Skip to main content

Table 3 Percent DNA methylation of elements in mutant lines1

From: Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis

   Genotype
   Ler (wt) Clk-st (wt) Ws (wt) cmt3 kyp ago4 drm1/2 drm1/2 cmt3
Locus Size CG CNG CNN CG CNG CNN CG CNG CNN CG CNG CNN CG CNG CNN CG CNG CNN CG CNG CNN CG CNG CNN
MU-48022 4.8 84 34 19 75 28 13 79 25 9 84 1 4.8 84 0.5 1 64 30 19 74 27 9.4 79 0.5 2.8
TA11-42173 6 - - - 81 62 12 88 77 12 75 7.5 10 80 42 13 82 65 12 81 60 5.5 9.6 0 0.2
SIN3-53004 0.2 80 78 38 80 70 59 88 72 58 90 10 6.8 83 73 54 58 2.5 0 58 1.7 0 15 2.5 0
MU-PCR5 >7 88 47 8 80 43 7.5 - - - 63 1.1 4.8 74 16 7 85 43 8 81 54 7.5 89 0.5 4.9
ATSN16 0.2     75 70 24     49 8.7 8.7 82 53 29 42 14 0.8 53 30 3.3 28 0 0.2
SUP7 1.2     16 55 16     8.9 0 5.7 5.9 1.7 1.9 16 20 3.6 14 39 8.7 10 0 0
MEA-ISR8 1.3     95 58 26 87 47 18 89 13 13 92 25 17 81 0 0.7 87 0 0 87 0 0
FWA9 0.5     84 16 6.8 89 18 4.2 93 2.9 6.4     87 2.5 0.7 81 0 0 88 0 0
NOS-PRO10 0.4 71* 45* 38*        54 19 24     77 21 10 77 23 3.2 61 1.3 0.3
SIN3-1119311 0.2 N/A N/A N/A N/A N/A N/A 91 90 56 N/A N/A N/A N/A N/A N/A N/A N/A N/A 81 2.5 0.3 N/A N/A N/A
229R112 ? - - - 93 58 13 93 58 7 83 1 1.7 88 17 6.3 88 54 5.1 87 49 1.9 76 0.5 0.5
229R212 ? - - - - - - 94 48 2.1 - - - - - - - - - 73 0 0 - - -
  1. 1The fraction methylated reported in Figure 5 is the ratio of mutant to wild-type. For example, the fraction of TA11-4217 that is methylated in ago4 is 65% (ago4)/62% (Clk-st) = 1.05. Numbers in bold are from previously published work. All loci except for 229R1 and 229R2 were used in the scatter plots in Figure 5. We determined the size of each element based on the Repbase consensus sequence, except for published examples, in which we used the information provided in the references below. 2MU-4802 is an isolated Mutator-like element annotated as At1g17275. 3TA11-4217 is an isolated LINE element annotated as At1g29650 with very close homology to TA11. 4SIN3-5300 is a SINE3 element located between At3g60130 and At3g60140. 5MU-PCR is a complex locus of multiple transposable elements inserted into one another present at the hk4S heterochromatic knob on chromosome 4 in Ws and in pericentric heterochromatin on chromosome 4 in Ler [19]. 6AtSN1 is a SINE1 element [33]. Bisulfite sequencing data derived from [12]. 7SUP is the Arabidopsis SUPERMAN gene [45]. Bisulfite sequencing data derived from [12,16,27,46]. 8MEA-ISR is a locus composed of tandem direct repeats located downstream of the Arabidopsis MEDEA gene [46]. Bisulfite sequencing data derived from [12,46]. 9FWA is the Arabidopsis FWA gene [47]. Bisulfite sequencing data derived from [11,46]. 10NOS-PRO is a transgenic nopaline synthase promoter [32]. Bisulfite sequencing data derived from [10,29]. 11SIN3-11193 is a SINE3 element located between At3g22060 and At3g22070. 12229R1 and 229R2 are intergenic sequences within 2 kb of one another located between At1g36940 and At1g36950. Dashes indicate that it is not done; N/A, sequence absent in Ler; asterisks indicate that the numbers are for the transgenic NOS-PRO line, Col ecotype; question marks indicate that the size of the methylated sequence cannot be accurately predicted.