unme H3k9m H3k9m2 H3K9m3 H3K27m H3K27m2

Peptides

pmoles0

2

10

50

0 4.5 5 6

Minutes

500

300

100

bp

A B

Supplementary Figure 1: MNase digestion conditions and specificity of anti-H3K9m2antibody. (a) Nuclear DNA digested with MNase for various periods of time. Six-minute digestion was used for ChIP assays. (b) Western blot analysis of interaction of anti-H3K9me2 antibody with different methylated peptides.

Supplementary Figure 2: Distribution of H3K9m2 levels (Z-scores) for probes correspondingto each of the five Arabidopsis nuclear chromosomes. Histogram shows the distribution ofthe numbers of probes relative to their Z-score. Black line (0.2) indicates the cut offvalue used for determining H3K9m2 positive probes..

Num

ber o

f pro

bes

Z-score

4000

3000

2000

1000

0420-2

chrom osom e 1 chrom osom e 2 chrom osom e 3 chrom osom e 4 chrom osom e 5 chloroplast

0.2

2

2

MNaseCrosslink

2

2

MNaseCrosslink

2

2

MNaseCrosslink

2

2MNaseCrosslink

5kbGenes Transposons

Supplementary Figure 3: Examples of H3K9m2 patterns observed using two differenttechniques for chromatin immunoprecipitation, micrococcal nuclease digested chromatin(MNase) or crosslinked and sonicated chromatin (Crosslink). Each gray bar corresponds tothe z-score of an individual probe. Genes are in green and transposons are in red.

13326000

241300

9936000

chr1

chr4

chr5

20

genes and transposonsK9H3m2

Interspersed repeats

DNA methylation (positive strand)

DNA methylation (negative strand)

1 kb

1 kb

1 kb

Supplementary Figure 4: Correlation of H3K9m2 methylation with CHG DNA methylation.Examples show the tight association between H3K9m2 positive regions (represented by grey signal), and CHG methylation as determined by whole genome bisulfite sequencing. Bright blue rectangles represent CHG methylation and green and red rectangles represent CG and CHH methylation respectively.

20

genes and transposonsK9H3m2

Interspersed repeats

DNA methylation (positive strand)

DNA methylation (negative strand)

20

genes and transposonsK9H3m2

DNA methylation (positive strand)

DNA methylation (negative strand)

2

0

13255000 13260000 13265000

AT4G26160.1AT4G26170.1

AT4G26180.1AT4G26190.1

3310000 3315000 3320000

AT1G10130.1

2

0

chr 4 genes

H3K9m2DNA methylaiton(positive strand)

DNA methylation(negative strand)

DNA methylaiton(positive strand)

DNA methylation(negative strand)

chr1 genes

H3K9m2

Supplementary Figure 5: Genes are devoid of H3K9m2 and CHG methylation and have highfrequency of CG methylation. Examples show the lack of association between H3K9m2 positive regions(represented by grey signal), and CG only methylated regions associated with the transcribed regions of genes, as determined by whole genome bisulfite sequencing. Green rectangles represent CG methylation and blue and red rectangles represent CHG and CHH methylation respectively.

1.0 11.5 17.7 30.0

1.1 7.2 19.7

1.0 10.3 17.3 23.5

1.0 9.0 16.0 27.0

1.5 2.3 2.8 6.3 18.6

chr1

chr2

chr3

chr4

chr5

Supplementary Figure 6: Chromosome-wide coordinates for pericentromeric (dark) andeuchromatic arm regions in megabases. Pericentromeric regions were assigned based on thedistribution of repetitive elements, genes and DNA methylation across chromosomes..

Supplementary Figure 7: Distribution of Z-scores of probes found in pericentromericregions or euchromatic arms of the chromosomes. Data was generated by conventional(crosslinked) ChIP.

1.5

1.0

0.5

0.04.44.03.63.22.82.42.01.61.20.80.4

Z - scores

perc

ent o

f pro

bes