Supplementary Figure S7. Orthologs of the A. thaliana IBM1 gene containing a large intron. Boxes represent exons, with coding regions in black and ...
CG
CHG
CHH
100
Met hyl at i on( %)
80
60
40
20
0
Col 0
c mt 3
k y p
F1Lerxc mt 3
F1Lerxk y p
Suppl ement ar yFi gur eS1.Bi s ul f i t es equenc i nganal y s i sofc y t os i nemet hy l at i onatt hemet hy l at edz oneoft he l ar geI BM1i nt r oni nwi l dt y pe,c mt 3andk y ppl ant s ,andoft hec mt 3der i v edandt hek y pder i v edal l el esi n Lerxc mt 3andLerxk y pF1hy br i ds ,r es pec t i v el y . Pr opor t i onsofmet hy l at edc y t os i nesatCG ( r ed) ,CHG ( bl ue)andCHH( gr een)s i t esar ei ndi c at edasper c ent ages .
WT
met 1 R1F1 R2F1 R3F2 R4F4 R5F3 R5F5 R7F6 R8F6
WT
met 1 F4R4 F5R5 F5R6
ant i s ens et r ans c r i pt i on
R10F8 UBQ1 s ens et r ans c r i pt i on
Suppl e me nt ar yFi gur eS2.RTPCRa na l ys i sofs e ns e( l e f tpa ne l )a nda nt i s e ns e( r i ght )I BM1Lt r a ns c r i pt i oni n wi l dt ypea ndme t 13pl a nt s ,us i ngpr i me rs e t sde s i gne da l ongt hel e ngt hoft hel a r gei nt r onoft heI BM1ge ne ( mi ddl e ) .Pr i me rpos i t i ons ,i nt r on,e xonsa ndt heme t hyl a t e di nt r oni cr e gi ona r ei ndi c a t e dbybl a c kt r i a ngl e s ,abl a c k l i ne ,ye l l owboxe sa ndar e dba r ,r e s pe c t i ve l y.Thea mpl i f i c a t i onofUBQ1wa sus e dt onor ma l i z et heRNAt e mpl a t e l e ve l s .
1
8
12
i bm14
WT
Bgl I I Undi ges t ed
Suppl ement ar yFi gur eS3.CHG met hy l at i onatt heBNSl oc usi n3i ndependenti bm1: : I BM1Ll i nes andi ni bm1andwi l dt y pepl ant s .DNAmet hy l at i onwasanal y z edbyr es t r i c t i ondi ges t i onwi t ht he met hy l at i ons ens i t i v eenz y meBgl I If ol l owedbyPCRwi t hBNSF2/ R3pr i mer s( Suppl ement ar yT abl e1) .
AT2G24370
AT2G19520
AT1G27000
AT5G14060
CMT3
AT2G42600
AT1G58030
AT3G23750
Met hyl at i on( %)
A
AT5G39960
B
i bm1
met 1: : I BM1L
met 1
WT
i bm1
met 1
met 1: : I BM1L
WT i bm1
met 1: : I BM1L
met 1
AT1G26400
i bm1
met 1: : I BM1L
met 1
ROS1
WT
C
WT
i bm1
met 1: : I BM1L
met 1
AT4G24740
WT
Met hyl at i on( %)
Met hyl at i on( %)
AT3G47860
Ta3
At GP31
AT5G19097
At Mu1
CAC2
AT2G12490
AT3G45446
Met hyl at i on( %)
At SN1
EVD
i bm1
met 1: : I BM1L
met 1
WT
i bm1
met 1: : I BM1L
met 1
WT
i bm1
met 1: : I BM1L
met 1
WT
i bm1
met 1: : I BM1L
met 1
WT
i bm1
met 1: : I BM1L
met 1
WT
Met hyl at i on( %)
At COPI A4
Suppl e me nt ar yFi gur eS4.Bi s ul f i t es e que nc i nga na l ys i soft heDNAme t hyl a t i onpa t t e r nsa te l e ve n ge ne s( A) ,t e nt r a ns pos a bl ee l e me nt s( B)a nda tt heROS1ge nea ndt heAT1G26400ROS1t a r ge t l oc us( C) ,i nwi l dt ype , me t 1,me t 1: : I BM1La ndi bm1pl a nt s .Pr opor t i onsofme t hyl a t e dc yt os i ne sa t CG( r e d) ,CHG( bl ue )a ndCHH( gr e e n)s i t e sa r ei ndi c a t e da spe r c e nt a ge s .
