1. Map-based cloning of ASI4 gene
4,750, ,150, ,900, ,610,000
4/ / / /176
TFL TT NGA PHYC LFY3
Chr.5
Marker
Coordinate
Recombination
xpo1a-4
xpo1a-5
At5G17020
V L S A S Q R Q D
GTC CTC TCA GCT TCT CAA AGA CAG GAT
V L S A S *
GTC CTC TCA GCT TCT TAA AGA CAG GAT
WT CDS
Xpo1a-4 CDS
acatattcagAGAGCTGCTG
acatattcaaAGAGCTGCTG
WT DNA
Xpo1a-5 DNA
Supplementary Figure 1
Map-based cloning of ASI4 gene
The recombination frequencies of the genetic mapping are shown here. There is a C-to-T mutation in asi4-1and thus produces a stop codon, and a G-to-A mutation in asi4-2 which produces wrong splicing.

2. F AT5G17020 asi4-2 (xpo1a-5) R2 R1 M Supplementary Figure 2
WT asi WT asi4-2
F+R F+R2 F R2 R1 M
Supplementary Figure 2
asi4-2 mutation leads to wrong splicing of XPO1A transcript
Two different transcripts were detected in asi4-2 compared to WT. Total RNA was extracted from 10-d-old WT and asi4-2 seedlings and then was reverse transcribed as PCR template.

3. Supplementary Figure 3.
Relative expression levels of ROS1 in xpo1a mutants.
xpo1a mutations do not affect the expression levels of ROS1 mRNA. Data were normalized to amplification of the Arabidopsis ACTIN2 gene.

4. 35S promoter
35S region B
Cytosine methylation %
Supplementary Figure 4
xpo1a mutation increases DNA methylation levels in the promoter region of 35S::SUC2 transgene
DNA methylation levels at region A and region B of 35S-SUC2 promoter are calculated from WGBS data. Region A and B are marked in figure 3

5. A B 35S-XPO1A-GFP/xpo1a-3 Bright Field XPO1A-GFP Merged
Supplementary Figure 5
XPO1A localizes to both nucleus and cytoplasm
(A) XPO1A-YFP fusion protein (driven by 35S promoter) was transiently expressed in Arabidopsis protoplasts, and YFP fluorescence was detected after 14 h of transformation. 35S:YFP-NbFib2 was co-transformed as a nuclolar localization marker. (B) Detection of GFP fluorescence in the root tip of 35S-XPO1A-GFP/xpo1a-3 transgenic plants.

6. Supplementary Figure 6
hda6 mutant displays reduced DNA methylation level in selected XPO1A target loci
A snapshot of published DNA methylome (Stroud et al., 2013) showing that DNA methylation levels are reduced in had6-7 mutant in comparison with its wild-type in the tested XPO1A target loci (Figure 3C and 3E).

7. Col xpo1a-3
Col-0 xpo1a-3
Supplementary Figure 7
xpo1a mutation increases the expression of XPO1B gene
Total RNA was extracted from 10-d-old Col-0 and xpo1a-3 (Col-0 background) seedlings and mRNA levels of XPO1A and XPO1B were determined by quantitative RT-PCR analysis.