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Series GSE21821 Query DataSets for GSE21821
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
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.
 
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.
 
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
Submission date May 13, 2010
Last update date May 15, 2019
Contact name matteo Pellegrini
E-mail(s) [email protected]
Phone 310-825-0012
Organization name UCLA
Department MCD Biology
Lab Matteo Pellegrini
Street address 621 Charles Young Drive South
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platforms (3)
GPL9062 Illumina Genome Analyzer (Arabidopsis thaliana)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL9302 Illumina Genome Analyzer II (Arabidopsis thaliana)
Samples (4)
GSM543295 Arabidopsis Mnase-Seq (seq, prb)
GSM543296 Arabidopsis Mnase-Seq (qseq)
GSM543297 Arabidopsis H3 ChIP-Seq
This SubSeries is part of SuperSeries:
GSE21673 Relationship between nucleosome positioning and DNA methylation
Relations
BioProject PRJNA129325
SRA SRP002544

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE21821_RAW.tar 3.0 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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