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Exon 1

(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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Exon 1

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  1. (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

  2. (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

  3. Figure S3 will be provided as Word or PDF file

  4. (a) (b) Relative transcript abundance Relative transcript abundance Relative transcript abundance Relative transcript abundance At4g19240 At5g05290 (d) (c) At1g23960 At1g03950 Figure S4

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