a jumonji protein with e3 ligase and histone h3 binding activities … · 4 89 chromatin structure...

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Short title: E3 ubiquitin ligase JMJ24 and TE silencing 1

Corresponding author: Isabel Bäurle 2

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A jumonji protein with E3 ligase and histone H3 binding activities 5

affects transposon silencing in Arabidopsis 6

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Tina Kabelitz1, Krzysztof Brzezinka1, Thomas Friedrich1, Michał Górka2, Alexander Graf2, 8

Christian Kappel1, Isabel Bäurle1* 9

10 1Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany 11 2 Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany 12

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*Corresponding author email: [email protected] 14

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One sentence summary: 18

A conserved jumonji protein with E3 ubiquitin ligase activity affects transposon silencing. 19

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Funding information 23

This work was supported by a Sofja-Kovalevskaja-Award from the Alexander-von-Humboldt-24

Foundation and the Deutsche Forschungsgemeinschaft (Grant SFB 973, Project A2) to I.B.. 25

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Author contributions 27

TK and IB conceived and designed research. TK, KB, TF, MG, AG, IB performed research. 28

TK, KB, AG, CK, IB analyzed the data. TK and IB wrote the manuscript with input from all 29

authors. 30

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Plant Physiology Preview. Published on March 15, 2016, as DOI:10.1104/pp.15.01688

Copyright 2016 by the American Society of Plant Biologists

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Abstract 33

Transposable elements (TEs) make up a large proportion of eukaryotic genomes. As their 34

mobilization creates genetic variation that threatens genome integrity, TEs are epigenetically 35

silenced through several pathways and this may spread to neighboring sequences. 36

JUMONJI (JMJ) proteins can function as anti-silencing factors and prevent silencing of genes 37

next to TEs. Whether TE silencing is counterbalanced by the activity of anti-silencing factors 38

is still unclear. Here, we characterize JMJ24 as a regulator of TE silencing. We show that 39

loss of JMJ24 results in increased silencing of the DNA transposon AtMu1c, while 40

overexpression of JMJ24 reduces silencing. JMJ24 has a JumonjiC (JmjC) domain and two 41

RING domains. JMJ24 auto-ubiquitinates in vitro, demonstrating E3 ligase activity of the 42

RING domain(s). JMJ24-JmjC binds the N-terminal tail of histone H3 and full-length JMJ24 43

binds histone H3 in vivo. JMJ24 activity is anti-correlated with histone H3 lysine 9 44

dimethylation (H3K9me2) levels at AtMu1c. Double mutant analyses with epigenetic 45

silencing mutants suggest that JMJ24 antagonizes histone H3K9me2, and requires H3K9 46

methyltransferases for its activity on AtMu1c. Genome-wide transcriptome analysis indicates 47

that JMJ24 affects silencing at additional TEs. Our results suggest that the JmjC domain of 48

JMJ24 has lost demethylase activity but has been retained as a binding domain for histone 49

H3. This is in line with phylogenetic analyses indicating that JMJ24 [with the mutated JmjC 50

domain] is widely conserved in angiosperms. Taken together, this study assigns a role in TE 51

silencing to a conserved JmjC-domain protein with E3 ligase activity, but no demethylase 52

activity. 53



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Introduction 54

Eukaryotic genomes contain a large proportion of transposable elements (TEs) and repetitive 55

sequences (Tenaillon et al., 2010; Fedoroff, 2012). Through their mobilization and 56

transposition, these sequences have a high mutagenic potential. This threatens genome 57

integrity but also provides an important source of genetic variation for selection to act upon 58

(Levin and Moran, 2011; Bennetzen and Wang, 2014). Thus, organisms have evolved 59

mechanisms to limit TE activity. These mechanisms mostly involve DNA methylation, small 60

RNAs and histone modifications (Law and Jacobsen, 2010; Castel and Martienssen, 2013; 61

Matzke and Mosher, 2014). TEs can be silenced to different degrees depending on which 62

pathways dominate at individual loci. Many TEs are silenced through CG methylation that 63

requires METHYLTRANSFERASE 1 (MET1) and DECREASED DNA METHYLATION 1 64

(DDM1) for maintenance in A. thaliana (Saze et al., 2003; Zemach et al., 2013). In RNA-65

dependent DNA methylation (RdDM), the generation of small-interfering RNA (siRNA) 66

triggers the deposition of chromatin-associated silencing marks such as DNA methylation in 67

CHG and CHH contexts (where H is A, C or T) and histone H3 lysine 9 dimethylation 68

(H3K9me2) at targeted loci (Castel and Martienssen, 2013; Matzke and Mosher, 2014). This 69

involves the DNA methyltransferase DOMAINS REARRANGED METHYLTRANSFERASE 70

(DRM1, DRM2) and CHROMOMETHYLASE (CMT2, CMT3) proteins (Cao and Jacobsen, 71

2002; Stroud et al., 2013; Stroud et al., 2014). H3K9me2 is a repressive chromatin mark 72

associated with the silencing of repeats and TEs (Jackson et al., 2002; Ebbs et al., 2005; 73

Ebbs and Bender, 2006). The H3K9 methyltransferases KRYPTONITE (KYP/ SUVH4), 74

SUVH5 and SUVH6 regulate CHH methylation in an siRNA-independent manner and have 75

been shown to be required for CMT3-dependent CHG methylation (Jackson et al., 2002; 76

Ebbs et al., 2005; Ebbs and Bender, 2006; Stroud et al., 2013). CHG methylation and 77

H3K9me2 reinforce each other through a positive feedback loop (Du et al., 2012). 78

The class II transposon Robertson’s Mutator element has originally been isolated from 79

maize, where it transposes frequently (Lisch, 2012). Mutator elements from Arabidopsis 80

thaliana have been characterized (Singer et al., 2001). For AtMu1 it was shown that it is 81

targeted by several epigenetic silencing pathways including RdDM (Lippman et al., 2003; 82

Bäurle et al., 2007) and AtMu1 transposition was found in DNA methylation-deficient 83

backgrounds and in the vegetative nucleus of pollen, where global reactivation of TEs occurs 84

(Singer et al., 2001; Slotkin et al., 2009). AtMu1c is the most active of the three AtMu1 copies 85

(Kabelitz et al., 2014). At the phylogenetic level AtMu1c transposition was found in the A. 86

thaliana lineage (Kabelitz et al., 2014). AtMu1c contains two highly homologous Terminal 87

Inverted Repeats (TIRs) and a conserved transposase gene. 88



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Chromatin structure is an important regulator of gene expression in all organisms. It is 89

regulated to a large extent by the composition, localization and posttranslational modification 90

of nucleosomes (Struhl and Segal, 2013; Zentner and Henikoff, 2013). Nucleosomes consist 91

of octamers of H2A, H2B, H3 and H4 proteins. All histones, but especially histone H3, can be 92

modified at several residues with various modifications including methylation, acetylation and 93

ubiquitination. Many of these modifications are reversible, thus contributing to the dynamic 94

regulation of gene expression. For example, in the case of histone lysine methylation histone 95

methyltransferases perform mono-, di- or tri-methylation of lysine (Black et al., 2012). 96

Conversely, the recently discovered histone demethylases reverse methylation. Two histone 97

lysine demethylase classes are present in animals, plants and yeast (Lu et al., 2008; Hong et 98

al., 2009; Liu et al., 2010; Mosammaparast and Shi, 2010; Chen et al., 2011). The JMJ gene 99

class is characterized by the catalytic JmjC domain and contains Fe2+- and α-ketoglutarate-100

dependent dioxygenases (Klose et al., 2006; Mosammaparast and Shi, 2010). Animal JMJ 101

proteins have been implicated in many processes regulating development and disease 102

(Klose et al., 2006; Landeira and Fisher, 2011). In A. thaliana, there are 21 JMJ genes, which 103

can be categorized into five groups, namely the KDM3/JHDM2, KDM4/JHDM3/JMJD2, 104

KDM5/JARID1, JMJD6 and JmjC domain-only groups, based on sequence analysis and 105

domain architecture (Lu et al., 2008; Hong et al., 2009). Members of the same clade tend to 106

have similar target specificities (Klose et al., 2006). About half of these genes have been 107

functionally characterized so far and they act in development and responses to endogenous 108

and exogeneous cues. For example, several characterized JMJ genes regulate flowering 109

time through repression or activation of different target genes and different modifications 110

(Noh et al., 2004; Yang et al., 2012; Crevillen et al., 2014; Gan et al., 2014). The histone H3 111

K4 demethylase JMJ14 is required for RNA-mediated DNA methylation (Deleris et al., 2010; 112

