IC4R002-Epigenomic-2010-20937895 - Revision history

Xysj1990: /* Plant Materials & Treatment */

2016-06-22T07:36:56Z

‎Plant Materials & Treatment

Xysj1990: /* Plant Materials & Treatment */

2016-06-22T07:36:44Z

‎Plant Materials & Treatment

Xysj1990: /* The Background of This Project */

2016-06-22T07:35:43Z

‎The Background of This Project

Xysj1990: /* The Background of This Project */

2016-06-22T07:35:31Z

‎The Background of This Project

Xysj1990: /* Research Findings */

2016-06-22T07:32:00Z

‎Research Findings

Xysj1990: /* Plant Materials & Treatment */

2016-06-22T07:30:25Z

‎Plant Materials & Treatment

Xysj1990 at 04:51, 22 June 2016

2016-06-22T04:51:34Z

Xysj1990: /* The Background of This Project */

2016-06-22T04:22:19Z

‎The Background of This Project

Xysj1990: /* The Background of This Project */

2016-06-22T04:21:52Z

‎The Background of This Project

Xysj1990 at 04:20, 22 June 2016

2016-06-22T04:20:18Z

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 ==Plant Materials & Treatment==
-* Our custom NimbleGen microarray consists of 2,154,325 45-bp to 85-bp probes that are tiled across the entire sequenced rice genome (Oryza sativa ssp. japonica cultivar Nipponbare, Michigan State University release 5, http://rice.plantbiology.msu.edu) without repeat masking. Each probe is se- lected to have a predicted melting temperature close to 76 °C. The array design is deposited in Gene Expression Omnibus (GEO) with accession number GSE22591. cDNA samples were prepared and labeled as described (24), with hybridization and data extraction preformed at the Fred Hutchinson Cancer Research Center (www.fhcrc.org) DNA array facility (25). Two independent cDNA samples for each tissue were labeled with Cy5 and cohybridized with sonicated genomic DNA labeled with Cy3. The two replicates were averaged, and outlier probes were removed by median smoothing (three-probe window). An expression score for each gene was calculated by averaging the signal of all probes within the gene’s exons.
+* Our custom NimbleGen microarray consists of 2,154,325 45-bp to 85-bp probes that are tiled across the entire sequenced rice genome (Oryza sativa ssp. japonica cultivar Nipponbare, Michigan State University release 5, http://rice.plantbiology.msu.edu) without repeat masking. Each probe is se- lected to have a predicted melting temperature close to 76 °C. The array design is deposited in Gene Expression Omnibus (GEO) with accession number GSE22591. cDNA samples were prepared and labeled as described (24), with hybridization and data extraction preformed at the Fred Hutchinson Cancer Research Center (www.fhcrc.org) DNA array facility (25). Two independent cDNA samples for each tissue were labeled with Cy5 and cohybridized with sonicated genomic DNA labeled with Cy3. The two replicates were averaged, and outlier probes were removed by median smoothing (three-probe window). An expression score for each gene was calculated by averaging the signal of all probes within the gene’s exons.<br><br>
 [[File:IC4R002-Epigenomic-2010-20937895-2.png |center |thumb |1000px |'''Figure 2. MITEs are the predominant target of CHH methylation. (A) Box plots showing methylation levels of different TE classes in rice embryo (Em), shoot (St), root (Rt), and endosperm (En). Each box encloses the middle 50% of the distribution, with the horizontal line marking the median. The lines extending from each box mark the minimum and maximum values that fall within 1.5 times the height of the box. MITE mean length = 189 bp; maximum length = 500 bp. SINE mean length = 141 bp; maximum length = 487 bp. LTR mean length = 855 bp; maximum length = 11 kb. (B–D) Rice genes were aligned as in Fig. 1, and TE frequency (B and C) or average methylation levels (D) for each 100-bp interval are plotted. In C and D, genes were grouped into quintiles by transcription.''']]<br>

