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Series GSE17554 Query DataSets for GSE17554
Status Public on Aug 11, 2009
Title Nucleosome deposition and DNA methylation at coding region boundaries
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary We profiled CpG methylation for human T cells and compared this pattern with public T cell nucleosome (H2A.Z) and polymerase II profiles (SRA000234). Focusing on DNA regions surrounding the start codon and stop codon, instead of the transcription start and end sites, we discovered a very intriguing pattern, namely methylation and nucleosomal peaks at those regions, more prominent than peaks near transcript boundaries. Elongating polymerases tend to pause near both coding ends immediately upstream of the epigenetic peaks, causing a significant reduction in elongation efficiency, suggesting their role in control of RNA splicing. Conserved features in underlying protein coding sequences seem to dictate their evolutionary conservation across multiple species. The nucleosomal and methylation marks are commonly associated with high sequence-encoded DNA-bending propensity but differentially with CpG density.

Keywords: Epigenetics
Overall design Sample submission examines CpG methylation from human T cells.
Contributor(s) Choi JK, Kim YJ
Citation(s) 19723310, 20602769
Submission date Aug 07, 2009
Last update date May 15, 2019
Contact name Jung Kyoon Choi
Organization name Genome Institute of Singapore
Street address 60 Biopolis Street
City Singapore
ZIP/Postal code 138672
Country Singapore
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (1)
GSM437544 Methyl-Seq_human T cells
SRA SRP001352
BioProject PRJNA118651

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Supplementary file Size Download File type/resource
GSE17554_RAW.tar 227.2 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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