met 1: : I BM1L WT met 1 23 22 I BM1L AT2G24370 AT2G19520 AT1G27000 ROS1 DME ACT2
Suppl ement ar yFi gur eS5.Tr ans c r i pt i onanal y s i si n2i ndependentmet 1: : I BM1Ll i nes .Repr es ent at i v ei magesof RTPCRanal y s esatI BM1L,AT2G24370,AT2G19520andAT1G27000,ROS1andDMEgenes .
A
B
C
Suppl e me nt ar yFi gur eS6.Abnor ma lf l owe rphe not ype sobs e r ve di ns omeme t 13l i ne s . I ma ge sofawhol ei nf l or e s c e nc es hoot( A)a ndma gni f i c a t i onoft woa bnor ma ls i l i que s( B&C) .
Identity with A. thaliana protein sequence (%)
Arabidopsis thaliana AT3G07610
Mean intron length (bp)
1974 bp
1 kb
2511 bp
1 kb
87
202 bp (Hu et al., 2011)
1 kb
50
141 bp (Park et al., 2010)
180 bp (AGI, 2000)
Arabidopsis lyrata XM_002882492.1
Brassica rapa Bra029664
2385 bp
Populus trichocarpa POPTRDRAFT_931816
8384 bp
POPTRDRAFT_890067
2585 bp
4 kb
47 200 bp (Jiang et al., 2011)
1 kb
46
Vitis vinifera GSVIVT0102608001
GSVIVT0133203001
2 kb
6211 bp
39830 bp
LOC100244450
20874 bp 25044 bp
LOC100261347
37
7102 bp
6212 bp
42
8 kb
4 kb
2 kb
42
1100 bp (Jiang et al., 2011)
38
Oryza sativa japonica LOC Os03g31594
8726 bp
2 kb
35
413 bp (Haberer et al., 2005)
44
436 bp (Paterson et al., 2009)
33
607 bp (Haberer et al., 2005)
Sorghum bicolor SORBIDRAFT_02g024010
8676 bp
2 kb
Zea mays GRMZM2G383210
13503 bp
2 kb
Apis mellifera
LOC408944
22347 bp
4 kb
20
1347 bp (from Apis mellifera NCBI Gnomon predictions rel. 4.0)
Supplementary Figure S7. Orthologs of the A. thaliana IBM1 gene containing a large intron. Boxes represent exons, with coding regions in black and untranslated regions in white. The region encoding the jmjC domain is shown in red (Saze et al, 2008). Length of the large introns and scale bars are indicated for each gene. The mean length of introns in each organism and the percentage of identity of each orthologous protein with Arabidopsis IBM1 protein are indicated. Orthologous genes were identified by blastp of the Arabidopsis IBM1 protein sequence against non-redundant protein sequences of the NCBI database (http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins). Additional genes annotated as orthologs of the IBM1 gene in the Gramene database were selected (http://www.gramene.org/). The percentage of identity of each orthologous protein with the Arabidopsis IBM1 protein sequence were determined by alignment of orthologous protein sequences using the ClustalW2 program (http://www.ebi.ac.uk/Tools/msa/clustalw2/).
45%
Total Genes ClassII
40%
ClassI
proportion of genes
35% 30% 25% 20% 15% 10% 5% 0%
n
