Trends in Genetics

Trends in Genetics

Volume 25, Issue 11, November 2009, Pages 511-517
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Review
Chromatin indexing in Arabidopsis: an epigenomic tale of tails and more

https://doi.org/10.1016/j.tig.2009.09.013Get rights and content

Packaging DNA into chromatin is pivotal for the regulation of genome activity in eukaryotes. This chromatin-level control relies on a range of histone modifications and variants, chromatin-remodeling proteins and DNA methylation in plants and mammals. High-resolution maps have recently been obtained for several chromatin modifications in Arabidopsis, which provide a first glimpse at the organization of plant epigenomes. These maps suggest a pervasive involvement of transcriptional activity in indexing chromatin with reference to the underlying DNA sequence. However, to assess the contribution of chromatin dynamics to plant development and phenotypic plasticity, it will be necessary to shift from a static to a dynamic view of the Arabidopsis epigenome.

Section snippets

Chromatin and the epigenome

Long considered mainly a DNA packaging device, chromatin is now viewed as a highly dynamic structure that affects all DNA transactions within the nucleus, namely transcription, replication, repair, recombination and transposition, as well as chromosome segregation. Thus, mutations that influence the composition of chromatin along the genome – the so-called epigenome – can induce strong phenotypic alterations or impaired viability, mainly caused by increased genome instability and/or

Epigenomic mapping in Arabidopsis

Over 20 chromatin marks and proteins have been analyzed in Arabidopsis at the cytological level by immunostaining or tagging 4, 5, 6, 7, 8, 10 of which have also been characterized at higher resolution through epigenomic mapping approaches (Box 2). Most epigenomic maps have been obtained using chromatin immunoprecipitation or methyl-cytosine immunoprecipitation, followed by hybridization to genomic tiling microarrays (ChIP-chip or MeDIP-chip, respectively) 9, 10, 11, 12, 13, 14, 15, 16. DNA

Heterochromatin and repeat elements

Despite its small size, the Arabidopsis genome contains many transposable elements and other repeats, most of which are clustered in pericentromeric or interstitial heterochromatin [27]. Consistent with immunostaining experiments, these heterochromatic regions were found by epigenomic mapping to be highly enriched in H3K9me2 and 5mC compared with euchromatin (Figure 1) 9, 10, 13, 14, 15, 17, 28. Thanks to their high resolution, these maps also revealed that the enrichment in H3K9me2 and 5mC was

Euchromatin and genes

The 125 Mb long Arabidopsis genome contains ∼28 000 genes, or 1 gene per ∼4 kb on average [27], a figure close to that of the highly compact genome of yeasts (1 gene/∼2 kb; [54]). Furthermore, most Arabidopsis genes are localized within euchromatin, which encompasses ∼100 Mb. Therefore, epigenomic mapping of this compartment equates with determining the distribution of chromatin marks over genes and their immediate surroundings, with few interspersed repeat elements. The emerging picture is one

Concluding remarks

The first epigenomic maps produced in Arabidopsis, mostly from whole seedlings or entire organs, have revealed an organization of chromosomes into small and well-demarcated chromatin domains that often coincide with single genes or individual repeat elements, irrespective of their location within euchromatin or heterochromatin. Significantly, a similar organization seems to prevail in plant species with more abundant repeat elements such as rice and maize, although the localization of DNA

Acknowledgments

We apologize to authors whose work could not be cited owing to space constraints. We thank Edith Heard for critical reading of this manuscript. F.K.T. was supported by a PhD studentship from the Brazilian government (Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior – CAPES). V.C. is a member of the European Union Network of Excellence “The Epigenome”. Work in the V.C. group is supported by grants from the French Agence Nationale de la Recherche (ANR Genoplante projects TAG and

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    These authors contributed equally to this work.

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