206, Supplementary table S2) of those reported 310

by Luo et al. (Luo et al., 2012) (Supplementary Figure S5A). H3K9me2 is mainly 311

localized on TEs (Supplementary Figure S5B). We also found 3697 genes that harbor 312

H3K9me2 (Supplementary table S3), and these genes overlap with 73% (836 of 1147) of 313



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those reported by Luo et al. (Supplementary Figure S5A) (Luo et al., 2012). Overall, 314

these results indicate that our ChIP-seq data are reliable. 315

Based on ChIP-seq data, we found 977 genes whose H3K27me3 levels were lower in 316

the pold2-1 mutant than in the wild type (P-value <0.01, false discovery rate (FDR) 317

<0.01, Supplementary table S4). After plotting the epigenetic profile of these 977 genes 318

with decreased levels of H3K27me3, we found that the H3K27me3 level was lower on 319

the gene body in the pold2-1 mutant than in the wild type (Figure 7A). The H3K4me3 320

levels in these 977 genes were relatively low. The H3K4me3 signal is mainly detected 321

after the transcriptional start site (TSS), the level of which was higher in pold2-1 than in 322

the wild type (Figure 7A). The total H3 was enriched on these gene body regions but 323

depleted on the TSS or transcription termination sites (TTS) (Figure 7A), which was 324

consistent with a previous report (Ha et al., 2011). The level of total H3 was slightly 325

lower in the pold2-1 mutant than in the wild type (Figure 7A). To determine whether 326

changes in H3K27me3 were correlated with changes in gene expression, we performed 327

RNA-seq of the wild type and the pold2-1 mutant (Supplementary table S5). Among the 328

977 genes with reduced levels of H3K27me3 in pold2-1, 385 were found to be expressed, 329

of which, 282 genes (73%) were up-regulated. After plotting these 385 expressed genes 330

using a heat map and a box plot, we found that the expression levels of these genes were 331

significantly higher in pold2-1 than in the wild type (P-value <0.0001, paired Student’s t-332

test, Figure 7B-C). These results suggest that pold2-1 leads to a decrease in H3K27me3 333

level, which in turn may increase gene expression. 334



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We found 343 genes that had a significantly higher level of H3K27me3 in the pold2-1 335

mutant than in the wild type (P-value <0.01, FDR <0.01, Supplementary table S6). The 336

increased H3K27me3 modification mainly occurred on the gene body regions (Figure 337

7D). Among these genes, there were no obvious changes in H3K4me3 or in H3 between 338

pold2-1 and the wild type (Figure 7D). Of the 343 genes with increased levels of 339

H3K27me3, 117 were expressed (71 down-regulated and 46 up-regulated), but the 340

expression was not significantly different between pold2-1 and the wild type (Figure 7E-341

F, P-value = 0.2292, paired Student’s t-test). These results suggest that the moderate 342

increase in H3K27me3 level in pold2-1 does not apparently change the gene expression. 343

We found 499 genes that had significantly higher H3K4me3 levels in the pold2-1 344

mutant than in the wild type (P-value <0.01, FDR <0.01, Supplementary table S7), and 345

21.4% (107 of 499) of these genes overlapped with genes with decreased levels of 346

H3K27me3. After plotting the epigenetic profiles of these 499 genes, we found that the 347

increased H3K4me3 signals began to occur just after the TSS (the first nucleosome in the 348

gene body) and then spread to the whole gene body, and that their level was lowest at the 349

TTS (Figure 8A). The H3 level was slightly lower in the pold2-1 mutant than in the wild 350

type (Figure 8A). Most of these 499 genes were expressed (455 of 499), and more than 351

76% (345 out of 455) genes were up-regulated. After statistical analysis, the expression 352

levels were significantly higher in the pold2-1 mutant than in the wild type (Figure 8B, 353

8C, P-value <0.0001, paired Student’s t-test). Only 32 of the genes were found to have a 354

lower H3K4me3 level (P-value <0.01, FDR <0.01, Supplementary table S8, Figure 8D). 355

Among these 32 genes, 30 were found to be expressed, of which 23 showed a lower 356



18

expression level in the pold2-1 mutant compared to the wild type. After boxplotting of 357

these 30 genes, they exhibited a lower expression level (Figure 8E-F; P-value = 0.0023, 358

paired Student’s t-test) in pold2-1 than in the wild type. These results suggest that the 359

pold2-1 mutation prominently increases the H3K4me3 level and gene expression. 360

We further selected some loci for validation by ChIP-PCR. SEP3 was recently 361

reported to be a target of the catalytic subunit POLD1, and its H3K4me3 level is 362

increased in the pold1 mutant (Iglesias et al., 2015). Consistent with our ChIP data 363

(Figure 9A), SEP3 together with eight other selected genes had decreased H3K27me3 364

levels and increased H3K4me3 levels. Two genes (AT2G39250 and AT1G06360) with 365

increased H3K27me3 and decreased H3K4me3 in pold2 -1 relative to the wild type were 366

also checked by ChIP-PCR (Figure 9B, 9C). The levels of total histone H3 among these 367

genes were similar between the pold2-1 mutant and the wild type (Figure 9D). UBI, 368

which has only a slight modification in H3K27me3 but a substantial modification in 369

H3K4me3, and H3 were used as controls. Consistently, six of nine genes that had 370

decreased H3K27me3 levels but increased H3K4me3 levels had higher expression levels 371

in pold2-1 than in the wild type (Figure 9E). In contrast, the expression levels of 372

AT2G39250 and AT1G06360 (with an increased level of H3K27me3 and a decreased 373

level of H3K4me3) were lower in pold2-1 than in the wild type (Figure 9E). Together, 374

these results suggest a critical role of POLD2 in mediating H3K27me3 and H3K4me3 375

levels and gene expression. 376

Discussion 377



19

Genetic screens for the release of the TGS of Pro35S:NPTII in either the ros1 or dms3-4 378

mutant has identified most of the core DNA-replication proteins including the DNA 379

single-strand-binding protein RPA2A (Xia et al., 2006), Pol α (Liu et al., 2010), Pol ε 380

(Yin et al., 2009), POLD2 (this study), RFC1 (Liu et al., 2010), and TOUSLED protein 381

kinase (Wang et al., 2007). Other studies have identified other DNA replication-related 382

proteins involved in mediating TGS including BRU1 (Takeda et al., 2004), chromatin 383

assembly factor (CAF-1) subunits FAS1 and FAS2 (Ono et al., 2006; Schonrock et al., 384

2006), and TEBICHI (Inagaki et al., 2009). The release of TGS by defects in the DNA-385

replication machinery suggests that these processes must have a common mechanism. In 386

this study, we found that POLD2 does not affect DNA methylation but plays crucial roles 387

in regulating H3K27me3 and H3K4me3 modification according to genome-wide ChIP-388

seq. The released silencing of NPTII in dms3-4 is mainly due to the change in histone 389

modifications by pold2-1. These results suggest that the DRR-TGS pathway is essential 390

for maintaining H3K27me3 and H3K4me3 inheritance and gene expression. 391

DNA Pol δ is conserved in eukaryotes and is important in regulating genomic 392

stability and development in Arabidopsis (Schuermann et al., 2009; Iglesias et al., 2015). 393