Searle et al., 2010; Le Masson et al., 2012; Greenberg et al., 2013). A H3K4 demethylase 113

from rice has been implicated in the repression of TE sequences (Cui et al., 2013). The H3 114

K9 me2/me1 demethylase IBM1 prevents genes from being silenced through invasion of 115

H3K9 methylation from neighboring TEs and repetitive elements (Saze et al., 2008; Inagaki 116

et al., 2010). IBM1/JMJ25 does not generally target TEs (Inagaki et al., 2010; Rigal et al., 117

2012) and indirectly represses TEs through the activation of DCL3 and RDR2 (Fan et al., 118

2012). Very recently, JMJ24 has been proposed to function in the base transcription of 119

silenced loci (Deng et al., 2015). However, its mode of action remains unclear. 120

Several members of the KDM3/JHDM2 clade from both kingdoms contain RING-finger 121

domains that may function in target protein ubiquitinylation (Lu et al., 2008; Zhou and Ma, 122

2008; Aiese Cigliano et al., 2013). However, in none of these proteins the RING domain has 123

been functionally characterized so far. Here, we functionally characterize the RING-finger- 124

and JmjC-domain containing protein JMJ24. Like IBM1, JMJ24 belongs to the KDM3 clade of 125



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putative histone H3 K9 demethylases. Interestingly, although the co-factor binding residues 126

of the JmjC domain indicate loss of catalytic activity, JMJ24 is conserved across the 127

angiosperm lineage and binds to histone H3 through this domain. JMJ24 also has 128

ubiquitination activity. JMJ24 has a role in transposon silencing by antagonizing H3K9me2 129

through locus-specific interactions. Taken together, JMJ24 likely functions in TE silencing 130

through ubiquitination of histones or associated target proteins. 131

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Results 134

JMJ24 counteracts transcriptional silencing of AtMu1c 135

In a reverse genetics screen for potential regulators of AtMu1c silencing, we found that a 136

mutant in the JMJ24 gene had a moderate but consistent decrease in AtMu1c transcript 137

levels (Fig. 1, Supplemental Fig. S1). At the morphological level the jmj24-2 mutant, which 138

carries a T-DNA insertion in the second exon (Supplemental Fig. S1), did not show any 139

apparent defects. To corroborate this observation, we generated lines expressing an artificial 140

miRNA against JMJ24 in the Col background. In these lines, JMJ24 transcript levels were 141

decreased to 76-20 % of the transcript levels in Col (Fig. 1). Correspondingly, AtMu1c 142

transcript levels were also decreased and the degree of reduction was correlated with the 143

strength of JMJ24 down-regulation. Thus, JMJ24 antagonizes AtMu1c silencing. We next 144

asked whether overexpression of JMJ24 was able to reduce AtMu1c silencing. To this end, 145

we generated transgenic plants overexpressing JMJ24 under the control of the 35S promoter 146

in the Col wild type background. We did not observe any obvious morphological alterations in 147

the 35S::JMJ24 plants. Indeed, we observed reduced silencing of AtMu1c as evidenced by 148

enhanced transcript levels (Fig. 1). The degree of reactivation correlated with the magnitude 149

of JMJ24 overexpression. The analysis of unspliced AtMu1c transcripts (Kabelitz et al., 2014) 150

in jmj24-2 and 35S::JMJ24 plants (Supplemental Fig. S2) suggests that the release of 151

silencing occurs at the level of transcription (i. e. before splicing). Together, our results 152

indicate that JMJ24 is both necessary and sufficient to antagonize AtMu1c silencing. 153

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JMJ24 is conserved across angiosperms but has lost Fe2+-binding activity 155

We next sought to determine the molecular function of JMJ24. JMJ24 contains a JmjC 156

domain and two RING finger domains as well as a nuclear localization signal (NLS, Fig. 2A). 157

JMJ24 is a single copy gene in A. thaliana and is most closely related to the KDM3/JHDM2 158

clade of JmjC proteins, which also contains IBM1/JMJ25 (Hong et al., 2009). JMJ24 and 159

three additional members of this clade (JMJ26, 27, 29) contain two RING domains of the 160

RING-C2 type, which are potential E3 ubiquitin ligase enzymes (Lorick et al., 1999; Stone et 161

al., 2005; Hong et al., 2009; Aiese Cigliano et al., 2013). Based on sequence similarity, the 162

KDM3/JHDM2 clade is predicted to have histone H3 K9 demethylase activity. In line with this 163

prediction, histone H3 K9 demethylase activity was demonstrated for IBM1 (Inagaki et al., 164

2010). To function as a demethylase, the JmjC domain requires Fe2+ and α-ketoglutarate as 165

cofactors (Klose et al., 2006). In JMJ24, the two residues that are required for α-166

ketoglutarate binding are present (Fig. 2A, Supplemental Fig. S3A). However, two of the 167

three highly conserved residues that bind Fe2+ are not present, suggesting that JMJ24-JmjC 168



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may not be able to bind Fe2+ and thus may not be an active demethylase. Given this potential 169

inactivity, it was interesting to study whether there are JMJ24-related proteins with a similarly 170

mutated binding site in other species. We found potential JMJ24 orthologues in all 171

angiosperm families investigated, including the basal angiosperm Amborella trichopoda and 172

a representative selection of monocot and dicot families, but not in the moss Physcomitrella 173

patens and not outside the plant kingdom (Fig. 2B). These results confirm and extend a 174

recent phylogenetic study, which identified a putative JMJ24 orthologue in Amborella 175

trichopoda (Qian et al., 2015). Comparing the conservation of the five amino acid residues 176

that are essential for co-factor binding (F/T/YHD/EKH), we found that all JMJ24-like proteins 177

had a degenerated motif (e. g. THNKF in JMJ24, Fig. 2A). Moreover, in the JMJ24-like 178

proteins the second histidine of the Fe2+ -binding motif was always converted into a 179

phenylalanine and the aspartate at position three almost always into an asparagine or lysine. 180

Thus, although JMJ24 has lost the THDKH motif of the canonical KDM3-JmjC domain, the 181

high degree of conservation of the modified JMJ24 motif suggests that this motif continues to 182

be under positive selection and that the JMJ24-JmjC domain is functionally active, albeit 183

probably not as a demethylase. Together, our phylogenetic analysis of protein sequences 184

revealed that JMJ24 has evolved before the separation of monocotyledonous and 185

dicotyledonous plants during basal angiosperm evolution and may have a functional activity 186

differing from that of the canonical JmjC domain. 187

Next, we tested the ability of the JMJ24-JmjC-domain to bind Fe directly. JMJ24-JmjC was 188

expressed in E. coli and purified (Supplemental Fig. S3B). As a control, we also expressed 189

and purified JMJ18-JmjC, in which all important residues are conserved. JMJ18-JmjC was 190

previously shown to be a functional histone H3K4me3/me2 demethylase (Yang et al., 2012). 191



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Using inductively-coupled plasma optical emission spectrometry (ICP-OES), we analyzed the 192

presence of Fe in GST, GST-JMJ24-JmjC and GST-JMJ18-JmjC (Fig. 2C, Supplemental 193

Table S1). GST-JMJ18-JmjC had a near equimolar Fe content (70%) consistent with the 194

binding of one Fe2+ per JmjC molecule. For GST-JMJ24-JmjC and GST alone, only 195



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background levels were observed (17-18%). This is consistent with the notion that JMJ24 is 196

unable to bind Fe2+ and is therefore not an active histone demethylase. It is also consistent 197

with a previous report that did not find demethylase activity for JMJ24 using an in vitro assay 198

(Deng et al., 2015). 199

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Nuclear JMJ24 shows E3 ubiquitin ligase activity 201

We next sought to identify alternative molecular functions of JMJ24 by investigating the 202

potential E3 ubiquitin ligase activitiy of the two RING finger domains. As E3 ubiquitin ligases 203

are known to bind to E2 enzymes promiscuously (Kraft et al., 2005), we first tested whether 204

JMJ24 was able to interact with the AtUBC10 E2 enzyme in the Yeast-Two-Hybrid system. 205

Using ß-galactosidase activity as a read-out, we observed interaction of AtUBC10 with the 206

full-length JMJ24 protein (aa 6-945), or with truncated versions of JMJ24 containing an N-207

terminal fragment (aa 6-432), both RING domains (aa 205-432), or only RING1 (aa 205-281; 208

Supplemental Fig. S4). No interaction was found when JMJ24-RING2 (aa 337-441) was 209

used as bait. Thus, JMJ24 interacts with AtUBC10 through the N-terminal RING1 domain. To 210

test whether JMJ24 functions as an E3 ubiquitin ligase we next performed an in vitro 211

ubiquitination assay (Stone et al., 2005). The BB protein (Disch et al., 2006), which was used 212

as a positive control, underwent poly-ubiquitination under our assay conditions (Fig. 3A). For 213

