Methodological problems with evaluating change efficiency

Motivation: Changes result from a turbulent environment and internal situation of an organization. Rarely do changes happen spontaneously, usually they stem from decisions consciously shaped and taken by the management. Both the reasons as well as consequences of changes appear on multiple grounds and areas, often strongly interrelated. This leads to far-reaching consequences, mainly difficulties in practical operations as well as consequences for studies, analyses and related scientific generalizations and the conclusion-drawing process in both domains.Aim: Purpose of this article is to present and make a critical analysis of the existing achievements in the area of evaluating change efficiency, and indicate opportunities and difficulties in formulating new, in particular synthetic, indicators of change efficiency. Methodology applied in this paper is deductive and based on collected data and their critical analysis.Results: Managers need synthetic measures that are hard to develop. Various methods may be used in order to do it, starting from simple and complex point scales and ending up with methods applied in other sciences, e.g. the Geneva method or its variations applied to evaluate the standard of living and development. Still this requires the isolation of main analytical measures, their upper and lower thresholds, in subsequent change or process areas, and the application of statistical methods to calculate change status or effect. Such action requires longer change planning and preparation, readiness on the part of the managerial staff, and continuous monitoring with active participation of leaders and change managers

Identification of genes preventing transgenerational transmission of stress-induced epigenetic states.

Examples of transgenerational transmission of environmentally induced epigenetic traits remain rare and disputed. Abiotic stress can release the transcription of epigenetically suppressed transposons and, noticeably, this activation is only transient. Therefore, it is likely that mechanisms countering the mitotic and meiotic inheritance of stress-triggered chromatin changes must exist but are undefined. To reveal these mechanisms, we screened for Arabidopsis mutants impaired in the resetting of stress-induced loss of epigenetic silencing and found that two chromatin regulators, Decrease in DNA methylation1 (DDM1) and Morpheus' Molecule1 (MOM1), act redundantly to restore prestress state and thus erase "epigenetic stress memory". In ddm1 mutants, stress hyperactivates heterochromatic transcription and transcription persists longer than in the wild type. However, this newly acquired state is not transmitted to the progeny. Strikingly, although stress-induced transcription in mom1 mutants is as rapidly silenced as in wild type, in ddm1 mom1 double mutants, transcriptional signatures of stress are able to persist and are found in the progeny of plants stressed as small seedlings. Our results reveal an important, previously unidentified function of DDM1 and MOM1 in rapid resetting of stress induced epigenetic states, and therefore also in preventing their mitotic propagation and transgenerational inheritance.This work was supported by grants from the Swiss National Science Foundation (31003A-125005), the European Commission through the AENEAS collaborative project (FP7 226477), the Gatsby Charitable Foundation, and the European Research Council.This is the final version of the article. It first appeared from PNAS via http://dx.doi.org/10.1073/pnas.140227511

DNA methylation and epigenetic inheritance during plant gametogenesis

In plants, newly acquired epigenetic states of transcriptional gene activity are readily transmitted to the progeny. This is in contrast to mammals, where only rare cases of transgenerational inheritance of new epigenetic traits have been reported (FASEB J 12:949-957, 1998; Nat Genet 23:314-318, 1999; Proc Natl Acad Sci U S A 100:2538-2543, 2003). Epigenetic inheritance in plants seems to rely on cytosine methylation maintained through meiosis and postmeiotic mitoses, giving rise to gametophytes. In particular, maintenance of CpG methylation (mCpG) appears to play a central role, guiding the distribution of other epigenetic signals such as histone H3 methylation and non-CpG DNA methylation. The evolutionarily conserved DNA methyltransferase MET1 is responsible for copying mCpG patterns through DNA replication in the gametophytic phase. The importance of gametophytic MET1 activity is illustrated by the phenotypes of met1 mutants that are severely compromised in the accuracy of epigenetic inheritance during gametogenesis. This includes elimination of imprinting at paternally silent loci such as FWA or MEDEA (MEA). The importance of DNA methylation in gametophytic imprinting has been reinforced by the discovery of DEMETER (DME), encoding putative DNA glycosylase involved in the removal of mC. DME opposes transcriptional silencing associated with imprinting activities of the MEA/FIE polycomb group comple