To our knowledge, the biological functions of Arabidopsis POLD2 have not been studied 394

yet. In this study, we found that POLD2 is an essential gene that contributes to DNA 395

replication, genomic stability through maintaining HR, DNA damage repair and telomere 396

length. In addition, genetic analysis presents a synergistic role of POLD2 with ATR or 397

Pol α in controlling plant development (Figure 3). Similarly, a previous study reported 398



20

that TEBICHI protein containing both DNA helicase and polymerase domains genetically 399

interacts with ATR to regulate plant development (Inagaki et al., 2009). 400

DNA replication proteins play crucial roles in maintaining histone inheritance. RNA- 401

and ChIP-seq indicate that POLD2 mediates the expression of genes enriched in 402

H3K27me3 and H3K4me3 in gene bodies. We found a high correlation between reduced 403

H3K27me3 levels or increased H3K4me3 levels and increased gene expression, which is 404

consistent with previous studies in Arabidopsis (Zhang et al., 2009) and Drosophila 405

(Papp and Muller, 2006). However, the expression of genes with increased H3K27me3 406

levels in pold2-1 does not show a clear tendency toward reduced gene expression, 407

probably because their expression is already very low, or because the experimental 408

seedlings have mixed cell types; the obtained results might be over- or under-estimated. 409

In this case, we might not detect the difference if change only occurs in a small 410

proportion of the cells in the whole plant. Perhaps future studies on specific cell types or 411

cell cycles will be able to prove how DNA replication factors participate in epigenetic 412

regulation in Arabidopsis. Interestingly, in embryonic stem cells, a specific chromatin-413

modification pattern (chromatin areas with these patterns are termed bivalent domains 414

and harbor both H3K27me3 and H3K4me3) is important for cell differentiation and 415

memory (Bernstein et al., 2006). Our results indicate that the POLD2 mutation altered the 416

levels of H3K27me3 and H3K4me3 of 107 bivalent genes (Figure S6, Supplementary 417

table S9). These results suggest that POLD2 is involved in regulating the bivalent histone 418

modifications, and that the DNA replication machinery could contribute to cell 419

differentiation and cell-type transition. 420



21

So far, the intrinsic mechanism that DNA replication affected H3K27me3 or 421

H3K4me3 was not clear, although several lines of evidence suggest that DNA replication 422

or related factors help regulate PcG target genes. Our RNA-seq data indicate that the 423

POLD2 mutation did not change the expression of genes responsible for the 424

establishment and maintenance of H3K4me3 and H3K27me3 significantly 425

(Supplementary table S10). Western blot analyses indicate that the total levels of 426

H3K4me3 and H3K27me3 were not changed in pold2 mutant (Figure S7). These results 427

suggest that POLD2 does not affect the expression of genes for establishment and 428

maintenance of H3K4me3 and H3K27me3 modification, or the global H3K4me3 and 429

H3K27me3 levels. It was previously proposed that DNA polymerase δ may play a role in 430

preventing replication stress or HR and in depositing active H3K4me3 marks (Iglesias et 431

al., 2015). Meanwhile, some studies indicate that the catalytic subunit of DNA 432

polymerase α interacts with (Barrero et al., 2007) or perturbs the binding of like-433

heterochromatin protein 1 (LHP1) (Hyun et al., 2013), which is the main reader/effector 434

for H3K27me3 in Arabidopsis (Barrero et al., 2007; Zhang et al., 2007). Another link 435

between DNA replication and H3K27me3 is MSI1 (multicopy suppressor of ira1), a 436

chromatin assembly factor in Arabidopsis, which interacts with PcG protein and LHP1 437

(Derkacheva et al., 2013). So, it is possible that a dysfunctional Pol δ may disturb the 438

entire replication machinery, which would interfere with the recruitment of LHP1 or PcG 439

proteins to PcG targets. In mammalian cells, PcG proteins can be phosphorylated by 440

cyclin-dependent kinases (CDK) in a cell cycle-dependent manner (Chen et al., 2010). 441

Because pold2-1 exhibits an abnormal cell cycle (Figure 4D), it is also possible that a 442



22

disordered cell cycle machinery in the DNA replication-related mutants may influence 443

the activity of PcG proteins and subsequently epigenetic silencing. Further studies will be 444

needed to dissect the molecular mechanisms for how each component of DNA replication 445

machinery participates in this process. 446

Materials and methods 447

Plant materials and growth conditions 448

pold2-1, hda6-11, ubp26-5, and rfc1-4 were isolated from an EMS-mutagenized 449

population of dms3-4 in this study. ros1 (ros1-1), polε (abo4), polα, rpa2a-2 (ror1-2), 450

dms3-4, nrpd1-8, nrpe1-14, and ros4 are C24 ecotypes carrying homozygous 451

PRORD29A:LUC and 35S-NPTⅡ transgenes. GK-762B02 (pold2-2) (Rosso et al., 2003), 452

atr-2 (SALK_032841C), and atm (SALK_040423C) are T-DNA insertion mutants 453

ordered from ABRC. dms3-1 (Col-0, (Kanno et al., 2008)) is a gift from Dr. Matzke. 454

Seeds were sterilized and grown on MS medium plates supplemented with 20 g/L 455

sucrose and 0.8% agar at 22°C under long-day (23 h) illumination. When 7 days old, 456

seedlings were transferred to soil and were grown in a greenhouse at 22°C under long-457

day (16 h) conditions. 458

Map-based cloning of POLD2 459

Approximately 12,000 dms3-4 (C24 background and kanamycin-sensitive) seeds were 460

mutated with EMS. The putative mutants were isolated from M2 seedlings that survived 461

on MS medium containing 50 mg/L kanamycin. For map-based cloning of the POLD2 462

gene, pold2-1 dms3-4 (in C24) was crossed with dms3-1 (Col-0) (Kanno et al., 2008), and 463

250 kanamycin-resistant plants selected from the F2 progeny were analyzed with SSLP 464



23

markers based on the polymorphism data (http://1001genomes.org/). POLD2 was 465

narrowed to an area between BAC clone F18O19 and T28M21. Based on previous results 466

with DNA polymerases, the POLD2 gene was selected and sequenced, and a point 467

mutation was determined. 468

For complementation, a 4.9-kbp length of POLD2 genomic DNA containing 1932 bp 469

(promoter + 5’UTR) and 254 bp 3’UTR was cloned into pCAMBIA1391. The plasmid 470

was introduced into pold2-1 dms3-4 mutants by Agrobacterium tumefaciens strain 471

