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Series GSE5974 Query DataSets for GSE5974
Status Public on Nov 26, 2006
Title Interdependence between DNA methylation and transcription
Organism Arabidopsis thaliana
Experiment type Expression profiling by genome tiling array
Genome binding/occupancy profiling by genome tiling array
Methylation profiling by array
Summary Cytosine methylation, a common form of DNA modification that antagonizes transcriptional initiation, is found at transposons and repeats in vertebrates, plants, and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within about 20% of Arabidopsis genes. Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit. Genic methylation is strongly influenced by transcription: moderately transcribed genes are most likely to be methylated, while genes at either extreme are least likely. Small RNAs are enriched at methylated genes, which suggests that aberrant transcription triggers genic methylation. Transcription is in turn influenced by methylation: short methylated genes are poorly expressed, and loss of methylation in the body of a gene leads to enhanced transcription. Our results indicate that genic transcription and DNA methylation are closely interwoven processes.
Keywords: whole genome profiling, DNA methylation, met1-6 expression
Overall design All experiments were done using two channels per chip. Two microarray experiments compared immunoprecipitated, methylated DNA to control genomic DNA. A third microarray experiment used a methylation sensitive restriction enzyme (HpyCH4 IV) to determine regions of differential DNA methylation in met1-6 mutant plants. Two microarray experiments for expression analysis of met1-6 mutants were done using biological replicates. Oligo (dT) primed cDNA from mutant plants was compared to oligo (dT) primed cDNA from wild type plants.
Contributor(s) Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S
Citation(s) 17128275
Submission date Oct 05, 2006
Last update date Aug 30, 2012
Contact name Jorja Henikoff
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
Platforms (1)
GPL3371 FHCRC Arabidopsis Tiling Array
Samples (5)
GSM138295 Met1-6_Hpy/Col_Hpy
GSM138296 methylation_IP/total_DNA 60930
GSM138297 methylation_IP/total_DNA 60935
BioProject PRJNA97449

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Supplementary file Size Download File type/resource
GSE5974_RAW.tar 46.6 Mb (http)(custom) TAR (of GFF, TXT)

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