GST-JMJ24-RING1 we observed a size shift of about 10 kDa, consistent with mono-214

ubiquitination of the protein (Fig. 3A, lane 4, bottom panel). A band of the same size 215

appeared in the corresponding lane in an immunoblot against the FLAG-tagged ubiquitin 216

(Fig. 3A, top panel). A similar but weaker band shift was found for GST-JMJ24-RING2 (lane 217

8). Thus, JMJ24 is a functional E3 ubiquitin ligase with RING1 being the primarily active 218

RING domain. 219

To test whether the predicted NLS in form of a Trp-Arg-Cys-motif (WRC-motif) near the N-220

terminus is functional, we determined the subcellular localization of JMJ24-YFP. In A. 221

thaliana plants stably transformed with JMJ24::JMJ24-YFP, we observed nuclear 222

fluorescence (Fig. 3B) as indicated by the overlap of YFP and DAPI signals. This transgenic 223

line complemented the jmj24-2 mutant phenotype as evidenced by restoration of AtMu1c 224

transcript levels (Supplemental Fig. S5). Taken together, our results indicate that JMJ24 is 225

an E3 ubiquitin ligase localized to the nucleus. 226

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JMJ24-JmjC binds histone H3 228

Even if JMJ24-JmjC is not an active demethylase, the domain may still function as a histone 229

binding module. We therefore tested whether differently modified histone H3 peptides were 230



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able to interact with GST-JMJ24-JmjC purified from E. coli (Shi et al., 2006). As controls, we 231

used GST-PHD-AtING1, for which a very high affinity for histone H3K4me3 was reported 232

(Lee et al., 2009), and GST. GST-JMJ24-JmjC was precipitated by unmodified H3 aa 1-20 or 233

H3 aa 1-20 that was mono-, di- or tri-methylated at either K4 or K9 (Fig. 4A). In contrast, 234

GST-JMJ24-JmjC was not precipitated by unmodified H3 aa 21-44. GST alone was not 235

precipitated by the tested H3 peptides (aa 21-44 or aa 1-20 K4me3). Thus, JMJ24-JmjC 236



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binds to the very N-terminus of histone H3 irrespective of the methylation states of K4 and 237

K9 in vitro. It can, however, not be excluded that in vivo the substrate specificity is further 238

determined by other parts of JMJ24, by modifications of the protein that are missing in 239

recombinant JMJ24-JmjC or by interacting molecules, as was reported for other JMJ proteins 240

(Hou and Yu, 2010). 241



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To identify JMJ24-interacting proteins in vivo, we performed purification of native protein 242

complexes followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) using 243

7 d old seedlings of a complementing 35S::JMJ24-vYFP transgenic A. thaliana line in the 244

jmj24-2 background (Supplemental Fig. S5). In two separate experiments with two technical 245

replicates each, we identified JMJ24 peptides with a very high score. We also identified 246

histone peptides of H2A, H2B, H3.1/H3.3, H3.3 and H4 with high scores (Fig. 4B). Neither of 247

these peptides was found in a control experiment using Col-0. Among the H3 peptides, we 248

found one peptide specific for H3.3 and several others that were redundant between H3.1 249

and H3.3 isoforms (Stroud et al., 2012; Shu et al., 2014). 250

We next investigated whether the binding of JMJ24 to histone H2B was likely direct or via 251

H3. To this end, we repeated the co-immunoprecipitation of JMJ24-YFP with crosslinking 252

under mild conditions to preserve protein-protein interactions. The co-precipitated proteins 253

were analyzed by immunoblotting for the presence of H3 and H2B. We were able to 254

precipitate H3 but not H2B with JMJ24-YFP, indicating that JMJ24 binds H3, but not H2B 255

(Fig. 4C). In summary, these results suggest that full-length JMJ24 interacts with 256

nucleosomes in vivo via binding to H3. 257

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Genetic interaction of JMJ24 with histone methyltransferases at AtMu1c 259

TEs are silenced through a number of silencing pathways involving RdDM and histone H3 K9 260

methylation. In order to begin to place JMJ24 within the existing silencing pathways, we 261

analyzed the interaction of JMJ24 with the histone H3K9 methyltransferases KYP, SUVH5 262

and SUVH6 (Jackson et al., 2002; Ebbs et al., 2005; Ebbs and Bender, 2006). To this end, 263

we crossed T-DNA insertion mutants of these genes with jmj24-2 and with 35S::JMJ24, 264

respectively. In kyp single mutants, we observed a loss of AtMu1c silencing using the kyp-7 265

and kyp-4/suvh4 alleles (Fig. 5). In kyp-7 jmj24-2 and kyp-4 jmj24-2, the silencing of AtMu1c 266

was partially restored. Conversely, in kyp-7 35S::JMJ24 and kyp-4 35S::JMJ24, AtMu1c 267

reactivation was stronger than in kyp single mutants or JMJ24 overexpressor lines. Thus, 268

JMJ24 still functions in a kyp mutant background. This is consistent with JMJ24 acting at 269

least in part independently of KYP. It was reported previously that SUVH5 and SUVH6 act 270

partially redundantly with KYP (Ebbs and Bender, 2006). In suvh5 suvh6 double mutants, 271

AtMu1c silencing was not affected (Fig. 5B), however, in the kyp-4 suvh5 suvh6 triple 272

mutant, AtMu1c transcript levels were massively induced, indicating that H3K9me2 is an 273

important component of AtMu1c silencing. Interestingly, modulation of JMJ24 activity by 274

mutation or overexpression in the kyp-4 suvh5 suvh6 background did not have an effect. 275

Surprisingly, the same was true for the suvh5 suvh6 double mutant background, although 276

AtMu1c levels in this background were overall low. These findings suggest that JMJ24 277



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requires SUVH5 and SUVH6 for its action. Together, these results are consistent with the 278

idea that JMJ24 opposes H3K9me2 by antagonizing the H3K9 histone methyltransferases 279

SUVH5 and SUVH6 (and possibly KYP). 280

281

JMJ24 represses H3K9me2 and CHG methylation at AtMu1c 282

To further test this idea, we analyzed H3K9me2 levels at the AtMu1c locus by chromatin 283

immunoprecipitation. In jmj24-2, there was a slight increase in H3K9me2 that tested not 284

significant (Fig. 6A). Conversely, in the JMJ24 overexpressor, we observed a significant 285



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reduction in H3K9me2 levels. In kyp-7, the overall levels were much reduced, but a similar 286

effect of JMJ24 activity was observed, with increased levels in jmj24-2 kyp-7 and reduced 287

levels in 35S::JMJ24 kyp-7 compared to kyp-7 that tested significant for the comparison 288

between jmj24-2 kyp-7 and 35S::JMJ24 kyp-7 (Fig. 6A). Thus, JMJ24 antagonizes H3K9me2 289

levels at AtMu1c. 290

As H3K9me2 acts in a positive feedback loop with CHG methylation, we next analyzed DNA 291

methylation levels at the TIR of AtMu1c in different mutant backgrounds by bisulfite 292

sequencing. We observed reduced overall methylation in kyp-7 (Fig. 6B, Total). In kyp-7 293

35S::JMJ24 CHG methylation was reduced compared to kyp-7 (Fig. 6B), consistent with the 294

observed reduction in H3K9me2 (Fig. 6A). Total methylation levels in jmj24-2 were slightly 295

increased (Fig. 6B). Thus, modulation of JMJ24 activity affected the level of DNA methylation 296

at AtMu1c, possibly through its role in antagonizing H3K9me2. 297

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Genetic interaction with DNA methyltransferases 299

We next investigated the genetic interaction between jmj24-2 and genes that affect CHH and 300

CHG DNA methylation. To this end, we crossed jmj24-2 into the cmt3-11 and drm1-2 drm2-2 301

cmt3-11 backgrounds (Cao et al., 2003; Zhang et al., 2006), which both caused a strong loss 302

of AtMu1c silencing, suggesting that AtMu1c silencing is mainly controlled by CMT3 (Fig. 7A 303

and B). Loss of jmj24-2 suppressed this release in silencing markedly, consistent with what 304

we observed in the wild-type background and suggesting that JMJ24 and CMT3 largely act in 305

parallel (Fig. 7A). However, jmj24-2 suppressed the effect of the drm1-2 drm2-2 cmt3-11 306

mutant much more strongly than it did with any other mutant tested (10-fold repression, Fig. 307