GV3101. 472

Subcellular localization of POLD2–GFP fusion protein 473

Three fragments, i.e., the 1932-bp promoters of POLD2, POLD2 cDNA without the TAA 474

stop codon, and GFP cDNA, were obtained using paired primers and were separately 475

cloned into the pCAMBIA1300 vector with POLD2 fused in frame with GFP. The vector 476

was introduced into pold2-1 dms3-4 plants by A. tumefaciens strain GV3101. This 477

construct was able to complement the pold2-1 mutant, indicating that the POLD2-GFP 478

fusion protein was functional. Three-day-old seedlings of the T2 progeny were examined 479

and photographed with a confocal laser scanning microscope (Leica sp5). 480

GUS staining 481

A 1932-bp genomic fragment of POLD2 upstream of ATG was amplified and cloned into 482

the pCAMBIA1391 vector. This ProPOLD2:GUS plasmid was then transformed into the 483

wild type (C24 ecotype) by A. tumefaciens strain GV3101. At least 25 independent 484

transgenic lines were selected for GUS staining. Transgenic plants at different growth 485

stages were collected and stained with freshly made GUS staining buffer (1× PBS, 0.1% 486



24

Triton X-100, 0.5 mM K3Fe(CN)6, 1 mg/mL X-Gluc) at 37 °C, and were then washed 487

several times with 70% ethanol. 488

Histochemical assay of ProCYCB1;1:GUS 489

Arabidopsis plants transformed with ProCYCB1;1:GUS (Colon-Carmona et al., 1999) 490

were crossed with the pold2-1 mutant. Three independent lines homozygous for both 491

GUS reporter and pold2-1 were selected from F4 progeny and subjected to histochemical 492

GUS staining. Homozygous GUS reporter wild-type lines selected from F4 progeny were 493

used as the control. 494

Intrachromosomal homologous recombination (HR) assay 495

The intrachromosomal recombination reporter line 651 (Molinier et al., 2006) (in C24) 496

was crossed with the pold2-1dms3-4 double mutant. At least three independent F4 plants 497

homozygous for the mutant pold2-1 (DMS3/DMS3×pold2-1/pold2-1) or wild type 498

(DMS3/DMS3×POLD2/POLD2) and homozygous for the GUS transgene were selected. 499

Seedlings were subjected to histochemical GUS staining as mentioned above. 500

Bisulfite sequencing 501

A whole-genome bisulfite sequencing library was prepared mainly according to (Urich et 502

al., 2015). Genomic DNAs were extracted from seedlings using the DNeasy Plant Mini 503

Kit (QIAGEN) according to the manufacturer’s instructions. A 2-μg quantity of genomic 504

DNAs was sonicated (20 cycles of 30 s on, 30 s off, at low intensity) into 200-bp 505

fragments with a Bioruptor (Diagenode, USA), end repaired, 3’-dA-tailed and ligated to 506

methylated adapters. After purification, the ligated DNA fragments were treated with the 507

EZ Methylation-Gold Kit (Zymo Research). The eluted bisulfite-treated DNAs were 508



25

amplified using barcoded primers for sequencing (CGCTGT for the wild type and 509

ACAGTG for the pold2 mutant). High-throughput sequencing of the BS-seq library was 510

performed on the Illumina NextSeq 500 System with single-end 75-bp reads. The raw 511

sequence data were demultiplexed and converted to fastq files using bcl2fastq2 512

Conversion Software (version v2.16.0) under default parameters. The DNA methylation 513

was analyzed according to (Zhao et al., 2014)(Wang et al., 2015). 514

For locus-specific bisulfite sequencing, 500-ng of DNA was treated with the EZ 515

Methylation-Gold Kit (Zymo Research). Two eluted fractions (10 µL each) were used as 516

PCR templates for amplifying the target sequence; the primers were the same as 517

previously reported (Zhao et al., 2014). Products were cloned into the pMD18-T vector 518

(TaKaRa), and 10-15 independent clones of each sample were sequenced (Lifetech-519

China). 520

Analysis of RNA-seq data 521

Total RNAs extracted from seedlings using the RNeasy Plant Mini Kit (QIAGEN) were 522

used for sequencing on the Illumina platform. Three biological replicates were performed 523

for pold2-1 and the wild type. Paired-end reads were selected and aligned to the 524

Arabidopsis reference genome (version: TAIR10) (Lamesch et al., 2012) using TopHat 525

and Cuffdiff (Trapnell et al., 2012). Values of each sample used for heatmap and boxplot 526

were log2(FPKM)-transformed. FPKM (fragments per kilobase of transcript per million 527

mapped reads) was generated from the output of the Cuffdiff software. 528

Chromatin immunoprecipitation (ChIP) assay 529



26

ChIP assay was based on the previous studies (Zhang et al., 2007; Lu et al., 2011) with 530

some modifications. A 2-g quantity of 10-day-old seedlings was fixed in 1% 531

formaldehyde. The seedlings were ground into power with liquid nitrogen and 532

homogenized with nuclei extraction buffer (1 M hexylene glycol, 20 mM Tris-HCl (pH 533

8.0), 0.15 mM spermine, 5 mM 2-mercaptoethanol, 1% Triton X-100, 0.1 mM PMSF, 534

and protease inhibitor cocktail). The homogenates were filtered through Miracloth and 535

centrifuged at 2,000 g for 10 min at 4°C. The pellets were washed two times with nuclei 536

extraction buffer and resuspended in 300 μL of nuclei lysis buffer (50 mM Tris-HCl (pH 537

8.0), 10 mM EDTA, 1% SDS and protease inhibitor cocktail). The chromatin was 538

sonicated (15 cycles of 30 s on with 30 s off, at high intensity) into fragments of about 539

300 bp using a Bioruptor. The antibodies used were anti-H3K27me3 (Ab6002, Abcam), 540

anti-H3 (ab1791, Abcam), anti-H3K4me3 (ab8580, Abcam), and anti-H3K9me2 (ab1220, 541

Abcam). Dynabeads (10001D, Life Technologies) were used for immunoprecipitation. 542

After RNase A and Proteinase K treatment, DNAs were recovered using the QIAquick 543

PCR purification kit (QIAGEN). The DNA concentration was determined using the Qubit 544

2.0 system (Life Technologies). The ChIP and input samples were adjusted with dH2O to 545

a concentration of 50 pg/μL, and used for qRT-PCR. Real-time PCR was performed in 20 546

μL with 1 μL of immunoprecipitated or input DNA in SYBR Green Master Mix 547

(TaKaRa). The reaction conditions were as follows: 95°C for 5 min and 40 cycles of 548

95°C for 30 s and 60°C for 1 min. 549

A 10-ng quantity of ChIP or input DNA was used to prepare a high-throughput 550

sequencing library. End repair, dA-tailing, adapter ligation, and amplification were 551



27

carried out using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina 552

(E6240, NEB) according to the manufacturer’s protocol. Index primers used for each 553

sample were as follows: ATCACG for WT-H3K27me3, CGATGT for WT-H3K4me3, 554

TTAGGC for WT-H3K9me2, TGACCA for WT-H3, ACAGTG for WT-Input, 555

GCCAAT for pold2-H3K27me3, CAGATC for pold2-H3K4me3, ACTTGA for pold2-556

H3K9me2, GATCAG for pold2-H3, and TAGCTT for pold2-Input. High-throughput 557

sequencing of the ChIP-seq library was carried on the Illumina NextSeq 500 System with 558

single-end 75-bp reads. The raw sequence data were demultiplexed and converted to fastq 559

files using bcl2fastq2 Conversion Software (Version v2.16.0) under default parameters. 560

