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(a). ATG. +1. 3’ UTR. 5’ UTR. Ex 4. Promoter. phyA’. Ex 1. Ex 2. Ex 3. mCG. demethylation. mCG. (b). phyA’. Exon 1. WT. ATG. phyA’. = Hypermethylation at CG sites. Exon 2. WT. = Background (WT) mCG. phyA’. Exon 3. WT.

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(a)

ATG

+1

3’ UTR

5’ UTR

Ex 4

Promoter

phyA’

Ex 1

Ex 2

Ex 3

mCG

demethylation

mCG

(b)

phyA’

Exon 1

WT

ATG

phyA’

= Hypermethylation at CG sites

Exon 2

WT

= Background (WT) mCG

phyA’

Exon 3

WT

WT (Col-0) methylation profile from http://epigenomics.mcdb.ucla.edu/BS-Seq/index.html

Exon 4

TAG

Figure S1


(a)

Ex 2

Ex 3

Promoter

Ex 1

Ex 4

5’ UTR

3’ UTR

# WT

+phyA-sps1

#

#

249

329

370

725

1421

701

617

617

1077

E

E

H1

H2

H4

H3

H8

H5

H6

H7

+

+

+

Probe 3

F2 (sps1 x WT)

Sps1

WT

1

2

3

4

(b)

2.3 kb

1.7 kb

Probe 3

Figure S2



(a)

(b)

Relative transcript abundance

Relative transcript abundance

Relative transcript abundance

Relative transcript abundance

At4g19240

At5g05290

(d)

(c)

At1g23960

At1g03950

Figure S4