7B), indicating that upon loss of asymmetric DNA methylation JMJ24 activity becomes 308

critical. This may reflect an increased sensitivity to changes in H3K9me2 in this background. 309

Taken together, our results are consistent with a model where JMJ24 suppresses epigenetic 310

silencing at AtMu1c by antagonizing histone H3K9me2, possibly by binding to histones and 311

mono-ubiquitinating an as yet unknown target protein. 312

313

JMJ24 widely affects silencing of transposons and repetitive elements 314

We next asked whether JMJ24 affected the expression/silencing of other TEs apart from 315

AtMu1c. To this end, we performed transcriptome analysis using ATH1 microarrays 316

comparing seedlings of three genotypes with increasing doses of JMJ24 (jmj24-2, Col, 317

35S::JMJ24). To efficiently analyze the TEs contained on the microarray we used a refined 318

probeset annotation (Slotkin et al., 2009). To maximize the effects of modulated JMJ24 319

activity and minimize potential background effects, we compared transcript levels in the 320

jmj24-2 mutant with those in an overexpressor line that was created in the jmj24-2 mutant 321

background. Several categories of DNA transposons and one class of LTR retrotransposons 322

(Gypsy AtGP1) were significantly affected (Fig. 8A and Table 1). Among the affected DNA 323

transposons, there were both MuDR (ARNOLD, VANDAL) and non-MuDR elements 324

(CACTA). Interestingly, at the global scale most TEs showed a release of silencing in the 325

jmj24-2 mutant compared to the overexpressor line 35S::JMJ24. Thus, JMJ24 can have 326

opposite effects on different TEs. This may depend on the chromosomal environment of the 327

element, and on the type and level of silencing present at the locus. 328



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To further characterize the effect of JMJ24 at the level of individual TEs, we selected six TEs 329

from the microarray analysis (VANDAL2, IS112A (Eisen et al., 1994; Slotkin et al., 2009)) 330

and from previous studies (Bäurle et al., 2007; Zheng et al., 2009; Deleris et al., 2010) for 331

expression analysis by qRT-PCR. The selected TEs fell into two classes (Fig. 8B and C). 332

The first class, containing IG/LINE, COPIA2 and MEA/ISR, displayed reduced transcript 333

levels in jmj24-2 and increased transcript levels in 35S::JMJ24, reminiscent of what we 334

observed for AtMu1c (Fig. 8B). Conversely, the second class, containing IS112A, a CACTA 335

TE and VANDAL2, displayed increased transcript levels in jmj24-2 and reduced transcript 336

levels in 35S::JMJ24 (Fig. 8C). These findings corroborate our observation that JMJ24 can 337

have apparently opposing outcomes both at the level of TE classes and at the single element 338

level. The transcriptome analysis suggests that globally the negative function of JMJ24 may 339

prevail as the affected TE categories indicate an increased expression in jmj24-2. The 340

different outcome may be caused by the context of the elements and the contribution of 341

individual silencing pathways to each locus. Notably, transcript levels of members of various 342

silencing pathways were not affected in jmj24-2 mutants. In summary, JMJ24 acts as an anti-343

silencing factor at some loci including AtMu1c, but as a silencing enhancer at others. 344



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Discussion 347

Here, we reported the characterization of the JmjC- and RING-domain containing protein 348

JMJ24 from A. thaliana. We have investigated the activity of the functional domains and the 349

global role of JMJ24 in TE silencing during seedling development. The JmjC domain is 350

conserved from yeast to humans and belongs to the superfamiliy of Fe2+-dependent 351

dioxygenases (Hou and Yu, 2010). Using Fe2+ and α-ketoglutarate as cofactors and in the 352

presence of oxygen, the methyl group of a methyl lysine is converted to hydroxymethyl, 353

which is then released as formaldehyde. Both co-factors are absolutely essential for 354

demethylase activity (Klose et al., 2006). JMJ24 belongs to the KDM3/JHDM2 group, as 355

does the closely related H3K9me2/me1 demethylase IBM1, indicating a specificity for 356

H3K9me2/me1 (Inagaki et al., 2010). Five well characterized residues are required to bind 357

the two cofactors. In JMJ24, the two amino acid residues required for α-ketoglutarate binding 358

are conserved, but only one of three residues required for Fe2+-binding is present. 359

Accordingly, no Fe-binding was detected experimentally for JMJ24-JmjC. Thus, it is highly 360

unlikely that JMJ24 is an active demethylase. Despite this apparent loss of functionality, 361

JMJ24 is conserved during angiosperm evolution with clear orthologues in all dicotyledonous 362

and monocotyledonous species examined. Interestingly, the two essential amino acids, 363

which are required for Fe2+-binding and are substituted in JMJ24, are highly conserved 364

among JMJ24 orthologues across monocotyledonous and dicotyledonous plants, suggesting 365

that they are functionally important and under positive selection. This function may be to bind 366

histones; its exact nature remains to be investigated. To our knowledge, JMJ24 is the first 367

JmjC-domain protein from plants with an inactive JmjC domain that has been functionally 368

characterized. 369

Interestingly, the founding member of the JMJ family, Jarid2 also lacks histone demethylase 370

activity (Klose et al., 2006; Landeira and Fisher, 2011). Jarid2 plays important roles in 371

development and disease as a component of the PRC2 silencing complex. Jarid2 is required 372

to target and assemble PRC2 onto target genes and may do so through association with 373

non-coding RNA and methylation by PRC2 (Kaneko et al., 2014; Sanulli et al., 2015). Thus, 374

there is precedent for the notion that the JmjC domain can degenerate, yet be maintained in 375

functionally active proteins. An attractive hypothesis is that the JMJ24 JmjC domain has 376

been retained as a histone H3 reader domain that binds modified or unmodified H3 in order 377

to target H3 or associated proteins for ubiquitination. Our in vivo immunoprecipitation 378

experiments confirmed that histone H3 is associated with JMJ24. It is a likely explanation 379

that we recovered all four nucleosome-constituting histones in the more sensitive LC-MS/MS 380

analysis because the conditions of purification were mild enough to leave nucleosomes 381

intact. Our analyses do not support the notion that JMJ24 binds a particular H3 modification 382



19

with high specificity. The in vitro binding studies indicated a broad binding of modified N-383

terminal H3 peptides. However, it is probable that other parts of the protein, unknown binding 384

partners, combinatorial histone modifications or modifications of JMJ24 itself affect the 385

binding specificity in vivo. It is well established for other histone lysine demethylases such as 386

PHF8, KDM7A and KDM4 that they have dual specificity depending on the chromatin context 387

and the presence of other binding factors (Klose et al., 2006; Horton et al., 2010; Lin et al., 388

2010; Liu et al., 2010; Yang et al., 2010). 389

In contrast to the JmjC domain, the RING-domains of JMJ24 have E3 ubiquitin ligase activity, 390

as demonstrated in vitro using AtUBC10 as E2 enzyme. Interestingly, RING1 was much 391

more active than RING2. Moreover, we only detected mono-ubiquitination in our 392

experiments. So far, the target of JMJ24 E3 ligase activity remains elusive. One interesting 393

possibility is that histone H3 or another histone protein is the target of this activity. Poly-394

ubiquitination is generally regarded as a signal for proteasomal degradation. In contrast, 395

mono-ubiquitination is a stable protein modification. So far, H3 ubiquitination has only been 396

reported for centromeric H3 variants in yeast and mammals (Hewawasam et al., 2010; 397

Niikura et al., 2015). Mono-ubiquitination of H2A and H2B and their role in activating gene 398

expression and PRC2 silencing, respectively, are well established (Weake and Workman, 399

2008). However, as we did not observe association with H2B (and H2A) and neither 400

modification was associated with the regulation of TEs, they are unlikely target proteins. 401

Alternatively, the target of ubiquitination may be a protein that is associated with histone H3 402

and histone H3 may serve to (negatively) regulate E3 ligase activity. RNA-DEPENDENT 403

RNA POLYMERASE 2 (RDR2) was very recently reported to interact with JMJ24 (Deng et 404

al., 2015). RDR2 was not found in our immunoprecipitation experiments; however, one 405

possible scenario is that JMJ24 binds RDR2 transiently in order to ubiquitinate it. Future 406

studies are required to test these possibilities. There is precedent for the combination of 407

histone demethylation and E3 ligase activity. Very recently, the animal histone demethylase 408

