The Evolution of Epitype

Meagher, Richard B.

doi:10.1105/tpc.110.075481

Cited by 11 publications

(14 citation statements)

References 85 publications

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“…Genotype and phenotype describe the relationship between DNA sequence and differences in gene expression and development at different levels. In the field of epigenetics, epitype and phenotype describe the parallel relationships between information in chromatin structure/DNA modifications and its manifestation during development (Meagher, 2010). The epitype of a single gene or entire genome is determined by cis -linked differences in chromatin structure (Meagher, 2010).…”

Section: Adaptive Value Of An Epigenetic Memorymentioning

confidence: 99%

“…In the field of epigenetics, epitype and phenotype describe the parallel relationships between information in chromatin structure/DNA modifications and its manifestation during development (Meagher, 2010). The epitype of a single gene or entire genome is determined by cis -linked differences in chromatin structure (Meagher, 2010). Progeny originating from warm and cold temperatures during embryogenesis should be considered as epitypes.…”

Section: Adaptive Value Of An Epigenetic Memorymentioning

confidence: 99%

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An adaptive epigenetic memory in conifers with important implications for seed production

Yakovlev¹,

Fossdal²,

Skrøppa³

et al. 2012

Seed Sci. Res.

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Conifers are evolutionarily more ancient than their angiosperm counterparts, and thus some adaptive mechanisms and features influenced by epigenetic mechanisms appear more highly displayed in these woody gymnosperms. Conifers such as Norway spruce have very long generation times and long life spans, as well as large genome sizes. This seemingly excessive amount of genomic DNA without apparent duplications could be a rich source of sites for epigenetic regulation and modifications. In Norway spruce, an important adaptive mechanism has been identified, called epigenetic memory. This affects the growth cycle of these trees living in environments with mild summers and cold winters, allowing them to adapt rapidly to new and/or changing environments. The temperature during post-meiotic megagametogenesis and seed maturation epigenetically shifts the growth cycle programme of the embryos. This results in significant and long-lasting phenotypic change in the progeny, such as advance or delay of vital phenological processes of high adaptive value, like bud break and bud set. This phenomenon is not only of important evolutionary significance but has clear practical implications for forest seed production and conservation of forest genetic resources. The underlying molecular mechanism that causes the ‘memory’ in long-lived woody species is currently under investigation. Here we summarize the information related to epigenetic memory regulation in gymnosperms, with special emphasis on conifers. The molecular mechanism behind this is still unknown but transcriptional changes are clearly involved. Epigenetic regulation may be realized through several mechanisms, including DNA methylation, histone modification, chromatin remodelling, small non-coding RNAs and transposable element regulation, of which non-coding RNAs might be one of the most important determinants.

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Section: Adaptive Value Of An Epigenetic Memorymentioning

confidence: 99%

Section: Adaptive Value Of An Epigenetic Memorymentioning

confidence: 99%

An adaptive epigenetic memory in conifers with important implications for seed production

Yakovlev¹,

Fossdal²,

Skrøppa³

et al. 2012

Seed Sci. Res.

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“…Expression divergence of duplicated/expanded genes is a subject of great interest to geneticists and evolutionary biologists because it may contribute to the retention and functional divergence of duplicated/expanded genes [10]. Meagher (2010) proposed the hypothesis that epitype and associated phenotypes evolved by gene duplication, divergence, and subfunctionalization [11]. To investigate the contribution of gene duplication and expansion to expression divergence, we have identified tandemly or segmentally duplicated as well as expanded sorghum genes by mobile elements in a genome-wide level and subsequently investigated their expression divergence under normal growth conditions and sucrose treatments.…”

Section: Introductionmentioning

confidence: 99%

Genetic variation and expression diversity between grain and sweet sorghum lines

Jiang

Jeevanandam

et al. 2013

BMC Genomics

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BackgroundBiological scientists have long sought after understanding how genes and their structural/functional changes contribute to morphological diversity. Though both grain (BT×623) and sweet (Keller) sorghum lines originated from the same species Sorghum bicolor L., they exhibit obvious phenotypic variations. However, the genome re-sequencing data revealed that they exhibited limited functional diversity in their encoding genes in a genome-wide level. The result raises the question how the obvious morphological variations between grain and sweet sorghum occurred in a relatively short evolutionary or domesticated period.ResultsWe implemented an integrative approach by using computational and experimental analyses to provide a detail insight into phenotypic, genetic variation and expression diversity between BT×623 and Keller lines. We have investigated genome-wide expression divergence between BT×623 and Keller under normal and sucrose treatment. Through the data analysis, we detected more than 3,000 differentially expressed genes between these two varieties. Such expression divergence was partially contributed by differential cis-regulatory elements or DNA methylation, which was genetically determined by functionally divergent genes between these two varieties. Both tandem and segmental duplication played important roles in the genome evolution and expression divergence.ConclusionSubstantial differences in gene expression patterns between these two varieties have been observed. Such an expression divergence is genetically determined by the divergence in genome level.

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“…For example, marks such as H3K9me2/3 and H3K4me2/3, although enriched on either silenced or actively transcribed genes, respectively, are also present in the reciprocal states (Cloos et al, 2008;Mosammaparast and Shi, 2010). Therefore the association between a specific epigenome and its transcriptional status is more complicated (Feil, 2008;Meagher, 2010).…”

Section: Discussionmentioning

confidence: 99%

Chromatin dynamics of the developmentally regulatedP. lividus neural alpha tubulin gene

Emanuele¹,

Costa²,

Ragusa³

et al. 2011

Int. J. Dev. Biol.

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Over 40 years ago, Allfrey and colleagues (1964) suggested that two histone modifications, namely acetylation and methylation, might regulate RNA synthesis. Nowadays it is universally accepted that activation of gene expression strictly depends on enzymatic mechanisms able to dynamically modify chromatin structure. Here, using techniques including DNaseI hypersensitive site analysis, chomatin immunoprecipitation and quantitative PCR analysis, we have analyzed the dynamics of histone post-translation modifications involved in developmentally/spatially controlled activation of the sea urchin PlTalpha2 tubulin gene. We have demonstrated that only when the PlTalpha2 core promoter chromatin is acetylated on H3K9, tri-methylated on H3K4 and not di-methylated on H3K27, RNA pol II can be enrolled. In contrast, we have shown that when chromatin is methylated both on H3K9 (me2/3) and H3K27 (me2) and mono methylated on H3K4 the promoter is not accessible to RNA pol II. Our results suggest that, during P. lividus embryogenesis, both HAT/HDAC and HMT/HDM activities, which are able to regulate accessibility of the PlTalpha2 basal promoter to RNA polymerase II, are coordinately switched-on.

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The Evolution of Epitype

Cited by 11 publications

References 85 publications

An adaptive epigenetic memory in conifers with important implications for seed production

An adaptive epigenetic memory in conifers with important implications for seed production

Genetic variation and expression diversity between grain and sweet sorghum lines

Chromatin dynamics of the developmentally regulatedP. lividus neural alpha tubulin gene

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