ChIP-seq analysis 561

Reads were mapped to the Arabidopsis genome (TAIR10) using bowtie1 (version 0.12.9) 562

(Langmead et al., 2009) allowing two nucleotide mismatches using following parameters: 563

bowtie -q -k 1 -n 2 -l 36 --best -S -p 2. Mapped reads were de-duplicated and sorted by 564

samtools (version 0.1.19-44428cd) (Li et al., 2009). Then the reads were normalized to 565

reads depth and used for further analysis. Peaks were found using MACS software 566

(version 1.4.2) (Zhang et al., 2008) using H3 as a background. For H3K27me3 peaks 567

finding in the wild type as an example, the parameters were as follow: macs14 -t 568

WT_K27ME3.sorted.bam –c WT_H3.sorted.bam –f BAM -g 1.30e+8 -n WT_K27ME3 569

--shiftsize 73 --pvalue 1e-5 --bw=300 --mfold=10,30. Gene annotation was used 570

BEDTools (Quinlan and Hall, 2010) according to TAIR10. 571

Histone modification changes between the wild type and pold2-1 mutant were determined 572

with SICER software (version 1.1) (Zang et al., 2009). For H3K4me3, the parameters 573



28

were as follows: SICER-df.sh pold2-1-H3K4me3.bed pold2-1-input.bed WT-574

H3K4me3.bed WT-input.bed 200 200 0.05 0.05; this means that the Window size and 575

Gap size were set at 200 bp. Then filtered by P-value < 0.01, FDR < 0.01 and fold 576

change > 1.5. For H3K27me3, the parameters were as follows: SICER-df.sh pold2-1-577

H3K27me3.bed pold2-1-input.bed WT-H3K27me3.bed WT-input.bed 200 200 0.05 0.05, 578

then filtered by P-value < 0.01, FDR < 0.01. Different regions were annotated with 579

BEDTools. Figure 7 and 8 were made using R packages (ggplot2, Rmisc, and reshape) 580

and homemade script. 581

Real-time PCR 582

Total RNAs were extracted from 0.1 g of seedlings using the RNeasy Plant Mini Kit 583

(QIAGEN). After RNase-free DNaseⅠ(TaKaRa) digestion at 37°C, 4 µg of RNA was 584

reverse transcribed with M-MLV reverse transcriptase (Promega) in a 30-μL volume. A 585

2-µL volume of five-fold-diluted cDNA was added to a 20-µL real-time PCR reaction 586

system in SYBR Green Master Mix (TaKaRa). The reaction was running by StepOnePlus 587

Real-Time PCR System (Applied Biosystems, USA), and the procedure was as follows: 588

95°C for 2 min followed by 40 cycles of 95°C for 5 s and 60°C for 30 s. Specific primers 589

for each gene are listed in Supplementary table S11. UBIQUITIN-CONJUGATING 590

ENZYME 21 (UBI, AT5G25760) was used as the reference gene as previously described 591

(Huettel et al., 2006). Three technical replicates were performed per biological replicate, 592

and two to three biological replicates were used in all experiments. 593

DNA-damage assay 594



29

A DNA-damage assay was performed as previously described (Liu et al., 2010). Seeds 595

were sterilized and grown on MS medium or MS medium supplemented with one of three 596

DNA-damaging reagents: 25 µM CIS (cis-diamineplatinum (II) dichloride, SIGMA, 597

479306); 50 ppm (0.005%) MMS (methyl methanesulfonate, SIGMA, 129925); or 200 598

mg/L HU ( , SIGMA, H8627). After they were grown for 15 days at 22°C under long-599

day (23 h) illumination, seedlings were imaged and weighed. The fresh weight relative to 600

untreated controls after treatment with DNA-damaging reagents was calculated. Three 601

biological replicates were carried out. 602

Telomere length 603

Genomic DNAs were extracted from 14-day-old seedlings using the DNaesy Plant Mini 604

Kit (QIAGEN) according to the manufacturer’s instructions. A 3-µg quantity of DNA 605

was digested with HinfI or MseI in a 100-μL system at 37 °C. Southern blot was 606

performed with the DIG-High Prime DNA Labeling and Detection Starter Kit II (Roche). 607

The synthesized telomere repeat (TTTAGGG), which was labeled with digoxigenin using 608

the DIG Oligonucleotide 3'-End Labeling Kit (Roche), was used as the probe. 609

Accession numbers 610

Sequence data from this article can be found in the EMBL/GenBank data libraries under 611

accession numbers: POLD2 (AT2G42120), RFC1 (AT5G22010), POLA (AT5G67100), 612

POLE (AT1G08260), ROR1 (AT2G24490), ROS1(AT2G36490), DMS3 (AT3G49250), 613

NRPD1 (AT1G63020), NRPE1 (AT2G40030), ROS4 (AT3G14980), ATM 614

(AT3G48190), ATR (AT5G40820), HDA6 (AT5G63110), UBP26 (AT3G49600), , SEP3 615



30

(AT1G24260), UBI (AT5G25760), BRCA1 (AT4G21070), RAD51 (AT5G20850), 616

PARP1 (AT2G31320), PARP2 (AT4G02390), and CYCB1;1 (AT4G37490). 617

RNA-seq, BS-seq, and ChIP-seq data have been deposited in the National Center for 618

Biotechnology Information Gene Expression Omnibus (GEO) database under accession 619

number GSE79259. 620

Supplemental Data 621

The following supplemental materials are available. 622

Supplemental Figure S1. Diagrams of hda6-11, ubp26-5, rfc1-4, and pold2-1 mutations. 623

Supplemental Figure S2. Genetic analysis of pold2-1 with pold2-2. 624

Supplemental Figure S3. POLD2 is a nuclear protein and is ubiquitously expressed. 625

Supplemental Figure S4. ChIP-qPCR in rfc1-4, ubp26-5 and hda6-11 samples. 626

Supplemental Figure S5. Validation of ChIP-seq data. 627

Supplemental Figure S6. Epigenetic profile of bivalent genes affected by pold2-1 mutant. 628

Supplemental Figure S7. Western blot to check global H3K27me3 and H3K4me3 in the 629

pold2-1 mutant. 630

Supplementary table S1. List of genes that harbor H3K27me3 in the C24 ecotype. 631

Supplementary table S2. List of genes that harbor H3K4me3 in the C24 ecotype 632

Supplementary table S3. List of genes that harbor H3K9me2 in the C24 ecotype. 633

Supplementary table S4. List of genes with decreased levels of H3K27me3 in the pold2-1 634

mutant. 635

Supplementary table S5. RNA-seq data. 636



31

Supplementary table S6. List of genes with increased levels of H3K27me3 in the pold2-1 637

mutant. 638

Supplementary table S7. List of genes with increased levels of H3K4me3 in the pold2-1 639

mutant. 640

Supplementary table S8. List of genes with decreased levels of H3K4me3 in the pold2-1 641

mutant. 642

Supplementary table S9. Bivalent genes changed in the pold2-1 mutant. 643

Supplementary table S10. The expression of genes responsible for H3K27me3 and 644

