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| Status |
Public on Apr 21, 2008 |
| Title |
Highly integrated single base resolution maps of the epigenome in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by genome tiling array
Methylation profiling by array
Methylation profiling by high throughput sequencing
|
| Summary |
Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosine DNA methylation identified by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays, for wildtype Col-0.
Understanding the epigenetic regulatory mechanisms that mediate control of transcription at multiple levels is critical to understanding how plants develop and respond to their environment. We combined next-generation sequencing by synthesis (SBS) technology with novel methods for direct sequencing of the entire cytosine methylome (methylC-seq), transcriptome (RNA-seq), and the small RNA component of the transcriptome (smRNA-seq) to create a set of highly integrated epigenome maps for Arabidopsis thaliana, in conjunction with a set of informative mutants defective in DNA methyltransferase and DNA demethylase activity. At single-base resolution we discovered extensive, previously undetected, DNA methylation, identified the context and level of methylation at each site, and found that local composition has effects upon DNA methylation state. Deep sequencing of the smRNAome exposed a direct relationship between the location and abundance of smRNAs and DNA methylation, perturbation of smRNA biogenesis upon loss of CpG DNA methylation, and a tendency for smRNAs to direct strand-specific DNA methylation in the region of RNA-DNA homology. Finally, strand-specific RNA-seq revealed changes in the transcript abundance of hundreds of genes upon alteration of the DNA methylation state, and enabled the identification of numerous previously unidentified genes regulated by DNA methylation.
This SuperSeries is composed of the SubSeries listed below.
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| Overall design |
Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosine DNA methylation identified by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays, for wildtype Col-0.
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| Contributor(s) |
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR |
| Citation(s) |
18423832 |
| |
| Submission date |
Mar 18, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL9062 |
Illumina Genome Analyzer (Arabidopsis thaliana) |
| GPL10977 |
[At35b_MR] Affymetrix Arabidopsis Tiling 1.0R Array |
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| Samples (16)
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| This SuperSeries is composed of the following SubSeries:
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| GSE10966 |
Highly integrated epigenome maps in Arabidopsis - whole genome shotgun bisulfite sequencing |
| GSE10967 |
Highly integrated epigenome maps in Arabidopsis - small RNA sequencing |
| GSE10968 |
Highly integrated epigenome maps in Arabidopsis - transcriptome sequencing |
| GSE10969 |
Highly integrated epigenome maps in Arabidopsis - methylcytosine immunoprecipitation |
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| Relations |
| BioProject |
PRJNA107265 |
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