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Series GSE3109 Query DataSets for GSE3109
Status Public on Oct 25, 2005
Title Chromatin and siRNA pathways cooperate to maintain DNA methylation
Organism Arabidopsis thaliana
Experiment type Methylation profiling by array
Methylation profiling by genome tiling array
Summary DNA methylation occurs at preferred sites in eukaryotes, although the basis for preference is not known. We use a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related RNA silencing component (AGO4) in methylating target loci. We find that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that corresponds to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants. Our results suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism. Thus, parallel pathways would be needed to maintain silencing of transposable elements.
Keywords: Methylation profiling using Msp I enzyme
 
Overall design Methylation profiling of Arabidopsis mutant in CNG methylation pathways on Arabidopsis oligo and random arrays.
 
Contributor(s) Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S
Citation(s) 16277745
Submission date Aug 10, 2005
Last update date Mar 16, 2012
Contact name Robert Tran
E-mail(s) rtran@fhcrc.org
Organization name Fred Hutchinson cancer research center
Street address 1100 Fairview Ave N; A1-111
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (2)
GPL1911 FHCRC Arabidopsis Oligo Array v1.0
GPL2726 FHCRC Arabidopsis Intergenic Array
Samples (60)
GSM69359 Methylation profiling of chromomethylase 3 (CMT3)-1 using Msp I enzyme
GSM69360 Methylation profiling of chromomethylase 3 (CMT3)-1R using Msp I enzyme
GSM69379 Methylation profiling of chromomethylase 3 (CMT3)-2 using Msp I enzyme
Relations
BioProject PRJNA93117

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