LSD2 implicated in cancer cell growth has been found to have E3 ubiquitin ligase activity 409

towards the O-GlcNAc transferase (Yang et al., 2015). JMJ24 shares the RING domains with 410

numerous KDM3 clade members (Zhou and Ma, 2008; Aiese Cigliano et al., 2013). Here, we 411

demonstrated for the first time E3 ubiquitin ligase activity for the RING domain of a JMJ 412

protein. 413

As described above JMJ24 falls into the KDM3/JHDM2 clade of JmjC proteins, indicating 414

specificity for H3K9me2/me1. In plants, H3K9me2 is associated with heterochromatin and 415

silenced TEs. Although JMJ24 has lost demethylase activity, it may still recognize and 416

antagonize H3K9me2. This hypothesis is confirmed by the H3K9me2 ChIP and the double 417

mutant analyses with the H3K9 methyltransferases KYP, SUVH5, SUVH6. Loss of JMJ24 418

activity correlated with enhanced H3K9me2 at AtMu1c and overexpression of JMJ24 419



20

correlated with reduced H3K9me2. This was especially true in the kyp-7 background, where 420

H3K9me2 levels were reduced but not abolished (because of redundancy with SUVH5 and 421

SUVH6). When SUVH5 and SUVH6 were simultaneously deleted, JMJ24 overexpression did 422

not have an effect. We found during this study that H3K9me2 strongly silences AtMu1c in the 423

Col accession. The sensitivity of transcript analysis by qRT-PCR and accession-specific 424

differences provide a plausible explanation for why previous studies did not observe such a 425

strong reactivation in suvh mutants (Lippman et al., 2003; Ebbs et al., 2005). Our findings 426

together with the phylogenetic grouping of JMJ24 suggest that H3K9me2 may be the 427

epigenetic mark that is targeted by JMJ24. 428

In summary, we propose a model where JMJ24 recognizes histone H3 through the 429

inactivated JmjC domain and subsequently mono- or poly-ubiquitinates H3 or an associated 430

protein (e. g. a histone H3 methyltransferase or reader protein), thereby marking it for 431

degradation or inactivation (Fig. 9). Thus, JMJ24 antagonizes the silencing mark H3K9me2 432

independently of demethylation and promotes basal level transcription. JMJ24 represents an 433

interesting new actor of the RdDM pathway. JMJ24 may play a role in TE reactivation during 434

development or during the establishment of silencing of new TE insertions. 435

JMJ24 antagonizes RdDM-mediated epigenetic silencing of the DNA transposon AtMu1c and 436

other TEs, and thus formally acts as an anti-silencing factor at these loci. IBM1/JMJ25 also 437

acts as an anti-silencing and boundary factor in A. thaliana, acting to protect genic regions 438

from the invasion of nearby heterochromatic marks and silencing (Saze et al., 2008; Inagaki 439

et al., 2010; Rigal et al., 2012). Another anti-silencing factor is the JMJ-domain protein Epe1 440

from Schizosaccharomyces pombe, which is required for heterochromatin boundary 441

formation (Trewick et al., 2007; Tamaru, 2010). Neither of them targets TEs. So far, we can 442

only speculate why plants may require an anti-silencing factor directed towards TEs. One 443

possibility is that this ensures low levels of transcription of a TE, which may be required to 444

sustain silencing by RNA-mediated recruitment of the silencing machinery (Fultz et al., 445

2015). Alternatively, it may act as a pre-adaptation to extreme environmental conditions and 446

allow rapid adaptation to changing environmental conditions (McClintock, 1984; Biemont and 447

Vieira, 2006; Lisch, 2013). It is thought that extreme environmental conditions cause 448

reactivation and transposition of TE, which increases genetic variability in the population and 449

may yield individuals with increased stress tolerance. Low level transcription may facilitate 450

reactivation during such extreme conditions. 451



21

Notably, some TE loci found to be regulated by JMJ24 in our microarray analysis were 452

affected in the opposite direction as AtMu1c. A recent study investigating the transcriptome 453

of jmj24-1 pollen by tiling arrays found that among 200 misregulated TEs, 80 % were 454

downregulated and 20 % upregulated (Deng et al., 2015), thus confirming our observations 455

in seedlings. Notably, in pollen TEs are globally hyperactivated compared to seedlings 456

(Slotkin et al., 2009), facilitating their experimental detection. This global reactivation together 457

with the different mode of transcript detection (tiling array vs. microarray) may explain why 458

slightly differing observations were made in the two studies. It is possible that the apparent 459

outcome of JMJ24 activity at individual loci depends on the locus-specific interplay of various 460

silencing pathways, as well as the developmental stage. For example, it is conceivable that 461

at loci (formally) repressed by JMJ24, the reduced transcription upon loss of JMJ24 causes 462

the overall activity of the locus to fall below a certain threshold so that the locus is no longer 463

targeted by another silencing pathway, thereby causing a net increase of transcript levels in 464

jmj24-2. Consequently, increased activity of the TE locus upon JMJ24 overexpression may 465

reinforce the acticity of the other silencing pathway, resulting in a net decrease of expression. 466

JMJ24 was found to be associated with the AtSN1, IG/LINE and SDC loci (Deng et al., 2015) 467

and may be associated with additional TEs investigated in this study. Identifying the target(s) 468



22

of ubiquitination remains an important question for future studies investigating the function of 469

JMJ24 in the RdDM pathway. 470

471

Materials and Methods 472

Plant material and growth conditions 473

Plants were grown in long day conditions on soil in a greenhouse or on GM plates (1 % (w/v) 474

glucose) at 23 °C day/ 21 °C night cycles for 10-14 d before analysis. All analyses were 475

performed in the Col-0 background. The jmj24-2 (SALK_021260), kyp-7 (SALK_069326 476

(Mathieu et al., 2007)), cmt3-11 (N16392) and drm1-2 drm2-2 cmt3-11 (N16384 (Henderson 477

and Jacobsen, 2008)) mutants were obtained from the European Arabidopsis Stock Centre. 478

suvh4/ kyp-4 (SALK_044606), suvh5 suvh6 (SALK_074957, SAIL_864_E08) and kyp-4 479

suvh5 suvh6 were obtained from J. Bender, Brown University (Ebbs and Bender, 2006). 480

481

Construction of transgenic lines 482

JMJ24 amiRNA, 35S::JMJ24 and JMJ24::JMJ24-vYFP lines were generated by 483

Agrobacterium-mediated transformation. The JMJ24 amiRNA construct was designed 484

according to (Ossowski et al., 2008). A PCR product containing the artificial JMJ24 miRNA 485

(oligonucleotides 297 – 300) (Supplemental Table S3) was subcloned into pGEM-T Easy 486

(Promega), sequenced and transferred to 35S::pBarM (ML595) using BamHI and XhoI. For 487

35S::JMJ24 and 35S::JMJ24-vYFP, the genomic sequence of JMJ24 encoding the full-length 488

protein was amplified with oligonucleotides 482 – 484, introducing BclI restriction sites. After 489

sequencing, the JMJ24 fragment was transferred via BclI into 35S::pBarM (ML595) and 490

35S::pBarM-vYFP (IB30), respectively. For JMJ24::JMJ24-vYFP, the genomic JMJ24 491

sequence was amplified in two fragments. The JMJ24 5’ region (containing promotor, 5’UTR 492

and the first half of the coding region) was amplified with oligonucleotides 417/418, 493

introducing SphI and PstI restriction sites. The JMJ24 3’ region (containing the second half of 494

the coding region and 3’UTR) was amplified with oligonucleotides 419/420, introducing KpnI 495

and PstI restriction sites. After sequencing, both fragments were assembled in pUC-ML939. 496

Venus YFP was amplified with oligonucleotides 477/ 478, introducing SalI restriction sites 497

and assembled with JMJ24::JMJ24 in pUC-ML939. The whole cassette was then transferred 498

via AscI into pBarMAP (ML516) (Adamski et al., 2009). 499

500

Gene expression analysis 501

RNA was extracted from 7-14 d old seedlings using a hot-phenol RNA extraction protocol 502

(Kabelitz et al., 2014). Total RNA was treated with TURBO DNAfree (Ambion), and 10 µg 503

were reverse transcribed with SuperScript III (Invitrogen) according to the manufacturers’ 504



23

instructions. cDNA was diluted 1:100 into qPCR reactions with GoTaq qPCR Master Mix 505

(Promega) and an Roche LightCycler 480 instrument was used for measurements. 506

Expression was normalized to TUBULIN6 using the comparative CT method. Primer 507

sequences are listed in Supplemental Table S3. For microarray analysis, RNA from 9 d-old 508

seedlings of three biological replicates per genotype was purified over an RNeasy Plant RNA 509

extraction column (Qiagen) and processed for hybridization of Affymetrix ATH1 GeneChips 510

(Atlas Biolabs, Berlin, Germany). Arrays were further processed using the R/Bioconductor 511

packages affy (Gautier et al., 2004) and limma (Ritchie et al., 2015) for rma normalization 512

and differential expression analysis. Significantly affected transposon categories based on 513

