Mechanisms and evolution of genomic imprinting in plants

Köhler, Claudia; Weinhofer-Molisch, I

doi:10.1038/hdy.2009.176

Cited by 77 publications

(59 citation statements)

References 62 publications

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“…Genomic imprinting has been discovered in both animals and plants (Kohler and Weinhofer-Molisch, 2010). In animals, genomic imprinting is only known in therian mammals, and most imprinted genes are expressed and imprinted in the brain and placenta (Pask, 2012;Keverne, 2013;Renfree et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Using next-generation RNA sequencing to identify imprinted genes

2014

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Genomic imprinting is manifested as differential allelic expression (DAE) depending on the parent-of-origin. The most direct way to identify imprinted genes is to directly score the DAE in a context where one can identify which parent transmitted each allele. Because many genes display DAE, simply scoring DAE in an individual is not sufficient to identify imprinted genes. In this paper, we outline many technical aspects of a scheme for identification of imprinted genes that makes use of RNA sequencing (RNA-seq) from tissues isolated from F1 offspring derived from the pair of reciprocal crosses. Ideally, the parental lines are from two inbred strains that are not closely related to each other. Aspects of tissue purity, RNA extraction, library preparation and bioinformatic inference of imprinting are all covered. These methods have already been applied in a number of organisms, and one of the most striking results is the evolutionary fluidity with which novel imprinted genes are gained and lost within genomes. The general methodology is also applicable to a wide range of other biological problems that require quantification of allele-specific expression using RNA-seq, such as cis-regulation of gene expression, X chromosome inactivation and random monoallelic expression.

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Section: Introductionmentioning

confidence: 99%

Using next-generation RNA sequencing to identify imprinted genes

2014

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“…Among Arabidopsis mutants in which AE has been observed in planta, Köhler et al (2003a) noted partly developed AE and embryo-like structure only in unpollinated MSI1/msi1 pistils cultured in vitro. Molecular research on the mechanisms controlling AE development in fie and met1 mutants of Arabidopsis strongly suggest that changes in genomic imprinting by DNA and histone methylation are essential for autonomous/apomictic development (Curtis and Grossniklaus, 2008;Köhler and Weinhofer-Molisch, 2010;Schmidt et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

THE INFLUENCE OF fie AND met1 MUTATIONS AND IN VITRO CULTURE CONDITIONS ON AUTONOMOUS ENDOSPERM DEVELOPMENT IN UNFERTILIZED OVULES OF ARABIDOPSIS THALIANA

Rojek¹,

Kuta²,

Kapusta³

et al. 2013

Acta Biologica Cracoviensia Series Botanica

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In flowering plants, seeds are produced both sexually (double fertilization is required) and asexually via apomixis (meiotic reduction and egg fertilization are omitted). An apomictic-like pattern of endosperm development in planta is followed by fis mutants of sexual Arabidopsis thaliana. In our experiments in planta, autonomous endosperm (AE) developed in met1 mutants. Furthermore we obtained autonomous endosperm formation in vitro not only in unfertilized ovules of fie mutants but also in wild genotypes (Col-0, MET1/MET1, FIE/FIE) and met1 mutants. AE induction and development occurred in all genotypes on the each of the media used and in every trial. The frequency of AE was relatively high (51.2% ovaries) and genotype-dependent. AE induced in vitro represents a more advanced stage of development than AE induced in fie mutants in planta. This was manifested by a high number of nuclei surrounded by cytoplasm and organized in nuclear cytoplasmic domains (NCDs), nodule formation, division into characteristic regions, and cellularization. The high frequency of AE observed in homozygous met1 (met1/met1) mutants probably is due to accumulation of hypomethylation as an effect of the met1 mutation and the in vitro conditions. AE development was most advanced in FIE/fie mutants. We suggest that changes in the methylation of one or several genes in the DNA of Arabidopsis genotypes caused by in vitro conditions resulted in AE induction and/or further AE development. K Ke ey y w wo or rd ds s: : Arabidopsis, fie and met1 mutants, apomixis, autonomous endosperm, in vitro culture, methylation.

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“…The observation that imprinted genes in flowering plants are located in the vicinity of transposable elements suggest that insertion of transposons is a prerequisite for imprinting of adjacent genes to control transposon activity in gametes, a hypothesis referred to as the defense hypothesis [7]. Liking imprinting to transposon activity, however, could not be accepted or justified unless solid evidence of parent of origin influence on transposon activity is clarified.…”

Section: Genomic Imprintingmentioning

confidence: 99%

Medical Genetics: Problems and Approaches

Salem¹

2013

Human Genet Embryol

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Radical prevention of genetic diseases and genetically-determined defects, through efficient prophylactic and effective curative approaches, represents the final goal of medical genetics. However, success in achieving this objective is totally dependent on comprehensive understanding of all structural and functional aspects of the human genome, transcriptome and proteome. A lot of perplexing phenomena and enigmatic problems in medical genetics, as well as in human genetics, are awaiting this understanding to be disclosed, e.g. genomic imprinting, spontaneous mutation, evolutionary adaptations, apoptosis, carcinogenesis, functions of pyknons, significance of transposons, roles of micro RNAs and many others. Although the human genome project is steadily progressing towards full structural characterization of the human genome, a parallel human genome function project is indispensable for finalizing our knowledge of our genetic constitution. Similarly, human proteome structure and human proteome function projects are necessary for the same purpose. The extreme complexity of the structure of the human genome and human proteome necessitates new accurate analytical methods to study and understand the behavior and capabilities of both of these structured biosystems. These methods should rely on laws of thermodynamics, principles of quantum mechanics and, even, concepts of nanosciences. It is hoped that these new research approaches will help in revealing and defining the underlying mechanisms responsible for maintaining integrity, stability and identity of the genome and proteome which represent prerequisite knowledge needed for controlling and directing the functions of both of them for attaining optimal health and welfare of human beings. The present article shortly addresses some of the aforementioned problems and tries to offer few hypotheses, interpretations and proposals that might prove helpful in this respect.

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Mechanisms and evolution of genomic imprinting in plants

Cited by 77 publications

References 62 publications

Using next-generation RNA sequencing to identify imprinted genes

Using next-generation RNA sequencing to identify imprinted genes

THE INFLUENCE OF fie AND met1 MUTATIONS AND IN VITRO CULTURE CONDITIONS ON AUTONOMOUS ENDOSPERM DEVELOPMENT IN UNFERTILIZED OVULES OF ARABIDOPSIS THALIANA

Medical Genetics: Problems and Approaches

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