Difference between revisions of "IC4R002-Epigenomic-2010-20937895"

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* '''Local DNA hypomethylation activates genes in rice endosperm'''
 
* '''Local DNA hypomethylation activates genes in rice endosperm'''
 
==The Background of This Project==
 
==The Background of This Project==
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* In eukaryotic nuclei, DNA associates with proteins to form chro- matin. It first wraps around core histones to form nucleosomes that, in turn, are often organized into higher-ordered structures. Chromatin structure plays an essential role in genome organization, transcriptional activity, and memory of developmental state (Bernstein et al., 2002). While all cells in an individual have the same nuclear genome, each cell type may harbor a distinct epigenome, which relies on heritable, often reversible, DNA methylation at cytosines and histone modifications (Richards, 1997).
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* Roughly 150 million y ago, flowering plants diverged to form the two dominant extant lineages, monocots and dicots (1). Arabidopsis thaliana, the preeminent plant genetic system, is a dicot, whereas cereal crops, such as rice, wheat, and maize, that feed much of the world are monocots. In both plant groups, pollen grains contain two sperm nuclei, one of which fertilizes a diploid central cell to give rise to triploid endosperm (2). A. thaliana endosperm is consumed by the developing embryo, whereas cereal endosperm persists and makes up the bulk of the mature seed— a developmental difference of particular practical importance (3). Developing seeds are genetic battlegrounds on multiple fronts: parents are proposed to be in conflict over resource allocation (2), whereas the embryo must repress parasitic transposable elements (TEs) to prevent damage to the genome.
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* Rice (Oryza sativa) is an important model species for cereals and other monocotyledonous plants. Two prominent features of most rice chromosomes are their clear organization into hetero- chromatic and euchromatic regions and the large amount of pericentromeric heterochromatin. For example, cytological studies using 49,6-diamidino-2-phenylindole staining indicate that approximately half of chromosomes 4 and 10 is the more densely stained heterochromatin, including their entire short arms and the proximal portions of their long arms (Cheng et al., 2001; Yan and Jiang, 2007). Global repression of transcription in rice heterochromatin has been observed, but the molecular basis is unknown (Jiao et al., 2005; Li et al., 2006). Completion of the rice genome sequence (International Rice Genome Sequencing Project, 2005) provides an unprecedented opportunity to examine epigenetic modifications comprehensively and correlate them with gene expression.
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* Most of our knowledge about DNA methylation in plant seeds is derived from A. thaliana. Processes involving genetic conflict tend to evolve rapidly (9), and therefore, methylation dynamics in cereal seeds may be quite different. Here, we use deep bisulfite se-
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quencing to examine DNA methylation in rice seeds. Wild-type rice endosperm methylation patterns—globally reduced non-CG methylation and local CG hypomethylation—resemble those of DME-deficient A. thaliana endosperm, a finding consistent with lack of DME in monocots. Reduced endosperm methylation is common in genes with preferential endosperm expression, in- dicating that demethylation is a major mechanism for gene activation in rice endosperm. Short TEs are hypermethylated at CHH sites in embryo, suggesting that endosperm demethylation func- tions to immunize the embryo against TEs through small RNAs.
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* '''In this project, the researchers describe high-resolution mapping of DNA methyla- tion and H3K4me2 and H3K4me3 patterns of rice (spp japonica cv Nipponbare) chromosomes 4 and 10 using tiling-path micro- arrays. We compare two developmental states: undifferentiated suspension-cultured cells and young light-grown shoots. The large heterochromatic regions on these chromosomes allow a genome-scale investigation of DNA methylation and histone modifications in heterochromatin. The completely sequenced rice centromeres of chromosomes 4 and 8 were also included in this analysis (Nagaki et al., 2004; Zhang et al., 2004). This indepth, genome-scale analysis provides unprecedented insights into the epigenetic signatures of the rice genome.'''
 
* '''In this project, the researchers describe high-resolution mapping of DNA methyla- tion and H3K4me2 and H3K4me3 patterns of rice (spp japonica cv Nipponbare) chromosomes 4 and 10 using tiling-path micro- arrays. We compare two developmental states: undifferentiated suspension-cultured cells and young light-grown shoots. The large heterochromatic regions on these chromosomes allow a genome-scale investigation of DNA methylation and histone modifications in heterochromatin. The completely sequenced rice centromeres of chromosomes 4 and 8 were also included in this analysis (Nagaki et al., 2004; Zhang et al., 2004). This indepth, genome-scale analysis provides unprecedented insights into the epigenetic signatures of the rice genome.'''
  

Revision as of 04:21, 22 June 2016

Project Title

  • Local DNA hypomethylation activates genes in rice endosperm

The Background of This Project

  • Roughly 150 million y ago, flowering plants diverged to form the two dominant extant lineages, monocots and dicots (1). Arabidopsis thaliana, the preeminent plant genetic system, is a dicot, whereas cereal crops, such as rice, wheat, and maize, that feed much of the world are monocots. In both plant groups, pollen grains contain two sperm nuclei, one of which fertilizes a diploid central cell to give rise to triploid endosperm (2). A. thaliana endosperm is consumed by the developing embryo, whereas cereal endosperm persists and makes up the bulk of the mature seed— a developmental difference of particular practical importance (3). Developing seeds are genetic battlegrounds on multiple fronts: parents are proposed to be in conflict over resource allocation (2), whereas the embryo must repress parasitic transposable elements (TEs) to prevent damage to the genome.
  • Most of our knowledge about DNA methylation in plant seeds is derived from A. thaliana. Processes involving genetic conflict tend to evolve rapidly (9), and therefore, methylation dynamics in cereal seeds may be quite different. Here, we use deep bisulfite se-

quencing to examine DNA methylation in rice seeds. Wild-type rice endosperm methylation patterns—globally reduced non-CG methylation and local CG hypomethylation—resemble those of DME-deficient A. thaliana endosperm, a finding consistent with lack of DME in monocots. Reduced endosperm methylation is common in genes with preferential endosperm expression, in- dicating that demethylation is a major mechanism for gene activation in rice endosperm. Short TEs are hypermethylated at CHH sites in embryo, suggesting that endosperm demethylation func- tions to immunize the embryo against TEs through small RNAs.


  • In this project, the researchers describe high-resolution mapping of DNA methyla- tion and H3K4me2 and H3K4me3 patterns of rice (spp japonica cv Nipponbare) chromosomes 4 and 10 using tiling-path micro- arrays. We compare two developmental states: undifferentiated suspension-cultured cells and young light-grown shoots. The large heterochromatic regions on these chromosomes allow a genome-scale investigation of DNA methylation and histone modifications in heterochromatin. The completely sequenced rice centromeres of chromosomes 4 and 8 were also included in this analysis (Nagaki et al., 2004; Zhang et al., 2004). This indepth, genome-scale analysis provides unprecedented insights into the epigenetic signatures of the rice genome.

Labs working on this Project

  • Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720

Corresponding Author

  • Daniel Zilberman (E-mail: danielz@berkeley.edu.)
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