ATH1 probeset annotations by Slotkin et al. (Slotkin et al., 2009) were identified using a 514

Wilcoxon Rank Sum test. P-values were Benjamini-Hochberg (BH) corrected. Empirical 515

cumulative distribution function (ECDF) plots were done using the R package Lattice. 516

517

Recombinant protein expression, Ubiquitin ligase assay and Fe binding 518

analysis 519

The JMJ24 RING domains were amplified from cDNA with oligonucleotides 552/667 (RING1) 520

and 668/669 (RING2), respectively, subcloned into pGEM-T Easy, sequenced and 521

transferred to pGEX-4T-1 (Amersham Biosciences). The JMJ24-JmjC domain was amplified 522

from cDNA with oligonucleotides 1000/1001, subcloned into pGEM-T Easy, sequenced and 523

transferred to pGEX-4T-1. The JMJ18-JmjC domain was amplified from cDNA with 524

oligonucleotides 1185/1186, subcloned into pGEM-T Easy, sequenced and transferred into 525

pGEX-5X-3. All recombinant proteins were expressed in E. coli strain BL21 (DE3). BB and 526

the AtUBC10 E2 were previously described and were expressed as His6-fusion proteins via 527

the pQE system and purified with Ni-NTA affinity resins (Qiagen) (Disch et al., 2006). The 528

JMJ24 RING domains, JMJ24- and JMJ18-JmjC-domains were expressed as GST fusions 529

via pGEX-4T-1 (Amersham Biosciences) and purified with a Glutathione affinity resin 530

(Pierce). The in vitro ubiquitin ligase assay was performed as previously described (Stone et 531

al., 2005). Twenty µl reactions containing 50 mM Tris-HCl, pH 7.5; 10 mM MgCl2; 0.05 mM 532

ZnCl2; 1 mM ATP; 0.2 mM dithiothreitol; 10 mM phosphocreatine; 2 units of creatine kinase 533

(Sigma); 200 ng of yeast E1 (Sigma); 500 ng of purified E2 HIS6-AtUBC10; 500 ng of purified 534

GST-JMJ24-RING or GST or HIS6-BB, and 10 µg FLAG-ubiquitin (Sigma) were incubated at 535

30° C for 2 h. Reactions were stopped by adding 6 µl of SDS-PAGE sample buffer (125mM 536

Tris-HCl, pH 6.8, 20% [v/v] glycerin, 4% [w/v] SDS, and 10% [v/v] β-mercaptoethanol) and 537

boiled for 5 min at 95°C. Reactions were analyzed by SDS-PAGE followed by 538

immunoblotting using anti-FLAG (Sigma), anti-GST or anti-His6 (both Novagen) and 539

secondary IR800 (Novagen) antibodies, followed by detection with the LI-COR ODYSSEY 540

system. For Fe binding analysis, 10 µmol protein was wet-ashed with nitric acid at 100°C 541



24

overnight and measured by inductively-coupled plasma optical emission spectrometry (ICP-542

OES) at 239.562 nm. The Fe concentration was normalized to the input protein concentration 543

to obtain the relative number of Fe molecules per protein molecule. 544

545

DNA methylation and ChIP analysis 546

Bisulfite sequencing and ChIP analysis were performed as described (Kabelitz et al., 2014). 547

For ChIP, chromatin was extracted from 7 d old seedlings, and sheared with a Bioruptor 548

(Diagenode). Chromatin immunoprecipitation was performed using anti-H3 (Abcam, ab1791) 549

or anti-H3K9me2 (Wako, 302-32369) antibodies. Precipitated DNA was quantified by qPCR 550

and normalized to Input and H3. 551

552

Histone peptide binding assay 553

The histone peptide binding assay was performed as described (Shi et al., 2006). In brief, 1 554

µg of biotinylated histone peptides (Millipore) were incubated with 10 µg of GST-fused 555

protein in binding buffer (50 mM Tris-HCl pH 7.5, 300 mM NaCl, 0.1 % NP-40, 1 mM PMSF 556

plus protease inhibitors) overnight at 4°C with rotation. After 1 h incubation with Streptavidin 557

Dynabeads (Invitrogen) and extensive washing with TBST, bound proteins were analyzed by 558

SDS-PAGE and immunoblotting with anti-GST antibodies (Novagen). 559

560

Pulldown and MS analysis 561

2 g of 7 d-old seedlings were collected and flash-frozen in liquid nitrogen. Protein 562

immunoprecipitation was performed using the μMACS GFP Isolation Kit (Miltenyi Biotec) and 563

a published protocol (Smaczniak et al., 2012). Immunoprecipitated proteins were digested 564

with trypsin (Trypsin Gold, Mass Spectrometry Grade; Promega), purified and desalted using 565

C18 columns (Teknokroma). The spectra acquired from the Easy-nLC coupled to a Q 566

Exactive Plus (Thermo Fisher Scientific) were analyzed using MaxQuant protein 567

quantification software (Cox and Mann, 2008). Immunoprecipitations from Col and 35S::YFP 568

were used as controls for unspecifically bound proteins. 569

For immunoblotting of JMJ24 pulldowns, 2 g of 7 d-old seedlings were crosslinked with 0.5 % 570

formaldehyde solution for 10 min, blocked with glycine and flash-frozen in liquid nitrogen. 571

Protein immunoprecipitation was performed as described above. Precipitated proteins were 572

analyzed by immunoblotting as described above and detected with antibodies against GFP 573

(Abcam, ab290), H3 (ab1791) and H2B (ab1790). Col-0 was used as a control to identify 574

non-specific binding. 575

576

Yeast-Two-Hybrid Analysis 577



25

Yeast-Two-Hybrid assays were performed with the DupLEX-A System (Origene) (Golemis et 578

al., 2008). Bait genes were cloned into pEG202 (lexA-DBD) and prey genes into pJG4-5 579

(B42-AD) vector. Yeast strain EGY48 (pSH18-34) was co-transformed by using the Frozen-580

EZ Yeast Transformation II Kit (Zymo Research). Three independent transformants per 581

combination were tested on appropriate dropout medium with Galactose, Raffinose, and X-582

Gal. 583

584

DAPI staining and confocal images 585

3 d old seedlings were fixed in PBST with 3 % glutaraldehyde for 6 h. DAPI staining was 586

done overnight in PBST with 5 % DMSO. After washing three times, pictures were taken 587

using a Zeiss LSM 710 confocal microscope. 588

589

Accession numbers 590

JMJ24 (At1g09060), AtMu1c (At5g27345), JMJ18 (At1g30810), KYP/SUVH4 (At5g13960), 591

SUVH5 (At2g35160), SUVH6 (At2g22740), DRM1 (At5g15380), DRM2 (At5g14620), CMT3 592

(At1g69770), IG/LINE (At5g27845), COPIA2 (At1g18930), MEA/ISR (At1g02580), IS112A 593

(At1g43590), CACTA TE (At4g03745), VANDAL2 (At2g12170). Microarray data files are 594

available from the GEO database (accession number GSEXXX). 595

596

597

Tables 598

Table 1: JMJ24 widely affects TE silencing. 599

TE categories with changed transcript level in 35S::JMJ24 compared to jmj24-2. Transcript 600

levels of jmj24-2 and 35S:JMJ24 were determined by ATH1 microarrays. TE annotation and 601

categorization were adopted from (Slotkin et al., 2009). p-values are Benjamini-Hochberg 602

(BH) corrected. n, number of probes in this category. Arrows indicate the direction of 603

transcript level difference in 35S::JMJ24 compared to jmj24-2. 604

TE Category n p (BH corrected) Retrotransposon.LTR.Gypsy.ATGP1I 10 0.0319 ↓ DNA-Transposon 575 0.0000 ↓ DNA-Transposon.MuDR 306 0.0052 ↓ DNA-Transposon.MuDR.nonTIR 44 0.0001 ↓ DNA-Transposon.MuDR.nonTIR. ARNOLD1 11 0.0271 ↓ DNA-Transposon.nonMuDR 269 0.0000 ↓ DNA-Transposon.nonMuDR.CACTA 85 0.0001 ↓ DNA-Transposon.nonMuDR.CACTA. ATENSPM1 29 0.0041 ↓ DNA-Transposon.nonMuDR.CACTA. ATENSPM1A 6 0.0361 ↓ 605

606



26

Supplemental Data 607

Supplemental Figure S1. JMJ24 gene structure and expression level in jmj24-2. 608

609

Supplemental Figure S2. JMJ24 affects AtMu1 silencing at the level of transcription. 610

