Difference between revisions of "IC4R009-Epigenomic-2013-23562565"

Revision as of 13:54, 27 July 2016

Rice is one of the most important food crops in the world and has been established as a model for plant genome study. Genomic sequences of two of the three subspecies of rice are available [1,2]. With its accurate genomic sequences, abundant genetic resources and availability of highly efficient reverse genetic tools, rice has become a model for cereal epigenomics and epigenetics as well. Epigenomics refers to genome-wide chromatin modification profiles mainly including DNA methylation and histone modifications, which control chromatin accessibility to DNA replication and repair and transcription machineries, thereby modulating the genome activities. Epigenetics studies mechanisms that are involved in variation and inheritance of epigenomic modifications. A wealth of trait variations among different rice species, subspecies and cultivars related to epigenomic variations, which may have been accumulated during the long history of rice evolution, domestication and selection, provides unique opportunities for crop epigenetic study. The researchers summarize and discuss features of rice epigenomes and epigenetic variations and its possible implication in heterosis and genetic improvement.

DNA cytosine methylation is a hallmark of inactivation of repetitive sequences and transposable elements in plants and is associated with heterochromatin formation. DNA cytosine methylation in plants occurs in CG, CHG and CHH contexts (where H is A, C or T). Extensive genome-wide DNA methylation data have been recently generated in rice. Genome-wide histone modifications (e.g. H3K4me2 H3K4me3, H3K9ac, H4K12ac, H3K27me3 and H3K36me3) have been defined in rice seedlings.

The chromatin modification machinery is generally conserved between rice and other plant species (www.chromdb.org). Analysis of loss-of-function mutants and RNAi or over-expression transgenic plants revealed that rice chromatin regulators are involved in various developmental pathways and in diverse responses to environment (Table 1).

Table 1 Chromatin modifiers reported in rice.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
Institut de Biologie des Plantes, Universite´ Paris sud, 91405 Orsay, France

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 ==Research Findings==
+* DNA cytosine methylation is a hallmark of inactivation of repetitive sequences and transposable elements in plants and is associated with heterochromatin formation. DNA cytosine methylation in plants occurs in CG, CHG and CHH contexts (where H is A, C or T). Extensive genome-wide DNA methylation data have been recently generated in rice. Genome-wide histone modifications (e.g. H3K4me2 H3K4me3, H3K9ac, H4K12ac, H3K27me3 and H3K36me3) have been defined in rice seedlings.
+* The chromatin modification machinery is generally conserved between rice and other plant species (www.chromdb.org). Analysis of loss-of-function mutants and RNAi or over-expression transgenic plants revealed that rice chromatin regulators are involved in various developmental pathways and in diverse responses to environment (Table 1).
+[[File:IC4R009-Epigenomic-2013-23562565-t1.png |center |thumb |800px |'''Table 1 Chromatin modifiers reported in rice.''']]
 ==Labs working on this Project==