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

被引：105

作者：

Xing, Mei-Qing ^{[1
]}

Zhang, Yi-Jing ^{[1
]}

Zhou, Shi-Rong ^{[1
]}

Hu, Wen-Yan ^{[1
]}

Wu, Xue-Ting ^{[1
]}

Ye, Ya-Jin ^{[1
]}

Wu, Xiao-Xia ^{[2
]}

Xiao, Yun-Ping ^{[3
]}

Li, Xuan ^{[1
]}

Xue, Hong-Wei ^{[1
]}

机构：

[1] Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Plant Physiol & Ecol, Natl Key Lab Plant Mol Genet, Shanghai 200032, Peoples R China

[2] Yangzhou Univ, Coll Biosci & Biotechnol, Yangzhou 225009, Peoples R China

[3] Shanghai OEbiotech, Shanghai 201210, Peoples R China

来源：

PLANT PHYSIOLOGY | 2015年 / 168卷 / 04期

关键词：

PLANT DEVELOPMENT; ENDOSPERM; ARABIDOPSIS; DEMETHYLATION; GENES; DIFFERENTIATION; CELLULARIZATION; IDENTIFICATION; EMBRYOGENESIS; TRANSCRIPTION;

D O I：

10.1104/pp.15.00414

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

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 predominantly around non-transposable element (TE) genes, short DNA-TEs, and short interspersed TEs compared with endosperm, and non-TE genes have the most diverse methylation status across seed development. In addition, lowly expressed genes are significantly enriched in hypermethylated genes, but not vice versa, confirming the crucial role of DNA methylation in suppressing gene transcription. Further analysis revealed the significantly decreased methylation at early developing stages (from 2 to 3 d after pollination), indicating a predominant role of demethylation during early endosperm development and that genes with a consistent negative correlation between DNA methylation change and expression change may be potentially directly regulated by DNA methylation. Interestingly, comparative analysis of the DNA methylation profiles revealed that both rice indica and japonica subspecies showed robust fluctuant profiles of DNA methylation levels in embryo and endosperm across seed development, with the highest methylation level at 6 d after pollination (2 d after pollination of endosperm in japonica as well), indicating that a complex and finely controlled methylation pattern is closely associated with seed development regulation. The systemic characterization of the dynamic DNA methylome in developing rice seeds will help us understand the effects and mechanism of epigenetic regulation in seed development.

引用

页码：1417 / U1554

页数：24

共 46 条

[1] Transcription factors regulating the progression of monocot and dicot seed development [J].

Agarwal, Pinky ;

Kapoor, Sanjay ;

Tyagi, Akhilesh K. .

BIOESSAYS, 2011, 33 (03) :189-202

[2] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[3] Epigenetic control of plant stress response [J].

Boyko, Alex ;

Kovalchuk, Igor .

ENVIRONMENTAL AND MOLECULAR MUTAGENESIS, 2008, 49 (01) :61-72

[4] Development of the endosperm in rice (Oryza sativa L): Cellularization [J].

Brown, RC ;

Lemmon, BE ;

Olsen, OA .

JOURNAL OF PLANT RESEARCH, 1996, 109 (1095) :301-313

[5] The Rice Oligonucleotide Array Database: an atlas of rice gene expression [J].

Cao, Peijian ;

Jung, Ki-Hong ;

Choi, Daeseok ;

Hwang, Daehee ;

Zhu, Jun ;

Ronald, Pamela C. .

RICE, 2012, 5

[6] Rice epigenomics and epigenetics: challenges and opportunities [J].

Chen, Xiangsong ;

Zhou, Dao-Xiu .

CURRENT OPINION IN PLANT BIOLOGY, 2013, 16 (02) :164-169

[7] Abscisic Acid Regulates Early Seed Development in Arabidopsis by ABI5-Mediated Transcription of SHORT HYPOCOTYL UNDER BLUE1 [J].

Cheng, Zhi Juan ;

Zhao, Xiang Yu ;

Shao, Xing Xing ;

Wang, Fei ;

Zhou, Chao ;

Liu, Ying Gao ;

Zhang, Yan ;

Zhang, Xian Sheng .

PLANT CELL, 2014, 26 (03) :1053-1068

[8] Transcriptome and methylome interactions in rice hybrids [J].

Chodavarapu, Ramakrishna K. ;

Feng, Suhua ;

Ding, Bo ;

Simon, Stacey A. ;

Lopez, David ;

Jia, Yulin ;

Wang, Guo-Liang ;

Meyers, Blake C. ;

Jacobsen, Steven E. ;

Pellegrini, Matteo .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (30) :12040-12045

[9] Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning [J].

Cokus, Shawn J. ;

Feng, Suhua ;

Zhang, Xiaoyu ;

Chen, Zugen ;

Merriman, Barry ;

Haudenschild, Christian D. ;

Pradhan, Sriharsa ;

Nelson, Stanley F. ;

Pellegrini, Matteo ;

Jacobsen, Steven E. .

NATURE, 2008, 452 (7184) :215-219

[10] Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations [J].

Eichten, Steven R. ;

Briskine, Roman ;

Song, Jawon ;

Li, Qing ;

Swanson-Wagner, Ruth ;

Hermanson, Peter J. ;

Waters, Amanda J. ;

Starr, Evan ;

West, Patrick T. ;

Tiffin, Peter ;

Myers, Chad L. ;

Vaughn, Matthew W. ;

Springer, Nathan M. .

PLANT CELL, 2013, 25 (08) :2783-2797

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