Reprogramming the epigenome during germline and seed development

Brown University, Department of Molecular Biology, Cell Biology, and Biochemistry, Providence, RI 02912, USA.
Genome biology (Impact Factor: 10.47). 09/2009; 10(8):232. DOI: 10.1186/gb-2009-10-8-232
Source: PubMed

ABSTRACT Gene silencing by DNA methylation and small RNAs is globally reconfigured during gametogenesis in Arabidopsis, affecting transposon activity, gene regulation and development.

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    • "For example, the proteomic study of post-translational modification, phosphorylation, and ubiquitination, etc., during the process is still limited (Mayank et al., 2012). In addition, epigenetic regulation by small non-coding RNAs and modification of DNA and histone has emerged for with roles in male reproductive system development (Johnson and Bender, 2009; Slotkin et al., 2009). However, with the great improvements in RNA and protein detection technology, such as single molecular sequencing (Fang et al., 2012) and label-free MS (Levin and Bahn, 2010), and combined with laser capture microdissection technology, we would have the ability to achieve more subtle spatio-temporal expression profiles with less tissue. "
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    ABSTRACT: Rice is one of the most important model crop plants whose heterosis has been well-exploited in commercial hybrid seed production via a variety of types of male-sterile lines. Hybrid rice cultivation area is steadily expanding around the world, especially in Southern Asia. Characterization of genes and proteins related to male sterility aims to understand how and why the male sterility occurs, and which proteins are the key players for microspores abortion. Recently, a series of genes and proteins related to cytoplasmic male sterility (CMS), photoperiod-sensitive male sterility, self-incompatibility, and other types of microspores deterioration have been characterized through genetics or proteomics. Especially the latter, offers us a powerful and high throughput approach to discern the novel proteins involving in male-sterile pathways which may help us to breed artificial male-sterile system. This represents an alternative tool to meet the critical challenge of further development of hybrid rice. In this paper, we reviewed the recent developments in our understanding of male sterility in rice hybrid production across gene, protein, and integrated network levels, and also, present a perspective on the engineering of male-sterile lines for hybrid rice production.
    Frontiers in Plant Science 04/2013; 4:92. DOI:10.3389/fpls.2013.00092 · 3.95 Impact Factor
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    • "Alternatively, parental “mismatch” could be due to sequence divergence between TEs in different lineages, whereby small RNAs generated from one lineage may fail to recognize or to effectively interact with target sequences from the alternative lineage, due to base-pairing mismatches (Figure 2(b)). Although there is no direct empirical evidence, it has been suggested that sequence specificity plays an important role in TE suppression [38, 39] and the proteins that interact with small RNAs rely on sequence complementarity to target TEs for methylation and silencing [40]. Given this, transcripts from one TE copy may not be able to target slightly different TE copies, although currently it is not clear how much sequence divergence must occur before TE copies can no longer suppress one another. "
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    ABSTRACT: New models of TE repression in plants (specifically Arabidopsis) have suggested specific mechanisms by which TE misregulation in hybrids might result in the expression of hybrid inviability. If true, these models suggest as yet undescribed consequences for (1) mechanistic connections between hybrid problems expressed at different postzygotic stages (e.g., inviability versus sterility), (2) the predicted strength, stage, and direction of isolation between diverging lineages that differ in TE activity, and (3) the association between species attributes that influence TE dynamics (e.g., mode of reproduction, geographical structure) and the rate at which they could accumulate incompatibilities. In this paper, we explore these implications and outline future empirical directions for generating data necessary to evaluate them.
    02/2012; 2012:698198. DOI:10.1155/2012/698198
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    • "In contrast, female catkins did not show a distinctive pattern of DNA methylation or associated gene expression, even though genome-wide demethylation has been observed in endosperm relative to embryo tissue [58]. Active demethylation is brought about by DEMETER, which is expressed specifically in the central cell of the female gametophye and removes methylated cytosines via a mechanism involving single-strand break repair [63,64]. We believe the difference between male and female catkins was mainly because we collected female catkins during early pollen release, well before endosperm and embryo development was likely to have begun on a large scale. "
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    ABSTRACT: DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood. We surveyed DNA methylation from seven distinct tissue types (vegetative bud, male inflorescence [catkin], female catkin, leaf, root, xylem, phloem) in the reference tree species black cottonwood (Populus trichocarpa). Using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq), we mapped a total of 129,360,151 36- or 32-mer reads to the P. trichocarpa reference genome. We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data. Qualitative DNA methylation differences among tissues were obvious on a chromosome scale. Methylated genes had lower expression than unmethylated genes, but genes with methylation in transcribed regions ("gene body methylation") had even lower expression than genes with promoter methylation. Promoter methylation was more frequent than gene body methylation in all tissues except male catkins. Male catkins differed in demethylation of particular transposable element categories, in level of gene body methylation, and in expression range of genes with methylated transcribed regions. Tissue-specific gene expression patterns were correlated with both gene body and promoter methylation. We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined. In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.
    BMC Genomics 01/2012; 13(1):27. DOI:10.1186/1471-2164-13-27 · 4.04 Impact Factor
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