611

Supplemental Figure S3. JMJ24 JmjC-domain alignment and recombinant protein 612

expression. 613

614

Supplemental Figure S4. The JMJ24–RING1 domain interacts with AtUBC10. 615

616

Supplemental Figure S5. Complementation of transgenic lines used in this study. 617

618 Supplemental Figure S6. Biological replicate for jmj24-2 kyp-7 double mutant 619 analysis. 620 621

Supplemental Figure S7. Control amplicons for the anti-H3K9me2 chromatin 622

immuno-precipitation experiment shown in Fig. 6A. 623

624

Supplemental Table S1. Quantification of Fe analysis by ICP-OES. 625

626

Supplemental Table S2. Details of AtMu1c TIR bisulfite sequencing (cf. Fig. 6B). 627

628

Supplemental Table S3. List of primers used in this study. 629

630

Supplemental Table S4. List of peptides identified in JMJ24 immunoprecipitation. 631

632

633

Acknowledgements 634

We thank J. Bender, Brown University, and the European Arabidopsis Stock Centre for 635

seeds. We are grateful to E. Benke, K. Henneberger, J. Kurtzke and J. Markowski for 636

technical assistance. We thank M. Lenhard, University of Potsdam, for materials and helpful 637

suggestions, and S. Leimkühler, University of Potsdam, for help with the ICP-OES analysis. 638

639

640

Figure legends 641



27

Fig. 1 JMJ24 negatively regulates AtMu1 silencing. 642

Relative JMJ24 (grey) and AtMu1c (black) transcript levels were determined by qRT-PCR. 643

Expression values were normalized to TUB6 and Col. jmj24, jmj24-2 mutant; JMJ24 amiR, 644

lines carrying an artificial miRNA against JMJ24; 35S::JMJ24, JMJ24 overexpression 645

construct. For each construct, three independent homozygous T3 lines were analyzed. Data 646

shown are averages over six biological replicates with error bars representing SEM. 647

648

Fig. 2 Putative JMJ24 orthologues are present across the angiosperms. 649

(A) Schematic overview of the JMJ24 protein domains and cofactor binding sites. Numbers 650

indicate aa positions of domain start and end. Amino acid residues required for Fe2+-binding 651

and α-ketoglutarate-binding are shown above the protein schematic. Corresponding residues 652

in the JMJ24 sequence are shown below. NLS, nuclear localization signal; RING, RING 653

finger domain; JmjC, JumonjiC domain. 654

(B) Phylogenetic tree with the KDM3 clade from A. thaliana (ARATH, JMJ24, JMJ25/IBM1, 655

JMJ26, JMJ27, JMJ29), Homo sapiens KDM3A, KDM3B and putative orthologues of JMJ24 656

from the basal angiosperm Amborella trichopoda (AMBTR), monocotyledonous species 657

Sorghum bicolor (SORBI), Oryza sativa ssp. japonica (ORYSJ), Brachipodium distachion 658

(BRADI), Hordeum vulgare (HORVD), Zea mays (ZEAMA) and the dicotyledonous species 659

A. lyrata (ARALL), Solanum lycopersicon (SOLLC), Glycine max (SOYBN), Vitis vinifera 660

(VITVI), Populus trichocarpa (POPTR), Physcomitrella patens (PHYPA) using full-length 661

protein sequences. Putative orthologues were identified using Delta Blast and Inparanoid. 662

The A. thaliana JMJ18 sequence was used as outgroup. The phylogenetic tree was prepared 663

using Phylogeny.fr and the default settings. Right panel, conservation of the residues 664

required for Fe2+ and α-ketoglutarate binding in the aligned protein sequences. Red, aa 665

conserved in canonical JmjC sequence; cyan, aa conserved in JMJ24-related proteins but 666

deviating from consensus sequence. 667

(C) Iron binding analysis of JMJ24-JmjC. The amount of protein–bound iron was measured 668

by inductively coupled plasma optical emission spectrometry (ICP-OES) and normalized to 669

protein input. The analysis was performed in triplicate. GST served as a negative and 670

JMJ18-JmjC as a positive control (for protein inputs see Supplemental Fig. S3B). The Fe 671

concentration was normalized to the input protein concentration to obtain the number of Fe 672

molecules per protein molecule. 673

674

Fig. 3 JMJ24 is a nuclear protein with mono-ubiquitination activity. 675

(A) In vitro ubiquitin-ligase assay of JMJ24 RING domains. GST-tagged JMJ24-RING1 (lane 676

4), JMJ24-RING2 (lane 8) and His6-tagged BB (lane 13) undergo autoubiquitination as 677



28

evidenced by the shifts in electrophoretic mobility (arrowheads) in the presence of E1 and 678

E2. Immunoblots were processed with anti-FLAG antibodies (upper panel) to visualize 679

FLAG-ubiquitin, or anti-GST and anti-His6 (lower panel) antibodies, respectively. His6-BB 680

(Disch et al., 2006) served as a positive control and catalyzes the formation of high-681

molecular-weight ubiquitin chains. GST served as negative control. GST-tagged JMJ24-682

RING1 and RING2 catalyze the attachment of mono-ubiquitin (arrowheads). The intense 683

band at 25 kDa in lanes 4, 8, 10, 11 and 13 (arrow) likely represents an E2-ubiquitin adduct 684

formed independently of E3 activity. 685

(B) Confocal microscopy images of JMJ24 subcellular localization. JMJ24::JMJ24-vYFP was 686

stably transformed into jmj24-2 mutants and 3 d-old root tips were imaged. (a) DAPI-stained 687

nuclei (blue), (b) JMJ24-vYFP signal (yellow), (c) bright field signal and (d) merged image of 688

(a), (b) and (c). Size bar, 10 μm. 689

690

Fig. 4 JMJ24 interacts with histones. 691

(A) JMJ24-JmjC binds to N-terminal histone H3 peptides (aa 1-20) in vitro. GST-tagged 692

JMJ24-JmjC was immunoprecipitated with biotinylated histone peptides with different 693

modifications. GST served as a negative and GST-tagged AtING1 (Lee et al., 2009) as a 694

positive control for histone binding. no hist., control with no added histone peptides. 695

(B) In vivo JMJ24 protein interaction partners as isolated by immunoprecipitation and mass 696

spectrometry (LC-MS/MS). Native JMJ24-vYFP protein complexes were immunoprecipitated 697

from transgenic 35S::JMJ24-vYFP plants and co-precipitated proteins were subsequently 698

identified by LC/MS-MS (see also Supplemental Table S4). Two biological experiments with 699

two technical replicates each were performed and the number of individual peptides and the 700

cumulative score is shown for each experiment. 701

(C) JMJ24 specifically binds Histone H3 in vivo. JMJ24-YFP was purified from crosslinked 702

nuclear protein extracts of transgenic 35S:JMJ24-YFP and non-transgenic Col-0 seedlings. 703

Co-purification of histone H2B and H3 was assessed by immunoblotting with specific 704

antibodies. 705

706

Fig. 5 Genetic interaction of JMJ24 with KYP, SUVH5 and SUVH6. 707

Relative AtMu1c transcript levels as determined by qRT-PCR in seedlings with modified 708

JMJ24 activity and (A) loss of KYP activity (kyp-7) or (B) loss of KYP (kyp-4), SUVH5 and 709

SUVH6 activities, respectively. Expression values of AtMu1c were normalized to TUB6 and 710

Col. (A) Results of one representative experiment are shown. Error bars indicate SEM of 711

three technical replicates. A second experiment is shown in Supplemental Fig. S6. (B) 712

Average of three biological replicates is shown. Error bars represent SEM. Statistical 713



29

analysis was performed using ANOVA with log2-transformed data, followed by Tukey test. 714

Different letters indicate significant differences. 715

716

Fig. 6 Effect of loss of JMJ24 on H3K9me2 and DNA methylation. 717

(A) Histone H3K9me2 levels relative to global H3 at the AtMu1c transposase region as 718

determined by chromatin immunoprecipitation in seedlings with modified JMJ24 and KYP 719

activities. Overexpression of JMJ24 reduces H3K9me2, while loss of H3K9me2 enhances it. 720

Data from three biological replicates were normalized to input and H3, and averaged. Error 721

bars represent SEM. *, p<0.05; **, p<0.005 (Student’s t-test). Data for control amplicons with 722

previously described (Mathieu et al., 2005; Kabelitz et al., 2014) high (CACTA) or low 723

(ACTIN) H3K9me2 accumulation are shown in Supplemental Fig. S6. 724

(B) DNA methylation analysis of the AtMu1c TIR by bisulfite sequencing in seedlings with 725

modified JMJ24 and KYP activities. Percentages of DNA methylation were calculated from 726

