Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation

Eichten, Steven R.; Schmitz, Robert J.; Springer, Nathan M.

doi:10.1104/pp.113.234211

Cited by 129 publications

(110 citation statements)

References 211 publications

(255 reference statements)

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“…Biologically, as CHH methylation is continually established de novo, it may not show the same level of biological stability when compared to the symmetric methylation contexts that have maintenance methyltransferases to maintain fidelity over DNA replication (Law and Jacobsen 2010). A major question regarding the study of DNA methylation is the likelihood that observed patterns are either dependent on genetic state or act independently as a separate epigenetic layer of regulatory information (Richards 2006;Eichten et al 2014). By looking at high-quality SNPs across the reference lines sequenced (Gordon et al 2014), DNA methylation variation was correlated with increased levels of genetic variation (Fig.…”

Section: Dna Methylation Of Diversementioning

confidence: 99%

DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

et al. 2016

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DNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole-genome bisulfite sequencing was performed on genetically diverse lines of the model cereal Brachypodium distachyon. Although DNA methylation profiles are broadly similar, thousands of differentially methylated regions are observed between lines. An analysis of novel transposable element indel variation highlighted hundreds of new polymorphisms not seen in the reference sequence. DNA methylation and transposable element variation is correlated with the genome-wide amount of genetic variation present between samples. However, there was minimal evidence that novel transposon insertions or deletions are associated with nearby differential methylation. This study highlights unique relationships between genetic variation and DNA methylation variation within Brachypodium and provides a valuable map of DNA methylation across diverse resequenced accessions of this model cereal species.

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Section: Dna Methylation Of Diversementioning

confidence: 99%

DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

et al. 2016

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“…Among all identified epigenetic mechanisms, including histone modifications, DNA methylation, and small noncoding RNAs, DNA methylation is relatively stable with transgenerational heritability that can be independent of heritable genes (Bird, 2007; Eichten, Schmitz, & Springer, 2014), with the result that DNA methylation has attracted the most attention in epigenetic studies in ecology and evolution (Alvarez, Schrey, & Richards, 2015). The pattern of DNA methylation can affect ecologically important phenotypes and plasticity (Herrera & Bazaga, 2013; Nicotra et al., 2015; Zhang et al., 2013) and may play a significant role in adaptation to various habitat conditions (Foust et al., 2016; Richards et al., 2012; Schulz et al., 2014).…”

Section: Introductionmentioning

confidence: 99%

Genetic and epigenetic changes during the invasion of a cosmopolitan species (Phragmites australis)

Liu

Cuiping

Liu

et al. 2018

Ecology and Evolution

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While many introduced invasive species can increase genetic diversity through multiple introductions and/or hybridization to colonize successfully in new environments, others with low genetic diversity have to persist by alternative mechanisms such as epigenetic variation. Given that Phragmites australis is a cosmopolitan reed growing in a wide range of habitats and its invasion history, especially in North America, has been relatively well studied, it provides an ideal system for studying the role and relationship of genetic and epigenetic variation in biological invasions. We used amplified fragment length polymorphism (AFLP) and methylation‐sensitive (MS) AFLP methods to evaluate genetic and epigenetic diversity and structure in groups of the common reed across its range in the world. Evidence from analysis of molecular variance (AMOVA) based on AFLP and MS‐AFLP data supported the previous conclusion that the invasive introduced populations of P. australis in North America were from European and Mediterranean regions. In the Gulf Coast region, the introduced group harbored a high level of genetic variation relative to originating group from its native location, and it showed epigenetic diversity equal to that of the native group, if not higher, while the introduced group held lower genetic diversity than the native. In the Great Lakes region, the native group displayed very low genetic and epigenetic variation, and the introduced one showed slightly lower genetic and epigenetic diversity than the original one. Unexpectedly, AMOVA and principal component analysis did not demonstrate any epigenetic convergence between native and introduced groups before genetic convergence. Our results suggested that intertwined changes in genetic and epigenetic variation were involved in the invasion success in North America. Although our study did not provide strong evidence proving the importance of epigenetic variation prior to genetic, it implied the similar role of stable epigenetic diversity to genetic diversity in the adaptation of P. australis to local environment.

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“…This could directly affect future stress response if repression is maintained or inherited epigenetically. DNA methylation is associated with repressive chromatin states and a diverse range of environmental cues can alter the methylome (Eichten et al, 2014). Thus, whole-genome bisulfite sequencing was performed on four biological replicates for the control (I), excesslight (III), and 24-h recovery (X) samples.…”

Section: Excess-light Stress Dna Methylomementioning

confidence: 99%

“…Yet, the rules governing the selective formation and retention of environmental memories, including via potential epigenetic mechanisms, are poorly defined (Boyko and Kovalchuk, 2011;Eichten et al, 2014;Mirouze and Paszkowski, 2011;Gutzat and Mittelsten Scheid, 2012;Iwasaki and Paszkowski, 2014). An aspect of stress responses in plants that has received relatively little attention is stress recovery.…”

Section: Introductionmentioning

confidence: 99%

Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis

et al. 2017

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Stress recovery may prove to be a promising approach to increase plant performance and, theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, and PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as 3 min. We demonstrate that 87% of the stress-upregulated mRNAs analyzed exhibit very rapid recovery. For instance, HSP101 abundance declined 2-fold every 5.1 min. We term this phenomenon rapid recovery gene downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting. Decay constants (k) were modeled using two strategies, linear and nonlinear least squares regressions, with the latter accounting for both transcription and degradation. This revealed extremely short half-lives ranging from 2.7 to 60.0 min for 222 genes. Ribosome footprinting using degradome data demonstrated RRGD loci undergo cotranslational decay and identified changes in the ribosome stalling index during stress and recovery. However, small RNAs and 5ʹ-3ʹ RNA decay were not essential for recovery of the transcripts examined, nor were any of the six excess light-associated methylome changes. We observed recovery-specific gene expression networks upon return to favorable conditions and six transcriptional memory types. In summary, rapid transcriptome resetting is reported in the context of active recovery and cellular memory.

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Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation

Cited by 129 publications

References 211 publications

DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

Genetic and epigenetic changes during the invasion of a cosmopolitan species (Phragmites australis)

Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis

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