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Genome-wide maps of chromatin state in rice endosperm

ABSTRACT: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone H3 trimethylation in rice endosperm. By obtaining about four hundred million bases of sequence from rice chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of rice endosperm. We find that the presence of H3K27me3 in either upstream or downstream of a gene is predominately associated with repression of the gene, while its absence is mainly associated with high gene expression. Examination of Histone H3 lysine 27 trimethylation in rice endosperm.

ORGANISM(S): Oryza sativa

SUBMITTER: Feng Tan

PROVIDER: E-GEOD-27048 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data.

Malone Brandon M BM Tan Feng F Bridges Susan M SM Peng Zhaohua Z

PloS one 20110930 9

Chromatin immunoprecipitation coupled with high throughput DNA Sequencing (ChIP-Seq) has emerged as a powerful tool for genome wide profiling of the binding sites of proteins associated with DNA such as histones and transcription factors. However, no peak calling program has gained consensus acceptance by the scientific community as the preferred tool for ChIP-Seq data analysis. Analyzing the large data sets generated by ChIP-Seq studies remains highly challenging for most molecular biology labo ...[more]

PMID: 21984925

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