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| Status |
Public on May 29, 2010 |
| Title |
Relationship between nucleosome positioning and DNA methylation: Bisulfite-Seq, ChIP-Seq, and Mnase-Seq |
| Organisms |
Arabidopsis thaliana; Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana utilizing massively parallel sequencing of mononucleosomes. By combining this data with profiles of DNA methylation at single base resolution, we identified ten base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA. These results suggest that nucleosome positioning strongly influences DNA methylation patterning throughout the genome and that DNA methyltransferases preferentially target nucleosome-bound DNA. We also observed similar trends in human nucleosomal DNA suggesting that the relationships between nucleosomes and DNA methyltransferases are conserved. Finally, as has been observed in animals, nucleosomes were highly enriched on exons, and preferentially positioned at intron-exon and exon-intron boundaries. RNA Pol II was also enriched on exons relative to introns, consistent with the hypothesis that nucleosome positioning regulates Pol II processivity. We also found that DNA methylation enriched on exons, consistent with the targeting of DNA methylation to nucleosomes.
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| Overall design |
Genomic DNA from Arabidopsis thaliana was MNase digested, size selected and sequenced. Genomic DNA associated with H3 was isolated using ChIP and sequenced. Genomic DNA from human HSF1 embryonic stem cells was bisulfite converted and sequenced.
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| Contributor(s) |
Chodavarapu RK, Feng S, Bernatavichute Y, Chen P, Stroud H, Yu Y, Hetzel J, Kuo F, Kim J, Cokus SJ, Casero D, Bernal M, Huijser P, Clark AT, Krämer U, Merchant SS, Zhang X, Pellegrini M, Jacobsen SE |
| Citation(s) |
20512117 |
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| Submission date |
May 13, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
matteo Pellegrini |
| E-mail(s) |
[email protected]
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| Phone |
310-825-0012
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| Organization name |
UCLA
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| Department |
MCD Biology
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| Lab |
Matteo Pellegrini
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| Street address |
621 Charles Young Drive South
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platforms (3) |
| GPL9062 |
Illumina Genome Analyzer (Arabidopsis thaliana) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
| GPL9302 |
Illumina Genome Analyzer II (Arabidopsis thaliana) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE21673 |
Relationship between nucleosome positioning and DNA methylation |
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| Relations |
| BioProject |
PRJNA129325 |
| SRA |
SRP002544 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE21821_RAW.tar |
3.0 Gb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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