1. Exon 1 Exon 2 Exon 3 Exon 4 TAG = Hypermethylation at CG sites = Background (WT) mCG phyA’ WT WT (Col-0) methylation profile from http://epigenomics.mcdb.ucla.edu/BS- Seq/index.html ATG phyA’ WT phyA’ WT ATG 5’ UTR 3’ UTR Promoter Ex 1Ex 2Ex 3 Ex 4 +1 phyA’ mCG demethylation (a) (b) Figure S1

2. Figure S2 (b) Probe 3 1.7 kb 2.3 kb WT Sps1 Probe 3 Promoter 5’ UTR Ex 1 Ex 2Ex 3 Ex 4 3’ UTR 370 249 329 E H1H1 H2H2 H3H3 H4H4 H5H5 H6H6 H7H7 H8H8 7251421701617 1077 617 E # # (a) ++ + F2 (sps1 x WT) 1234 + phyA-sps1 # WT

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

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