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

Table 2 CNG methylation changes within transposable elements

Mutant	Total targets	Transposon targets*	p value^†
Random-PCR array
All loci	597	12
cmt3	5	2	0.01
kyp	4	3	<0.0001
ago4	1	0	1
drm1/2	2	0	1
drm1/2 cmt3	7	3	0.001
Gene-oligo array ^‡
All unambiguous loci	6,950	907 (13%)
cmt3 targets	164	104 (63%)	<0.0001
kyp targets	38	26 (68%)	<0.0001
ago4 targets	0	0	-
drm1/2 targets	6	4 (67%)	0.005
drm1/2 cmt3 targets	103	67 (65%)	<0.0001

*Total number of possible transposable element hits among the 597 loci on the random-PCR array or among the 26,090 loci on the gene-oligo array. ^†Using Fisher's exact test. ^‡All numbers represent only those loci for which the MspI cut site responsible for differential fractionation could be unambiguously determined.

ISSN: 1474-760X