Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming?

Gehring, Mary

doi:10.1111/nph.15856

Cited by 72 publications

(66 citation statements)

References 51 publications

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“…Another striking insight from the 5mC divergence patterns is that the increase in D is particularly pronounced for context CG but appears to be low, or even absent, at CHG and CHH loci. Similar observations have previously led to the hypothesis that the inheritance of spontaneous epimutations may be restricted to CG dinucleotides [11,12], perhaps as a consequence of the preferential reinforcement of CHG and CHH methylation during sexual reproduction [38,39]. Using heuristic arguments, it had been further suggested that CG epimutations accumulate neutrally, at least at the level of individual cytosines, meaning that 5mC gains and loss in this context are under no selective constraints [12].…”

Section: Spontaneous Epimutations Accumulate Neutrally Over Generationsmentioning

confidence: 56%

AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

et al. 2020

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Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stochastic events using pedigree-based DNA methylation data as input. We demonstrate how AlphaBeta can be employed to study transgenerationally heritable epimutations in clonal or sexually derived mutation accumulation lines, as well as somatic epimutations in long-lived perennials. Application of our method to published and new data reveals that spontaneous epimutations accumulate neutrally at the genome-wide scale, originate mainly during somatic development and that they can be used as a molecular clock for age-dating trees.

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Section: Spontaneous Epimutations Accumulate Neutrally Over Generationsmentioning

confidence: 56%

AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

et al. 2020

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“…Epigenetic regulatory processes which modify gene activity based on DNA methylation, histone modifications, and modulation of chromatin structure are involved in controlling diverse developmental and cell fate decisions. Epigenetic regulation is increasingly recognized to be important during plant germline development [129]. While long non-coding RNAs can act in modulating DNA methylation and histone modifications to regulate gene activity [130], future investigations are required to elucidate their specific importance during reproductive development in detail.…”

Section: Epigenetic Regulatory Pathways Are Involved In Regulation Ofmentioning

confidence: 99%

Controlling Apomixis: Shared Features and Distinct Characteristics of Gene Regulation

Schmidt

2020

Genes

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In higher plants, sexual and asexual reproduction through seeds (apomixis) have evolved as alternative strategies. As apomixis leads to the formation of clonal offspring, its great potential for agricultural applications has long been recognized. However, the genetic basis and the molecular control underlying apomixis and its evolutionary origin are to date not fully understood. Both in sexual and apomictic plants, reproduction is tightly controlled by versatile mechanisms regulating gene expression, translation, and protein abundance and activity. Increasing evidence suggests that interrelated pathways including epigenetic regulation, cell-cycle control, hormonal pathways, and signal transduction processes are relevant for apomixis. Additional molecular mechanisms are being identified that involve the activity of DNA- and RNA-binding proteins, such as RNA helicases which are increasingly recognized as important regulators of reproduction. Together with other factors including non-coding RNAs, their association with ribosomes is likely to be relevant for the formation and specification of the apomictic reproductive lineage. Subsequent seed formation appears to involve an interplay of transcriptional activation and repression of developmental programs by epigenetic regulatory mechanisms. In this review, insights into the genetic basis and molecular control of apomixis are presented, also taking into account potential relations to environmental stress, and considering aspects of evolution.

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“…Meiotic transmission of epigenetic markings resulting from environmental cues provides a mechanism through which plastic responses to the environment can be transmitted from one generation to the next (transgenerational plasticity [ 6 ]). While plant germline cells do undergo a number of rounds of epigenetic reprogramming prior to the formation of a new seed [ 7 ], it is clear that environmental conditions experienced by parents can alter phenotypes [ 8 , 9 , 10 , 11 ], epigenetic profiles [ 4 , 10 , 12 , 13 ] and gene expression [ 14 , 15 , 16 ] in the next generation. Importantly, autocorrelation between offspring and parent environment can favor mechanisms that establish such patterns of transgenerational plasticity [ 17 , 18 ], perhaps leading to natural selection that either favors or disfavors this transmission depending on local environmental patterns [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

Mimulus sRNAs Are Wound Responsive and Associated with Transgenerationally Plastic Genes but Rarely Both

Colicchio

Kelly

Hileman

2020

IJMS

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Organisms alter development in response to environmental cues. Recent studies demonstrate that they can transmit this plasticity to progeny. While the phenotypic and transcriptomic evidence for this “transgenerational plasticity” has accumulated, genetic and developmental mechanisms remain unclear. Plant defenses, gene expression and DNA methylation are modified as an outcome of parental wounding in Mimulus guttatus. Here, we sequenced M. guttatus small RNAs (sRNA) to test their possible role in mediating transgenerational plasticity. We sequenced sRNA populations of leaf-wounded and control plants at 1 h and 72 h after damage and from progeny of wounded and control parents. This allowed us to test three components of an a priori model of sRNA mediated transgenerational plasticity—(1) A subset of sRNAs will be differentially expressed in response to wounding, (2) these will be associated with previously identified differentially expressed genes and differentially methylated regions and (3) changes in sRNA abundance in wounded plants will be predictive of sRNA abundance, DNA methylation, and/or gene expression shifts in the following generation. Supporting (1) and (2), we found significantly different sRNA abundances in wounded leaves; the majority were associated with tRNA fragments (tRFs) rather than small-interfering RNAs (siRNA). However, siRNAs responding to leaf wounding point to Jasmonic Acid mediated responses in this system. We found that different sRNA classes were associated with regions of the genome previously found to be differentially expressed or methylated in progeny of wounded plants. Evidence for (3) was mixed. We found that non-dicer sRNAs with increased abundance in response to wounding tended to be nearby genes with decreased expression in the next generation. Counter to expectations, we did not find that siRNA responses to wounding were associated with gene expression or methylation changes in the next generation and within plant and transgenerational sRNA plasticity were negatively correlated.

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Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming?

Cited by 72 publications

References 51 publications

AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Controlling Apomixis: Shared Features and Distinct Characteristics of Gene Regulation

Mimulus sRNAs Are Wound Responsive and Associated with Transgenerationally Plastic Genes but Rarely Both

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