Genomics

Dataset Information

156

Nucleosome deposition and DNA methylation at coding region boundaries


ABSTRACT: 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.

INSTRUMENT(S): Illumina Genome Analyzer (Homo sapiens)

SUBMITTER: Jung Kyoon Choi  

PROVIDER: GSE17554 | GEO | 2009-08-11

SECONDARY ACCESSION(S): PRJNA118651

REPOSITORIES: GEO

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Publications

Nucleosome deposition and DNA methylation at coding region boundaries.

Choi Jung Kyoon JK   Bae Jae-Bum JB   Lyu Jaemyun J   Kim Tae-Yoon TY   Kim Young-Joon YJ  

Genome biology 20090901 9


BACKGROUND: Nucleosome deposition downstream of transcription initiation and DNA methylation in the gene body suggest that control of transcription elongation is a key aspect of epigenetic regulation. RESULTS: Here we report a genome-wide observation of distinct peaks of nucleosomes and methylation at both ends of a protein coding unit. Elongating polymerases tend to pause near both coding ends immediately upstream of the epigenetic peaks, causing a significant reduction in elongation efficiency  ...[more]

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