2016
DOI: 10.1105/tpc.15.00911
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Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

Abstract: ORCID IDs: 0000-0002-7301-4759 (N.M.S.); 0000-0003-3232-9479 (Q.L.)Flowering plants have strikingly distinct genomes, although they contain a similar suite of expressed genes. The diversity of genome structures and organization is largely due to variation in transposable elements (TEs) and whole-genome duplication (WGD) events. We review evidence that chromatin modifications and epigenetic regulation are intimately associated with TEs and likely play a role in mediating the effects of WGDs. We hypothesize that… Show more

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Cited by 92 publications
(86 citation statements)
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References 160 publications
(190 reference statements)
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“…Young NUMTs may have stronger deleterious effects and their toleration by nuclear genomes may be determined by conditions such as genome architecture and the strength of the genome immune system against foreign DNAs. Genes potentially involved in such epigenetic mechanisms show functional variation within species (Shen et al, 2014) or elevated amino acid substitution rates between species (Willing et al, 2015), suggesting differences in the genome immune system between species (Springer et al, 2016). In contrast, NUMTs that survived in the genome to an older age could have always been or could have become less deleterious, and the cumulative length of those NUMTs might be determined by the size of the nuclear genome.…”
Section: Resultsmentioning
confidence: 99%
“…Young NUMTs may have stronger deleterious effects and their toleration by nuclear genomes may be determined by conditions such as genome architecture and the strength of the genome immune system against foreign DNAs. Genes potentially involved in such epigenetic mechanisms show functional variation within species (Shen et al, 2014) or elevated amino acid substitution rates between species (Willing et al, 2015), suggesting differences in the genome immune system between species (Springer et al, 2016). In contrast, NUMTs that survived in the genome to an older age could have always been or could have become less deleterious, and the cumulative length of those NUMTs might be determined by the size of the nuclear genome.…”
Section: Resultsmentioning
confidence: 99%
“…However, a more global impact of stress on the efficiency of TE-silencing mechanisms has also been suggested (TittelElmer et al, 2010). In particular, genomic stress brought on by hybridization or polyploidization has global effects on epigenetic regulation and may thereby lead to TE reactivation (Kashkush et al, 2003;Madlung et al, 2005;Lopes et al, 2013;Springer et al, 2016;Edger et al, 2017). However, genome shock in polyploids has been studied primarily in allopolyploid contexts, where hybridization is the major contributor, as observed in Senecio cambrensis (Hegarty et al, 2006) and Spartina anglica (Parisod et al, 2009).…”
Section: Transposition Burst and The Generation Of A High-effect Mutamentioning
confidence: 99%
“…For example, the duplication of the HvHox2 gene, due to TE activity, and its neo-funzionalization, created a row-type spike [16]. If TE dynamics can heavily modify the genome structure, it has been suggested that chromatin modifications and, in general, epigenetic regulation, can shape the TE-induced effects [41]. Verisimilarly, a combination of these mechanisms is at the basis of the continuum of morphological variants that can be observed in a barley spike.…”
Section: Conclusive Remarksmentioning
confidence: 99%