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 ==Plant Materials & Treatment==
 * Our custom NimbleGen microarray consists of 2,154,325 45-bp to 85-bp probes that are tiled across the entire sequenced rice genome (Oryza sativa ssp. japonica cultivar Nipponbare, Michigan State University release 5, http://rice.plantbiology.msu.edu) without repeat masking. Each probe is se- lected to have a predicted melting temperature close to 76 °C. The array design is deposited in Gene Expression Omnibus (GEO) with accession number GSE22591. cDNA samples were prepared and labeled as described (24), with hybridization and data extraction preformed at the Fred Hutchinson Cancer Research Center (www.fhcrc.org) DNA array facility (25). Two independent cDNA samples for each tissue were labeled with Cy5 and cohybridized with sonicated genomic DNA labeled with Cy3. The two replicates were averaged, and outlier probes were removed by median smoothing (three-probe window). An expression score for each gene was calculated by averaging the signal of all probes within the gene’s exons.
 ==Research Findings==
 * To learn how cytosine methylation regulates cereal seed genomes, we quantified methylation in rice embryos, endosperm, and seedling shoots and roots by sequencing bisulfite-converted genomic DNA (bisulfite treatment converts unmethylated cytosine to uracil) to 11- to 15-fold coverage of the nuclear genome. The aggregate methylation patterns in all tissues are very similar to those of mature rice leaves (8) as well as those of A. thaliana (6)—CG methylation is common in gene bodies, except near the transcription start and termination sites, whereas TEs are methylated in all sequence contexts (Fig. 1). Overall CG methyl- ation patterns and levels are virtually indistinguishable between embryos, shoots, roots, and leaves (Fig. 1 A and B). CHG methylation increases modestly with age of the tissue: lowest in em- bryos, higher in young shoots and roots, and highest in mature leaves (Fig. 1 C and D), consistent with reports of increased methylation in older tissues of maize and petunia (10, 11). CHH methylation is also higher in leaves than in seedling tissues (Fig. 1 E and F).

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 ==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. In this project, the researchers use deep bisulfite sequencing 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.
+* 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. In this project, the researchers use deep bisulfite sequencing 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.<br><br>
 [[File:IC4R002-Epigenomic-2010-20937895-1.png |center |thumb |1000px |'''Figure 1.Patterns of DNA methylation in rice tissues. Rice genes (A, C, and E) or TEs (B, D, and F) were aligned at the 5′ end (Left) or the 3′ end (Right), and average methylation levels for each 100-bp interval are plotted. The dashed line represents the point of alignment.''']]

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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.
 * 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. In this project, the researchers use deep bisulfite sequencing 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.
 ==Plant Materials & Treatment==
 * Our custom NimbleGen microarray consists of 2,154,325 45-bp to 85-bp probes that are tiled across the entire sequenced rice genome (Oryza sativa ssp. japonica cultivar Nipponbare, Michigan State University release 5, http://rice.plantbiology.msu.edu) without repeat masking. Each probe is se- lected to have a predicted melting temperature close to 76 °C. The array design is deposited in Gene Expression Omnibus (GEO) with accession number GSE22591. cDNA samples were prepared and labeled as described (24), with hybridization and data extraction preformed at the Fred Hutchinson Cancer Research Center (www.fhcrc.org) DNA array facility (25). Two independent cDNA samples for each tissue were labeled with Cy5 and cohybridized with sonicated genomic DNA labeled with Cy3. The two replicates were averaged, and outlier probes were removed by median smoothing (three-probe window). An expression score for each gene was calculated by averaging the signal of all probes within the gene’s exons.

@@ Line 8: / Line 8: @@
 ==Research Findings==
 * To learn how cytosine methylation regulates cereal seed genomes, we quantified methylation in rice embryos, endosperm, and seedling shoots and roots by sequencing bisulfite-converted genomic DNA (bisulfite treatment converts unmethylated cytosine to uracil) to 11- to 15-fold coverage of the nuclear genome. The aggregate methylation patterns in all tissues are very similar to those of mature rice leaves (8) as well as those of A. thaliana (6)—CG methylation is common in gene bodies, except near the transcription start and termination sites, whereas TEs are methylated in all sequence contexts (Fig. 1). Overall CG methyl- ation patterns and levels are virtually indistinguishable between embryos, shoots, roots, and leaves (Fig. 1 A and B). CHG methylation increases modestly with age of the tissue: lowest in em- bryos, higher in young shoots and roots, and highest in mature leaves (Fig. 1 C and D), consistent with reports of increased methylation in older tissues of maize and petunia (10, 11). CHH methylation is also higher in leaves than in seedling tissues (Fig. 1 E and F).
 ==Labs working on this Project==

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 * '''Local DNA hypomethylation activates genes in rice endosperm'''
 ==The Background of This Project==
-* 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).
+* 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.
-* 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.
+* 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-
 * '''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.'''

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 ==Project Title==
-* '''High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression'''
+* '''Local DNA hypomethylation activates genes in rice endosperm'''
 ==The Background of This Project==
 * 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).
@@ Line 7: / Line 7: @@
 ==Labs working on this Project==
+* Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
 ==Corresponding Author==
-* '''Xing Wang Deng''' (E-mail: xingwang.deng@yale.edu)
+* '''Daniel Zilberman''' (E-mail: danielz@berkeley.edu.)