H3K4me3 in the wild type and pold2-1 mutant from RNA-seq data. 645

Supplementary table S11. Primers used in this study. 646

647

Acknowledgments 648

We would like to thank Dr. Marjori A. Matzke for providing dms3-1 mutant. We also 649

thank Arabidopsis Biological Resource Center for T-DNA mutant. 650

651



32

Figure legends 652

Figure 1. Isolation of mutants that suppress the kanamycin sensitivity of the dms3-4 653

mutant. 654

A. The phenotype of the wild type (WT), dms3-4, and suppressors of dms3-4 growing on 655

MS medium supplemented with 50 mg/L kanamycin. 656

B. Relative expression of NPTII in the WT, dms3-4, and suppressors of dms3-4. 657

C. Relative expression of ROS1 in the WT, dms3-4, and suppressors of dms3-4. 658

D. Relative expression of TSI in WT, dms3-4, and suppressors of dms3-4. For B, C, and 659

D, RNAs were extracted from 7-day-old seedlings. Values were normalized to the 660

expression level of the references gene (UBI). Two independent experiments (each with 661

three technical replicates) were done with similar results. Values are means ± SE, n=3, 662

from one experiment. 663

E. pold2-1 released the silencing of 35S:NPTII in ros1, ros4, nrpd1, and nrpe1. The 664

growth phenotype of the WT, pold2-1, ros1, ros4, nrpd1-8, nrpe1-14, and double mutants 665

pold2-1 ros1, pold2-1 ros4, pold2-1 nrpd1-8, and pold2-1 nrpe1-14 on MS containing 0 666

or 50 mg/L kanamycin (Kan). 667

F. pold2-1 could not restore the expression of silenced RD29A:LUC caused by the ros1 668

mutant. Luminescence imaging of the RD29A:LUC transgene. The indicated plants were 669

treated with 300 mM NaCl for 3 h, followed by luminescence imaging. 670

Figure 2. Map-based cloning of POLD2 671

A. Phenotypic analysis of F1 seedlings of dms3-4 pold2-1 backcrossed with dms3-4 on 672

kanamycin-containing medium. 673



33

B. The segregation of F2 seedlings growing on kanamycin-containing medium. 674

C. Map-based cloning of the pold2-1 mutation. The position of the POLD2 mutation was 675

narrowed to the bottom of chromosome 2 between BAC T28M21 and F18O19. The 676

mutation of pold2-1 occurred at splicing sites (G1170A). pold2-2 is a T-DNA insertion 677

allele. The domain structure of the POLD2 protein is indicated. OB, oligonucleotide-678

/oligosaccharide-binding domain; PDE, phosphodiesterase-like domain. 679

D. Spliced forms of cDNA caused by the pold2-1 mutation. Five kinds of transcripts were 680

identified from 23 independent clones amplified from cDNAs. Among them, four 681

transcripts would produce an earlier stop codon, and one would delete 6 bp and lead to 682

the deletion of two amino acids (delete QE) and to the mutation of one amino acid (from 683

original D to H). 684

E. Complementary analyses of pold2-1 with genomic DNA or Pro35S:FLAG-HA-685

POLD2 construct, or native promoter driving cDNA (ProPOLD2: POLD2-GFP). 686

Phenotypes of mutant and complementary lines growing on MS medium containing 0 687

mg/L kanamycin (left) or 50 mg/L kanamycin (right). 688

Figure 3. Phenotypic analyses of pold2-1 with other DNA replication-related 689

mutants. 690

A. Phenotype of the wild type (WT), pold2-1, pol α, and pold2-1 polα double mutant. 691

B. Phenotype of the WT, pol ε, pol α, and polε pol α double mutant. 692

C. Phenotype of the WT, pold2-1, ror1-2 (rpa2a), and pold2-1 ror1-2 double mutant. 693

D. Phenotype of the WT, polε, ror1-2 (rpa2a), and polε ror1-2 double mutant. 694

E. Phenotype of the WT, polε, pold2-1, and pold2-1 polε double mutant. 695



34

F. Phenotype of the WT, ror1-2 (rpa2a), pol α, and polα ror1-2 double mutant. 696

G. Phenotype of the WT, atr, pold2-1, and atr pold2-1 double mutant. 697

H. Phenotype of the WT, atm, pold2-1, and atm pold2-1 double mutant. Bar = 1 cM. 698

Figure 4. The pold2-1 mutant has increased sensitivity to DNA damage, a delayed 699

cell cycle, increased homologous recombination, and a reduced telomere length. 700

A. pold2-1 is hypersensitive to MMS. Wild-type, dms3-4, pold2-1 dms3-4, and pold2-1 701

seedlings that were grown for 15 days on MS medium alone or MS medium with 200 702

mg/L hydroxyurea (200 HU), 50 ppm methyl methanesulfonate (50 MMS), or 25 µM 703

cisplatin (25 CIS). P values were calculated using Paired Student’s t test. 704

B. Relative fresh weight of seedlings in (D). The fresh weight relative to untreated 705

controls after treatment with DNA-damaging reagents is shown. Values are means ± SE, 706

n=3. 707

C. Relative expression of DNA damage response genes in the wild type, dms3-4, pold2-1 708

dms3-4, and pold2-1 as determined by qRT-PCR. RNAs extracted from 7-day-old 709

seedlings were used for qRT-PCR. Values were normalized to the expression level of the 710

references gene (UBI). Two independent experiments (each with three technical 711

replicates) were done with similar results. Values are means ± SE, n=3, from one 712

experiment. 713

D. pold2-1 increases the expression of ProCYCB1;1:GUS. ProCYCB1;1:GUS was 714

introduced into the pold2-1 mutant by crossing the wild type carrying ProCYCB1;1:GUS 715

with the pold2-1 mutant. a–d show GUS staining in (a) a wild-type seedling; (b) a wild-716

type root tip; (c) a pold2-1 seedling; and (d) a pold2-1 root tip. (e) CYCB1;1 expression 717



35

as determined by qRT-PCR. RNAs were extracted from 7-day-old seedlings and used for 718

qRT-PCR. Values were normalized to the expression level of the references gene (UBI). 719

Two independent experiments (each with three technical replicates) were done with 720

similar results. Values are means ± SE, n=3, from one experiment. 721

E. pold2-1 increases homologous recombination (HR) in 14-day-old seedlings. The wild-722

type 651 carrying a homologous reporter GUS gene was crossed with the dms3-4 pold2-1 723

mutant. Homozygous pold2-1 plants carrying the homozygous GUS reporter were 724

isolated and used for GUS staining. 725

F-G. pold2-1 exhibits a reduced telomere length. Genomic DNAs of the wild type, dms3-726

4, pold2-1, and pold2-1 dms3-4 digested by HinfI (DNA-methylation sensitive, F) or 727