Methodological problems with evaluating change efficiency

Motivation: Changes result from a turbulent environment and internal situation of an organization. Rarely do changes happen spontaneously, usually they stem from decisions consciously shaped and taken by the management. Both the reasons as well as consequences of changes appear on multiple grounds and areas, often strongly interrelated. This leads to far-reaching consequences, mainly difficulties in practical operations as well as consequences for studies, analyses and related scientific generalizations and the conclusion-drawing process in both domains.Aim: Purpose of this article is to present and make a critical analysis of the existing achievements in the area of evaluating change efficiency, and indicate opportunities and difficulties in formulating new, in particular synthetic, indicators of change efficiency. Methodology applied in this paper is deductive and based on collected data and their critical analysis.Results: Managers need synthetic measures that are hard to develop. Various methods may be used in order to do it, starting from simple and complex point scales and ending up with methods applied in other sciences, e.g. the Geneva method or its variations applied to evaluate the standard of living and development. Still this requires the isolation of main analytical measures, their upper and lower thresholds, in subsequent change or process areas, and the application of statistical methods to calculate change status or effect. Such action requires longer change planning and preparation, readiness on the part of the managerial staff, and continuous monitoring with active participation of leaders and change managers.</p

Epigenetic memory in plants

Epigenetics refers to heritable changes in patterns of gene expression that occur without alterations in DNA sequence. The epigenetic mechanisms involve covalent modifications of DNA and histones, which affect transcriptional activity of chromatin. Since chromatin states can be propagated through mitotic and meiotic divisions, epigenetic mechanisms are thought to provide heritable ‘cellular memory’. Here, we review selected examples of epigenetic memory in plants and briefly discuss underlying mechanisms.This work was supported by the Gatsby Charitable Foundation and the European Research Council.This is the author accepted manuscript. The final version is available from EMBO Press via http://dx.doi.org/10.15252/embj.20148888

Epigenetic memory in plants.

Epigenetics refers to heritable changes in patterns of gene expression that occur without alterations in DNA sequence. The epigenetic mechanisms involve covalent modifications of DNA and histones, which affect transcriptional activity of chromatin. Since chromatin states can be propagated through mitotic and meiotic divisions, epigenetic mechanisms are thought to provide heritable 'cellular memory'. Here, we review selected examples of epigenetic memory in plants and briefly discuss underlying mechanisms.This work was supported by the Gatsby Charitable Foundation and the European Research Council.This is the author accepted manuscript. The final version is available from EMBO Press via http://dx.doi.org/10.15252/embj.20148888

Specific suppression of long terminal repeat retrotransposon mobilization in plants

The tissue culture passage necessary for the generation of transgenic plants induces genome instability. This instability predominantly involves the uncontrolled mobilization of LTR retrotransposons (LTR-TEs), which are the most abundant class of mobile genetic elements in plant genomes. Here, we demonstrate that in conditions inductive for high LTR-TE mobilization, like abiotic stress in Arabidopsis (Arabidopsis thaliana) and callus culture in rice (Oryza sativa), application of the reverse transcriptase (RT) inhibitor known as Tenofovir substantially affects LTR-TE RT activity without interfering with plant development. We observed that Tenofovir reduces extrachromosomal DNA accumulation and prevents new genomic integrations of the active LTR-TE ONSEN in heat-stressed Arabidopsis seedlings, and transposons of O. sativa 17 and 19 (Tos17 and Tos19) in rice calli. In addition, Tenofovir allows the recovery of plants free from new LTR-TE insertions. We propose the use of Tenofovir as a tool for studies of LTR-TE transposition and for limiting genetic instabilities of plants derived from tissue culture.</p

Virus-mediated export of chromosomal DNA in plants

Viruses are potential vectors for horizontal gene transfer. Here, studying viral infection of sugar beet plants, the authors report the generation of virus-host circular DNA hybrids and provide a picture of the initial steps in virus-mediated horizontal transfer of chromosomal DNA between plant species

Environmental and epigenetic regulation of Rider retrotransposons in tomato.

Transposable elements in crop plants are the powerful drivers of phenotypic variation that has been selected during domestication and breeding programs. In tomato, transpositions of the LTR (long terminal repeat) retrotransposon family Rider have contributed to various phenotypes of agronomical interest, such as fruit shape and colour. However, the mechanisms regulating Rider activity are largely unknown. We have developed a bioinformatics pipeline for the functional annotation of retrotransposons containing LTRs and defined all full-length Rider elements in the tomato genome. Subsequently, we showed that accumulation of Rider transcripts and transposition intermediates in the form of extrachromosomal DNA is triggered by drought stress and relies on abscisic acid signalling. We provide evidence that residual activity of Rider is controlled by epigenetic mechanisms involving siRNAs and the RNA-dependent DNA methylation pathway. Finally, we demonstrate the broad distribution of Rider-like elements in other plant species, including crops. Our work identifies Rider as an environment-responsive element and a potential source of genetic and epigenetic variation in plants