20 independent clones each (cf. Supplemental Table S2). 727

728

Fig. 7 Genetic interaction of JMJ24 with CMT3, DRM1 DRM2 CMT3. 729

Relative AtMu1c transcript levels in jmj24-2 double mutants with cmt3-11 (A), drm1 drm2 730

cmt3 (B) as determined by qRT-PCR. Expression values of AtMu1c were normalized to 731

TUB6 and Col. Averages of three biological replicates are shown. Error bars represent SEM. 732

733

Fig. 8 JMJ24 affects TE silencing positively and negatively. 734

(A) Empirical cumulative distribution function (ECDF) plots for DNA TEs, MuDR DNA TEs, 735

non-MuDR DNA TEs and CACTA DNA TEs (Slotkin et al., 2009). The distribution shows the 736

log2FC of 35S::JMJ24 against jmj24-2 based on ATH1 microarray data. A shift of the log2FC 737

distribution of the TE category specified in the header (magenta) compared to the log2FC 738

distribution of all TEs (blue) to the left indicates lower expression. 739

(B), (C) Relative transcript levels of several TEs behaving similar to AtMu1c (B) or opposite 740

(C) in jmj24-2 and 35S::JMJ24 as determined by qRT-PCR. Expression values were 741

normalized to TUB6 and Col. Error bars are SEM of n biological replicates. *, p<0.05, **, 742

p<0.005 (Student’s t-test). 743

744

Fig. 9 A Model for JMJ24 action during RdDM 745

JMJ24 encodes an inactive histone demethylase that associates with histone H3. At the 746

AtMu1c locus, JMJ24 antagonizes repressive H3K9me2 marks, which are deposited by KYP 747

and SUVH5/6 and promote DNA methylation. JMJ24 (genetically) antagonizes SUVH5/6 748



30

function and the positive effect of JMJ24 on AtMu1c expression depends on the presence of 749

SUVH5/6. An as yet unknown target protein is (mono-)ubiquitinated by JMJ24 and thus 750

inactivated. In the absence of JMJ24 this target protein promotes silencing of AtMu1c, likely 751

through the methylation of H3K9 or cytosine. Thus, the JMJ24 pathway acts to sustain basal 752

transcription of AtMu1c and other TE during development or the establishment of silencing at 753

novel TE insertions. 754

755

756

757



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http://scholar.google.com/scholar?as_q=Jumonji demethylases moderate precocious flowering at elevated temperature via regulation of FLC in Arabidopsis.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Gan&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

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http://scholar.google.com/scholar?as_q=Interplay between active chromatin marks and RNA-directed DNA methylation in Arabidopsis thaliana.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Greenberg&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

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

http://scholar.google.com/scholar?as_q=Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading&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=Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Henderson&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Mol Cell%5BTitle%5D%29 AND 40%5BVolume%5D AND 444%5BPagination%5D AND Hewawasam G%2C Shivaraju M%2C Mattingly M%2C Venkatesh S%2C Martin%2DBrown S%2C Florens L%2C Workman JL%2C Gerton JL%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=Psh1 is an E3 ubiquitin ligase that targets the centromeric histone variant Cse4&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hewawasam&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Mol Cells%5BTitle%5D%29 AND 27%5BVolume%5D AND 481%5BPagination%5D AND Hong EH%2C Jeong YM%2C Ryu JY%2C Amasino RM%2C Noh B%2C Noh YS%5BAuthor%5D&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hong EH, Jeong YM, Ryu JY, Amasino RM, Noh B, Noh YS (2009) Temporal and spatial expression patterns of nine Arabidopsis genes encoding Jumonji C-domain proteins. Mol Cells 27: 481-490

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

http://scholar.google.com/scholar?as_q=Temporal and spatial expression patterns of nine Arabidopsis genes encoding Jumonji C-domain proteins&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=Temporal and spatial expression patterns of nine Arabidopsis genes encoding Jumonji C-domain proteins&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hong&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Nat Struct Mol Biol%5BTitle%5D%29 AND 17%5BVolume%5D AND 38%5BPagination%5D AND Horton JR%2C Upadhyay AK%2C Qi HH%2C Zhang X%2C Shi Y%2C Cheng X%5BAuthor%5D&dopt=abstract

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Singer T, Yordan C, Martienssen RA (2001) Robertson's Mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1). Genes Dev 15: 591-602


Slotkin RK, Vaughn M, Borges F, Tanurdzic M, Becker JD, Feijo JA, Martienssen RA (2009) Epigenetic reprogramming and smallRNA silencing of transposable elements in pollen. Cell 136: 461-472


Smaczniak C, Immink RG, Muino JM, Blanvillain R, Busscher M, Busscher-Lange J, Dinh QD, Liu S, Westphal AH, Boeren S, ParcyF, Xu L, Carles CC, Angenent GC, Kaufmann K (2012) Characterization of MADS-domain transcription factor complexes inArabidopsis flower development. Proc Natl Acad Sci U S A 109: 1560-1565


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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


Stroud H, Otero S, Desvoyes B, Ramirez-Parra E, Jacobsen SE, Gutierrez C (2012) Genome-wide analysis of histone H3.1 and H3.3variants in Arabidopsis thaliana. Proc Natl Acad Sci U S A 109: 5370-5375


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Tamaru H (2010) Confining euchromatin/heterochromatin territory: jumonji crosses the line. Genes Dev 24: 1465-1478Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Tenaillon MI, Hollister JD, Gaut BS (2010) A triptych of the evolution of plant transposable elements. Trends Plant Sci 15: 471-478Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Trewick SC, Minc E, Antonelli R, Urano T, Allshire RC (2007) The JmjC domain protein Epe1 prevents unregulated assembly anddisassembly of heterochromatin. EMBO J 26: 4670-4682


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http://scholar.google.com/scholar?as_q=ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Shi&as_ylo=2006&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28Arabidopsis replacement histone variant H3%2E3 occupies promoters of regulated genes%2E%5BTitle%5D%29 AND Shu H%2C Nakamura M%2C Siretskiy A%2C Borghi L%2C Moraes I%2C Wildhaber T%2C Gruissem W%2C Hennig L%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=Arabidopsis replacement histone variant H3.3 occupies promoters of regulated genes.&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=Arabidopsis replacement histone variant H3.3 occupies promoters of regulated genes.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Shu&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=%28thaliana are regulated by the chromatin%2Dremodeling gene Decrease in DNA Methylation DDM1%2E Genes Dev%5BTitle%5D%29 AND 15%5BVolume%5D AND 591%5BPagination%5D AND Singer T%2C Yordan C%2C Martienssen RA%5BAuthor%5D&dopt=abstract

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http://www.ncbi.nlm.nih.gov/pubmed?term=%28Cell%5BTitle%5D%29 AND 136%5BVolume%5D AND 461%5BPagination%5D AND Slotkin RK%2C Vaughn M%2C Borges F%2C Tanurdzic M%2C Becker JD%2C Feijo JA%2C Martienssen RA%5BAuthor%5D&dopt=abstract

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

http://scholar.google.com/scholar?as_q=Epigenetic reprogramming and small RNA silencing of transposable elements in pollen&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 reprogramming and small RNA silencing of transposable elements in pollen&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Slotkin&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

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http://scholar.google.com/scholar?as_q=Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Smaczniak&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

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http://www.ncbi.nlm.nih.gov/pubmed?term=%28Nat Struct Mol Biol%5BTitle%5D%29 AND 21%5BVolume%5D AND 64%5BPagination%5D AND Stroud H%2C Do T%2C Du J%2C Zhong X%2C Feng S%2C Johnson L%2C Patel DJ%2C Jacobsen SE%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=A triptych of the evolution of plant transposable elements&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 triptych of the evolution of plant transposable elements&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tenaillon&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

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http://www.ncbi.nlm.nih.gov/pubmed?term=%28A companion cell%2Ddominant and developmentally regulated H3K4 demethylase controls flowering time in Arabidopsis via the repression of FLC expression%2E%5BTitle%5D%29 AND Yang H%2C Han Z%2C Cao Y%2C Fan D%2C Li H%2C Mo H%2C Feng Y%2C Liu L%2C Wang Z%2C Yue Y%2C Cui S%2C Chen S%2C Chai J%2C Ma L%5BAuthor%5D&dopt=abstract

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http://scholar.google.com/scholar?as_q=A companion cell-dominant and developmentally regulated H3K4 demethylase controls flowering time in Arabidopsis via the repression of FLC expression.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yang&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

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a jumonji protein with e3 ligase and histone h3 binding activities … · 4 89 chromatin structure...

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