MseI (DNA-methylation insensitive, G) were subjected to Southern blot with a telomere 728

probe. 729

Figure 5. pold2-1 releases the silencing of NPTII in dms3-4 independent on DNA 730

methylation. 731

A. IGV visualization of the DNA methylation level (CG, CHG, and CHH) at the 732

transgenic T-DNA locus in the wild type (WT) and pold2-1 mutant from whole-genome 733

bisulfite sequencing data. 734

B-C. Methylation level of the 35S (B) and NOS (C) regions of the wild type, dms3-4, 735

pold2-1, and dms3-4 pold2-1 as determined by bisulfite sequencing (10-15 clones were 736

analyzed for each sample). 737

D. Patterns of DNA methylation (CG, CHG, and CHH) across all genes in the wild type 738

(WT) and the pold2-1 mutant. Genes were aligned from the transcriptional start sites 739



36

(TSS) to the transcriptional termination sites (TTS), and average methylation for all 740

cytosines within each bin is plotted. 741

E. Patterns of DNA methylation (CG, CHG, and CHH) across all transposon elements 742

(TEs) in the wild type (WT) and the pold2-1 mutant. TEs were aligned from the 743

transcriptional start sites (TSS) to the transcriptional termination sites (TTS), and average 744

methylation for all cytosines within each bin is plotted. 745

Figure 6. pold2-1 decreases the H3K27me3 level at NPTII 746

A. Histone modification status of the transgene construct in the wild type (WT) and 747

pold2-1 mutant. Data of Histone H3 lysine 9 dimethylation (K9me2), Histone H3 lysine 748

27 trimethylation (K27me3), Histone H3 lysine 4 trimethylation (K4me3), total histone 749

H3 (H3), and input (Input) level were shown from whole genome ChIP-seq. The data 750

range of each modification was set to the same scale between the wild type and pold2-1 751

mutant. 752

B. Chart depicted the relative quantitative histone modification level of 35S or NPTII 753

region as shown in A. 754

C-E. Histone modification levels at 35S (C), NPTII (D), and UBI (E) in the wild type, 755

dms3-4, pold2-1 dms3-4, and pold2-1 as indicated by ChIP-PCR analysis. The histone 756

modification levels of H3K27me3, H3K4me3, H3K9me2, and total histone H3 on each 757

indicated locus were detected by ChIP-qPCR. UBI was used as a control locus enriched 758

in H3K4me3 but depleted in H3K27me3 or H3K9me2 modification. The error bars 759

represent the standard error of the means. 760



37

Figure 7. Correlation between H3K27me3 signals across the genes and mRNA 761

expression levels caused by the pold2-1 mutation. 762

A. Altered histone modification profiles of 977 H3K27me3-decreased genes by pold2-1. 763

Genes were aligned from the transcriptional start sites (TSS) to the transcriptional 764

termination sites (TTS) and divided into 60 bins. The 2,000-bp (2-kb) regions either 765

upstream of TSS or downstream TTS were also included and divided into 20 bins 766

respectively. Histone modification levels of each bin are plotted. 767

B. Gene expression profiles of H3K27me3-decreased genes in pold2-1 and the wild type. 768

Values were log2FPKM-transformed. FPKM (fragments per kilobase of transcript per 769

million mapped reads) were generated from RNA-seq using TopHat and Cufflinks 770

software. 771

C. Boxplot showing the expression (log2FPKM-transformed) of genes in B. The mean 772

value of the group was significantly higher in pold2-1 than in the wild type (*** 773

P<0.0001, two-tailed paired Student’s t-test). 774

D. Altered histone modification profiles of 343 H3K27me3-increased genes by pold2-1 775

mutant. Genes were aligned from the transcriptional start sites (TSS) to the transcriptional 776


upstream of TSS or downstream TTS were also included, and each was divided into 20 778

bins. Histone modification levels of each bin are plotted. 779

E. Gene expression profiles of H3K27me3-increased genes in pold2-1. Values shown are 780

log2FPKM-transformed. FPKM (fragments per kilobase of transcript per million mapped 781

reads) were generated from RNA-seq using TopHat and Cufflinks software. 782



38

F. Boxplot showing the expression (log2FPKM-transformed) of genes in B. The mean 783

value of the group in pold2-1 was not significantly different from that in the wild-type 784

group (n. s., not significant, paired Student’s t-test). 785

Figure 8. Correlation between H3K4me3 signals across the gene and mRNA 786

expression levels caused by pold2 mutant 787

A. Altered histone modification profiles of 499 H3K4me3-increased genes by pold2-1. 788

Genes were aligned from the transcriptional start sites (TSS) to the transcriptional 789




B. Gene expression profiles of H3K4me3-increased genes by pold2-1. Values shown are 793

log2FPKM. FPKM (fragments per kilobase of transcript per million mapped reads) was 794

generated from RNA-seq using TopHat and Cufflinks software. 795

C. Boxplot showing the expression (log2FPKM-transformed) of genes in B. The mean 796

value of the pold2-1 group was significantly higher than that of the wild-type group (*** 797

P<0.0001, two-tailed, paired Student’s t-test). 798

D. Altered histone modification profiles of 32 H3K4me3-decreased genes by pold2-1 799

mutant. Genes were aligned from the transcriptional start sites (TSS) to the transcriptional 800






39

E. Gene expression profiles of H3K4me3-decreased genes by pold2-1 mutant. Values are 804

log2FPKM-transformed. FPKM (fragments per kilobase of transcript per million mapped 805

reads) was generated from RNA-seq using TopHat and Cufflinks software. 806

F. Boxplot showing the expression (log2FPKM) of genes in B. The mean value of the 807

pold2-1 group was significantly lower than that of the wild-type group (** P<0.001, two-808

tailed paired Student’s t-test). 809

Figure 9. IGV visualization of selected histone modification altered genes, and 810

validation of ChIP-seq results. 811

A. IGV views of reads density (RPKM) of H3K27me3 (K27me3), H3K4me3 (K4me3), 812

H3, and Input from CHIP-seq data in the wild type (WT) and pold2-1 mutant. The data 813

range of each modification was set to the same scale for the WT and pold2-1 mutant. 814

AT2G39250 and AT1G06360 are examples of genes with increased levels of H3K27me3 815

and decreased levels of H3K4me3. UBI is a positive control for H3K4me3 and a negative 816

control for H3K27me3; the level of histone modification for UBI was similar for the wild 817

type (WT) and the pold2-1 mutant. The other genes had decreased levels of H3K27me3 818

and increased levels of H3K4me3. The red bars on the top of each gene indicate the 819

primer location used for validation. 820

B-D. ChIP-qPCR verified the selected histone modification changed genes. The histone 821

modification level of H3K27me3 (B), H3K4me3 (C), and total histone H3 (D) on each 822

indicated gene was measured by ChIP-qPCR between the wild type (WT) and pold2-1 823

mutant. Values presented are relative to the input, the error bars represent the standard 824



40

error of the mean (n=3). AT5G25760 (UBI) was used as a control locus enriched in 825

