High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression

X Li, X Wang, K He, Y Ma, N Su, H He, V Stolc… - The Plant …, 2008 - academic.oup.com
We present high-resolution maps of DNA methylation and H3K4 di-and trimethylation of two
entire chromosomes and two fully sequenced centromeres in rice (Oryza sativa) shoots and …

[HTML][HTML] Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

X Li, J Zhu, F Hu, S Ge, M Ye, H Xiang, G Zhang… - BMC genomics, 2012 - Springer
Background DNA methylation plays important biological roles in plants and animals. To
examine the rice genomic methylation landscape and assess its functional significance, we …

Genome‐wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice

H Yan, S Kikuchi, P Neumann, W Zhang… - The Plant …, 2010 - Wiley Online Library
We conducted genome‐wide mapping of cytosine methylation using methylcytosine
immunoprecipitation combined with Illumina sequencing. The chromosomal distribution …

Rice epigenomics and epigenetics: challenges and opportunities

X Chen, DX Zhou - Current opinion in plant biology, 2013 - Elsevier
During recent years rice genome-wide epigenomic information such as DNA methylation
and histone modifications, which are important for genome activity has been accumulated …

[HTML][HTML] Integrative analysis of reference epigenomes in 20 rice varieties

L Zhao, L Xie, Q Zhang, W Ouyang, L Deng… - Nature …, 2020 - nature.com
Epigenomic modifications are instrumental for transcriptional regulation, but comprehensive
reference epigenomes remain unexplored in rice. Here, we develop an enhanced chromatin …

Analysis of chromatin regulators reveals specific features of rice DNA methylation pathways

F Tan, C Zhou, Q Zhou, S Zhou, W Yang… - Plant …, 2016 - academic.oup.com
Plant DNA methylation that occurs at CG, CHG, and CHH sites (H= A, C, or T) is a hallmark
of the repression of repetitive sequences and transposable elements (TE s). The rice (Oryza …

Global analysis reveals the crucial roles of DNA methylation during rice seed development

MQ Xing, YJ Zhang, SR Zhou, WY Hu, XT Wu… - Plant …, 2015 - academic.oup.com
Seed development is an important process of reproductive development and consists of
embryo and endosperm development; both comprise several key processes. To determine …

[HTML][HTML] Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica

Z Du, H Li, Q Wei, X Zhao, C Wang, Q Zhu, X Yi, W Xu… - Molecular plant, 2013 - cell.com
While previous studies have shown that histone modifications could influence plant growth
and development by regulating gene transcription, knowledge about the relationships …

Asymmetric variation in DNA methylation during domestication and de-domestication of rice

S Cao, K Chen, K Lu, S Chen, X Zhang, C Shen… - The Plant …, 2023 - academic.oup.com
Hundreds of plant species have been domesticated to feed human civilization, while some
crops have undergone de-domestication into agricultural weeds, threatening global food …

Epigenetic inheritance in rice plants

K Akimoto, H Katakami, HJ Kim, E Ogawa… - Annals of …, 2007 - academic.oup.com
Abstract Background and Aims Epigenetics is defined as mechanisms that regulate gene
expression without base sequence alteration. One molecular basis is considered to be DNA …