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 …

Genome-wide profiling of histone H3K4-tri-methylation and gene expression in rice under drought stress

W Zong, X Zhong, J You, L Xiong - Plant molecular biology, 2013 - Springer
Histone modifications affect gene expression level. Several studies have shown that they
may play key roles in regulating gene expression in plants under abiotic stress, but genome …

Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm

JA Rodrigues, R Ruan, T Nishimura… - Proceedings of the …, 2013 - National Acad Sciences
Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits
extensive localized DNA demethylation on maternally inherited chromosomes …

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 …

The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres

T Zhang, PB Talbert, W Zhang, Y Wu… - Proceedings of the …, 2013 - National Acad Sciences
Plant and animal centromeres comprise megabases of highly repeated satellite sequences,
yet centromere function can be specified epigenetically on single-copy DNA by the presence …

Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene‐body DNA …

C Lafon‐Placette, P Faivre‐Rampant… - New …, 2013 - Wiley Online Library
DNA methylation is involved in the control of plant development and adaptation to the
environment through modifications of chromatin compaction and gene expression. In poplar …

Cytoplasmic organelle DNA preferentially inserts into open chromatin

D Wang, JN Timmis - Genome biology and evolution, 2013 - academic.oup.com
DNA transfer from chloroplasts and mitochondria to the nucleus is ongoing in eukaryotes but
the mechanisms involved are poorly understood. Mitochondrial DNA was observed to …

Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses

G Turco, JC Schnable, B Pedersen… - Frontiers in plant …, 2013 - frontiersin.org
Conserved non-coding sequences (CNS) are islands of non-coding sequence that, like
protein coding exons, show less divergence in sequence between related species than …

Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales

JA Fincher, DL Vera, DD Hughes, KM McGinnis… - Plant …, 2013 - academic.oup.com
The nucleosome is a fundamental structural and functional chromatin unit that affects nearly
all DNA-templated events in eukaryotic genomes. It is also a biochemical substrate for …

Epigenetic repression of male gametophyte-specific genes in the Arabidopsis sporophyte

RD Hoffmann, MG Palmgren - Molecular plant, 2013 - cell.com
Tissue formation, the identity of cells, and the functions they fulfill, are results of gene
regulation. The male gametophyte of plants, pollen, is outstanding in this respect as several …