H3K4me3 modification but depleted in H3K27me3 modification. 826

E. Relative gene expression level of these selected genes. RNAs extracted from 10-day-827

old seedlings were used for qRT-PCR. Values were normalized to the expression level of 828

the references gene (UBI). Two independent experiments (each with three technical 829

replicates) were done with similar results. Values are means ± SE, n=3, from one 830

experiment. 831

832

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834

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837

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841

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41

846

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Parsed CitationsAufsatz W, Mette MF, van der Winden J, Matzke M, Matzke AJ (2002) HDA6, a putative histone deacetylase needed to enhanceDNA methylation induced by double-stranded RNA. EMBO J 21: 6832-6841

Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Barrero JM, Gonzalez-Bayon R, del Pozo JC, Ponce MR, Micol JL (2007) INCURVATA2 encodes the catalytic subunit of DNAPolymerase alpha and interacts with genes involved in chromatin-mediated cellular memory in Arabidopsis thaliana. Plant Cell 19:2822-2838


Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A,Feil R, Schreiber SL, Lander ES (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells.Cell 125: 315-326


Burgers PM (2009) Polymerase dynamics at the eukaryotic DNA replication fork. J Biol Chem 284: 4041-4045Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Chen S, Bohrer LR, Rai AN, Pan Y, Gan L, Zhou X, Bagchi A, Simon JA, Huang H (2010) Cyclin-dependent kinases regulateepigenetic gene silencing through phosphorylation of EZH2. Nat Cell Biol 12: 1108-1114


Church DN, Briggs SE, Palles C, Domingo E, Kearsey SJ, Grimes JM, Gorman M, Martin L, Howarth KM, Hodgson SV,Collaborators N, Kaur K, Taylor J, Tomlinson IP (2013) DNA polymerase epsilon and delta exonuclease domain mutations inendometrial cancer. Hum Mol Genet 22: 2820-2828


Colon-Carmona A, You R, Haimovitch-Gal T, Doerner P (1999) Technical advance: spatio-temporal analysis of mitotic activity with alabile cyclin-GUS fusion protein. Plant J 20: 503-508


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http://www.ncbi.nlm.nih.gov/pubmed?term=%28Nat Genet%5BTitle%5D%29 AND 45%5BVolume%5D AND 136%5BPagination%5D AND Palles C%2C Cazier JB%2C Howarth KM%2C Domingo E%2C Jones AM%2C Broderick P%2C Kemp Z%2C Spain SL%2C Guarino E%2C Salguero I%2C Sherborne A%2C Chubb D%2C Carvajal%2DCarmona LG%2C Ma Y%2C Kaur K%2C Dobbins S%2C Barclay E%2C Gorman M%2C Martin L%2C Kovac MB%2C Humphray S%2C Consortium C%2C Consortium WGS%2C Lucassen A%2C Holmes CC%2C Bentley D%2C Donnelly P%2C Taylor J%2C Petridis C%2C Roylance R%2C Sawyer EJ%2C Kerr DJ%2C Clark S%2C Grimes J%2C Kearsey SE%2C Thomas HJ%2C McVean G%2C Houlston RS%2C Tomlinson I%5BAuthor%5D&dopt=abstract

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Ramirez-Parra E, Gutierrez C (2007) E2F regulates FASCIATA1, a chromatin assembly gene whose loss switches on the endocycleand activates gene expression by changing the epigenetic status. Plant Physiol 144: 105-120


Rosso MG, Li Y, Strizhov N, Reiss B, Dekker K, Weisshaar B (2003) An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics. Plant Mol Biol 53: 247-259


Schonrock N, Exner V, Probst A, Gruissem W, Hennig L (2006) Functional genomic analysis of CAF-1 mutants in Arabidopsisthaliana. J Biol Chem 281: 9560-9568


Schuermann D, Fritsch O, Lucht JM, Hohn B (2009) Replication stress leads to genome instabilities in Arabidopsis DNApolymerase delta mutants. Plant Cell 21: 2700-2714


Sridhar VV, Kapoor A, Zhang K, Zhu J, Zhou T, Hasegawa PM, Bressan RA, Zhu JK (2007) Control of DNA methylation andheterochromatic silencing by histone H2B deubiquitination. Nature 447: 735-738


Steimer A, Amedeo P, Afsar K, Fransz P, Mittelsten Scheid O, Paszkowski J (2000) Endogenous targets of transcriptional genesilencing in Arabidopsis. Plant Cell 12: 1165-1178


Stroud H, Greenberg MV, Feng S, Bernatavichute YV, Jacobsen SE (2013) Comprehensive analysis of silencing mutants revealscomplex regulation of the Arabidopsis methylome. Cell 152: 352-364


Takeda S, Tadele Z, Hofmann I, Probst AV, Angelis KJ, Kaya H, Araki T, Mengiste T, Mittelsten Scheid O, Shibahara K, Scheel D,Paszkowski J (2004) BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis. GenesDev 18: 782-793


Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential geneand transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7: 562-578


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http://www.ncbi.nlm.nih.gov/pubmed?term=%28Plant Cell%5BTitle%5D%29 AND 16%5BVolume%5D AND 1021%5BPagination%5D AND Probst AV%2C Fagard M%2C Proux F%2C Mourrain P%2C Boutet S%2C Earley K%2C Lawrence RJ%2C Pikaard CS%2C Murfett J%2C Furner I%2C Vaucheret H%2C Mittelsten Scheid O%5BAuthor%5D&dopt=abstract

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http://www.ncbi.nlm.nih.gov/pubmed?term=%28Bioinformatics%5BTitle%5D%29 AND 26%5BVolume%5D AND 841%5BPagination%5D AND Quinlan AR%2C Hall IM%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842

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http://search.crossref.org/?page=1&rows=2&q=Rosso MG, Li Y, Strizhov N, Reiss B, Dekker K, Weisshaar B (2003) An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics. Plant Mol Biol 53: 247-259

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http://www.ncbi.nlm.nih.gov/pubmed?term=%28Plant Cell%5BTitle%5D%29 AND 12%5BVolume%5D AND 1165%5BPagination%5D AND Steimer A%2C Amedeo P%2C Afsar K%2C Fransz P%2C Mittelsten Scheid O%2C Paszkowski J%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

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http://www.ncbi.nlm.nih.gov/pubmed?term=%28BRU%5BTitle%5D%29 AND 1%5BVolume%5D AND a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis%2E Genes Dev 18%3A 782%5BPagination%5D AND Takeda S%2C Tadele Z%2C Hofmann I%2C Probst AV%2C Angelis KJ%2C Kaya H%2C Araki T%2C Mengiste T%2C Mittelsten Scheid O%2C Shibahara K%2C Scheel D%2C Paszkowski J%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Takeda&as_ylo=2004&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Nat Protoc%5BTitle%5D%29 AND 7%5BVolume%5D AND 562%5BPagination%5D AND Trapnell C%2C Roberts A%2C Goff L%2C Pertea G%2C Kim D%2C Kelley DR%2C Pimentel H%2C Salzberg SL%2C Rinn JL%2C Pachter L%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Trapnell&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Nat Protoc%5BTitle%5D%29 AND 10%5BVolume%5D AND 475%5BPagination%5D AND Urich MA%2C Nery JR%2C Lister R%2C Schmitz RJ%2C Ecker JR%5BAuthor%5D&dopt=abstract

