Genomics

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Genome-wide maps of DNA methylation state in rice embryo and endosperm


ABSTRACT: We report the application of methylacytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq) for high-throughput profiling of DNA methylation in rice embryo 3, 6, 9 DAP and endosperm 2, 3, 6, 9 DAP. A total number of 12-14 million of 2×49 bp paired-end reads was generated for each sample, and BOWTIE2 was used for read mapping. We generated genome-wide DNA methylation profiles of rice embryo and endosperm. This study provides a framework to systemically characterize the effect of DNA methylation in developing seeds and will help to illustrate the epigenetic regulation of rice seed development. Rice embryo and endosperm were selected for DNA extraction and methylacytosine immunoprecipetation combined with Illumina sequencing. We sought to obtain the genome-wide DNA methylation profilings of embryo at 3,6,9 days after pollination(DAP) and endosperm at 2,3,6,9 DAP. To that end, we hand-selected embryo at 3,6,9 DAP and endosperm at 2,3,6,9 DAP according to morphological criteria.

ORGANISM(S): Oryza sativa  

SUBMITTER: yijing zhang   Hong-Wei Xue 

PROVIDER: E-GEOD-57706 | ArrayExpress | 2015-09-01

SECONDARY ACCESSION(S): SRP042015GSE57706PRJNA247779

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development.

Xing Mei-Qing MQ   Zhang Yi-Jing YJ   Zhou Shi-Rong SR   Hu Wen-Yan WY   Wu Xue-Ting XT   Ye Ya-Jin YJ   Wu Xiao-Xia XX   Xiao Yun-Ping YP   Li Xuan X   Xue Hong-Wei HW  

Plant physiology 20150705 4


Seed development is an important process of reproductive development and consists of embryo and endosperm development; both comprise several key processes. To determine and investigate the functions of the dynamic DNA methylome during seed development, we profiled the DNA methylation genome wide in a series of developmental stages of rice (Oryza sativa) embryo and endosperm by methylcytosine immunoprecipitation followed by Illumina sequencing. The results showed that embryo is hypermethylated pr  ...[more]

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