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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 03, 2008 |
| Title |
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by genome tiling array
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| Summary |
Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5' ends of genes where it promotes transcriptional competence. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation.
Keywords: Affinity-purification on microarray
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| Overall design |
All experiments were done using two channels per chip. DNA methylation experiments compared immunoprecipitated, methylated DNA to control genomic DNA. H2A.Z experiments compared whole micrococcal nuclease-treated affinity-purified chromatin to input chromatin used for affinity purification. Affinity purification was performed using either biotin-tagged H2A.Z, pulled down using streptavidin, or endogenous H2A.Z pulled down using an anti-H2A.Z antibody.
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| Contributor(s) |
Daniel Z, Steven H |
| Citation(s) |
18815594 |
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| Submission date |
Jul 23, 2008 |
| Last update date |
Mar 20, 2012 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
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| Phone |
206-667-4850
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| Organization name |
Fred Hutchinson Cancer Research Center
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| Department |
Basic Sciences
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| Lab |
Henikoff
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| Street address |
1100 Fairview AV N, A1-162
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
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| Platforms (1) |
| GPL3371 |
FHCRC Arabidopsis Tiling Array |
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| Samples (21)
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| GSM307373 |
Zilberman H2A.Z IP/total DNA 90984 (BLRP-1) |
| GSM307374 |
Zilberman H2A.Z IP/total DNA 1364702 (BLRP-2) |
| GSM307375 |
Zilberman H2A.Z IP/total DNA 1364902 (BLRP-3) |
| GSM307376 |
Zilberman H2A.Z IP/total DNA 1365602 (BLRP-4) |
| GSM307377 |
Zilberman H2A.Z IP/total DNA 1823502 (Ab-2 WT) |
| GSM307378 |
Zilberman H2A.Z IP/total DNA 1824902 (Ab-1 WT) |
| GSM307379 |
Zilberman H2A.Z IP/total DNA 1825002 (Ab-2 met1-6) |
| GSM307380 |
Zilberman H2A.Z IP/total DNA 1825302 (Ab-1 met1-6) |
| GSM307381 |
Zilberman Methylation IP/total DNA 103548 (met1-6 aerial) |
| GSM307382 |
Zilberman Methylation IP/total DNA 1862602 (WT root-2) |
| GSM307383 |
Zilberman Methylation IP/total DNA 1864302 (met1-6 root-2) |
| GSM307384 |
Zilberman Methylation IP/total DNA 1881802 (WT root-1) |
| GSM307385 |
Zilberman Methylation IP/total DNA 1882402 (met1-6 root-1) |
| GSM307386 |
Zilberman Methylation IP/total DNA PIE6-in (pie1-5 sample 1) |
| GSM307387 |
Zilberman Methylations IP/total DNA WT6 (WT sample 1) |
| GSM307388 |
Zilberman Methylation IP/total DNA PIE6-II (pie1-5 sample 2) |
| GSM307389 |
Zilberman Methylation IP/total DNA PIE6-III (WT sample 2) |
| GSM307390 |
Zilberman Methylation IP/total DNA WT6-II (pie1-5 sample 3) |
| GSM307391 |
Zilberman Methylation IP/total DNA WT6-III (WT sample 3) |
| GSM307392 |
Zilberman met1-6 RNA/WT RNA 102388 (met1-6/WT 1) |
| GSM307393 |
Zilberman met1-6 RNA/WT RNA 110048 (met1-6/WT 2) |
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| Relations |
| BioProject |
PRJNA113725 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE12212_RAW.tar |
347.0 Mb |
(http)(custom) |
TAR (of GFF, PAIR) |
| Processed data included within Sample table |
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