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Wang Y, Liu J, Xia R, Wang J, Shen J, Cao R, Hong X, Zhu JK, Gong Z (2007) The protein kinase TOUSLED is required formaintenance of transcriptional gene silencing in Arabidopsis. EMBO Rep 8: 77-83


Xia R, Wang J, Liu C, Wang Y, Wang Y, Zhai J, Liu J, Hong X, Cao X, Zhu JK, Gong Z (2006) ROR1/RPA2A, a putative replicationprotein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis. Plant Cell 18: 85-103


Yin H, Zhang X, Liu J, Wang Y, He J, Yang T, Hong X, Yang Q, Gong Z (2009) Epigenetic regulation, somatic homologousrecombination, and abscisic acid signaling are influenced by DNA polymerase epsilon mutation in Arabidopsis. Plant Cell 21: 386-402


Zang CZ, Schones DE, Zeng C, Cui KR, Zhao KJ, Peng WQ (2009) A clustering approach for identification of enriched domains fromhistone modification ChIP-Seq data. Bioinformatics 25: 1952-1958


Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE (2009) Genome-wide analysis of mono-, di- and trimethylation ofhistone H3 lysine 4 in Arabidopsis thaliana. Genome Biol 10: R62


Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE (2007) Whole-genome analysis of histoneH3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5: e129


Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers RM, Brown M, Li W, Liu XS (2008) Model-based Analysis of ChIP-Seq (MACS). Genome Biology 9


Zhao Y, Xie S, Li X, Wang C, Chen Z, Lai J, Gong Z (2014) REPRESSOR OF SILENCING5 Encodes a Member of the Small HeatShock Protein Family and Is Required for DNA Demethylation in Arabidopsis. Plant Cell 26: 2660-2675


Zhu JK (2009) Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet 43: 143-166Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title


http://www.ncbi.nlm.nih.gov/pubmed?term=%28Plant Physiol%5BTitle%5D%29 AND 167%5BVolume%5D AND 905%5BPagination%5D AND Wang C%2C Dong X%2C Jin D%2C Zhao Y%2C Xie S%2C Li X%2C He X%2C Lang Z%2C Lai J%2C Zhu JK%2C Gong Z%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Wang C, Dong X, Jin D, Zhao Y, Xie S, Li X, He X, Lang Z, Lai J, Zhu JK, Gong Z (2015) Methyl-CpG-binding domain protein MBD7 is required for active DNA demethylation in Arabidopsis. Plant Physiol 167: 905-914

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http://scholar.google.com/scholar?as_q=Methyl-CpG-binding domain protein MBD7 is required for active DNA demethylation in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wang&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28EMBO Rep%5BTitle%5D%29 AND 8%5BVolume%5D AND 77%5BPagination%5D AND Wang Y%2C Liu J%2C Xia R%2C Wang J%2C Shen J%2C Cao R%2C Hong X%2C Zhu JK%2C Gong Z%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Wang Y, Liu J, Xia R, Wang J, Shen J, Cao R, Hong X, Zhu JK, Gong Z (2007) The protein kinase TOUSLED is required for maintenance of transcriptional gene silencing in Arabidopsis. EMBO Rep 8: 77-83

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Wang&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=The protein kinase TOUSLED is required for maintenance of transcriptional gene silencing in Arabidopsis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=The protein kinase TOUSLED is required for maintenance of transcriptional gene silencing in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wang&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28ROR%5BTitle%5D%29 AND 2%5BVolume%5D AND functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis%2E Plant Cell 18%3A 85%5BPagination%5D AND Xia R%2C Wang J%2C Liu C%2C Wang Y%2C Wang Y%2C Zhai J%2C Liu J%2C Hong X%2C Cao X%2C Zhu JK%2C Gong Z%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Xia R, Wang J, Liu C, Wang Y, Wang Y, Zhai J, Liu J, Hong X, Cao X, Zhu JK, Gong Z (2006) ROR1/RPA2A, a putative replication protein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis. Plant Cell 18: 85-103

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Xia&hl=en&c2coff=1


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http://www.ncbi.nlm.nih.gov/pubmed?term=%28Plant Cell%5BTitle%5D%29 AND 21%5BVolume%5D AND 386%5BPagination%5D AND Yin H%2C Zhang X%2C Liu J%2C Wang Y%2C He J%2C Yang T%2C Hong X%2C Yang Q%2C Gong Z%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Yin H, Zhang X, Liu J, Wang Y, He J, Yang T, Hong X, Yang Q, Gong Z (2009) Epigenetic regulation, somatic homologous recombination, and abscisic acid signaling are influenced by DNA polymerase epsilon mutation in Arabidopsis. Plant Cell 21: 386-402

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Yin&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Epigenetic regulation, somatic homologous recombination, and abscisic acid signaling are influenced by DNA polymerase epsilon mutation in Arabidopsis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Epigenetic regulation, somatic homologous recombination, and abscisic acid signaling are influenced by DNA polymerase epsilon mutation in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yin&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Bioinformatics%5BTitle%5D%29 AND 25%5BVolume%5D AND 1952%5BPagination%5D AND Zang CZ%2C Schones DE%2C Zeng C%2C Cui KR%2C Zhao KJ%2C Peng WQ%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zang CZ, Schones DE, Zeng C, Cui KR, Zhao KJ, Peng WQ (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25: 1952-1958

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zang&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A clustering approach for identification of enriched domains from histone modification ChIP-Seq data&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A clustering approach for identification of enriched domains from histone modification ChIP-Seq data&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zang&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Genome%2Dwide analysis of mono%2D%2C di%2D and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana%2E%5BTitle%5D%29 AND Zhang X%2C Bernatavichute YV%2C Cokus S%2C Pellegrini M%2C Jacobsen SE%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE (2009) Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol 10: R62

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http://scholar.google.com/scholar?as_q=Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhang&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Whole%2Dgenome analysis of histone H3 lysine 27 trimethylation in Arabidopsis%2E%5BTitle%5D%29 AND Zhang X%2C Clarenz O%2C Cokus S%2C Bernatavichute YV%2C Pellegrini M%2C Goodrich J%2C Jacobsen SE%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5: e129


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http://www.ncbi.nlm.nih.gov/pubmed?term=%28Model%2Dbased Analysis of ChIP%2DSeq MACS%2E%5BTitle%5D%29 AND Zhang Y%2C Liu T%2C Meyer CA%2C Eeckhoute J%2C Johnson DS%2C Bernstein BE%2C Nussbaum C%2C Myers RM%2C Brown M%2C Li W%2C Liu XS%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers RM, Brown M, Li W, Liu XS (2008) Model-based Analysis of ChIP-Seq (MACS). Genome Biology 9


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http://www.ncbi.nlm.nih.gov/pubmed?term=%28Annu Rev Genet%5BTitle%5D%29 AND 43%5BVolume%5D AND 143%5BPagination%5D AND Zhu JK%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhu JK (2009) Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet 43: 143-166

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