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Epigenetics and Genomics
New and old papers of epigenetics and genomics
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ScienceDirect.com - Cell - Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA

ScienceDirect.com - Cell - Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA | Epigenetics and Genomics | Scoop.it

Epigenetic inheritance is more widespread in plants than in mammals, in part because mammals erase epigenetic information by germline reprogramming. We sequenced the methylome of three haploid cell types from developing pollen: the sperm cell, the vegetative cell, and their precursor, the postmeiotic microspore, and found that unlike in mammals the plant germline retains CG and CHG DNA methylation. However, CHH methylation is lost from retrotransposons in microspores and sperm cells and restored by de novo DNA methyltransferase guided by 24 nt small interfering RNA, both in the vegetative nucleus and in the embryo after fertilization. In the vegetative nucleus, CG methylation is lost from targets of DEMETER (DME), REPRESSOR OF SILENCING 1 (ROS1), and their homologs, which include imprinted loci and recurrent epialleles that accumulate corresponding small RNA and are premethylated in sperm. Thus genome reprogramming in pollen contributes to epigenetic inheritance, transposon silencing, and imprinting, guided by small RNA.

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Transgenerational inheritance of induced changes in the epigenetic state of chromatin in plants

Transgenerational inheritance of induced changes in the epigenetic state of chromatin in plants | Epigenetics and Genomics | Scoop.it

There is growing experimental evidence from both animals and plants that changes in the environment can have profound effects on the epigenetic state of chromatin in nuclei. The epigenetic state of chromatin and the cell-specific transcription profile of genes are mitotically stable and, sometimes, can be transmitted across generations. Plants often show stable transgenerational inheritance of induced alterations of epigenetic states that are associated with morphologically or physiologically distinctive phenotypes. This pattern of inheritance may be due to the fact that germ cells produced by terminal differentiation and to the absence of appreciable epigenetic reprogramming during the life cycle. Recent advances in mass sequencing technology have accelerated the decoding of the epigenomes of various tissues and cell types and provided new insights into the dynamics of epigenetic changes during the plant life cycle and in response to environmental challenges. As plants have a sessile nature, the epigenetic regulation of genes and transposable elements in response to environmental stresses might be crucial for the generation and inheritance of phenotypic variations in plants in natural populations.

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Chromatin remodeling: Activating ACL1 with a little help from 'friends'

Chromatin remodeling: Activating ACL1 with a little help from 'friends' | Epigenetics and Genomics | Scoop.it
Chromatin remodeling —- the packaging and unpackaging of genomic DNA and its associated proteins —- regulates a host of fundamental cellular processes including gene transcription, DNA repair, programmed cell death as well as cell fate.
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Auxin and Epigenetic Regulation of SKP2B, an F-Box That Represses Lateral Root Formation

Auxin and Epigenetic Regulation of SKP2B, an F-Box That Represses Lateral Root Formation | Epigenetics and Genomics | Scoop.it

In plants, lateral roots originate from pericycle founder cells that are specified at regular intervals along the main root. Here, we show that Arabidopsis (Arabidopsis thaliana) SKP2B (for S-Phase Kinase-Associated Protein2B), an F-box protein, negatively regulates cell cycle and lateral root formation as it represses meristematic and founder cell divisions. According to its function, SKP2B is expressed in founder cells, lateral root primordia and the root apical meristem. We identified a novel motif in the SKP2B promoter that is required for its specific root expression and auxin-dependent induction in the pericycle cells. Next to a transcriptional control by auxin, SKP2B expression is regulated by histone H3.1/H3.3 deposition in a CAF-dependent manner. The SKP2B promoter and the 5′ end of the transcribed region are enriched in H3.3, which is associated with active chromatin states, over H3.1. Furthermore, the SKP2B promoter is also regulated by H3 acetylation in an auxin- and IAA14-dependent manner, reinforcing the idea that epigenetics represents an important regulatory mechanism during lateral root formation.

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ScienceDirect.com - Trends in Genetics - Epigenetics and crop improvement

ScienceDirect.com - Trends in Genetics - Epigenetics and crop improvement | Epigenetics and Genomics | Scoop.it

There is considerable excitement about the potential for epigenetic information to contribute to heritable variation in many species. Our understanding of the molecular mechanisms of epigenetic inheritance is rapidly growing, and it is now possible to profile the epigenome at high resolution. Epigenetic information plays a role in developmental gene regulation, response to the environment, and in natural variation of gene expression levels. Because of these central roles, there is the potential for epigenetics to play a role in crop improvement strategies including the selection for favorable epigenetic states, creation of novel epialleles, and regulation of transgene expression. In this review we consider the potential, and the limitations, of epigenetic variation in crop improvement.

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