Plant epigenomics—deciphering the mechanisms of epigenetic inheritance and plasticity in plants
Claudia Köhler and Nathan Springer
Genome Biology 201718:132
https://doi.org/10.1186/s13059-017-1260-9 © The Author(s). 2017
Source/Fonte: The Scientist
EDITORIAL
Published: 6 July 2017
It is an exciting time to study plant epigenetics. Technological advances are providing unprecedented opportunities to monitor chromatin modifications, gene expression, and genome structure. Many classical epigenetic phenomena (transposable element inactivation, imprinting, paramutation, transgene silencing, and co-suppression) were first documented in plants. Combined with classical genetic studies, newly available sequencing technologies are facilitating the study of these and other epigenetic phenomena at a level of detail that was unthinkable only a few years ago. Studies of epigenetics in plants are of great importance. Plants are heavily dependent upon changes in gene expression in order to respond to environmental stimuli, and chromatin-based regulation of gene expression is likely crucial for these responses. Furthermore, the level of chromatin ‘resetting’ during sexual reproduction appears to be lower in plants in comparison with animal species [1, 2], potentially allowing inheritance of epimutations acquired during plant life. In addition, many plant species can propagate asexually and produce vegetative clones, providing opportunities for mitotic inheritance of epigenetic states leading to important traits. This issue of Genome Biology highlights exciting progress in many areas of plant epigenetics and epigenomics.
DNA methylation is a well-studied chromatin modification in animals and plants that can be stably inherited, both following cell divisions and, to some extent, across generations. DNA methylation can be monitored at high resolution by using sodium bisulfite treatment of DNA, followed by next-generation sequencing. Cytosines in different sequence contexts (CG, CHG, and CHH (where H is any base other than G)) and at different types of loci in plant genomes can be targeted by DNA methylation. This modification has likely evolved as a mechanism to silence transposons, which are ‘genomic parasites’ invading the genome of their hosts. The vast majority of transposons are highly methylated and are likely a primary target for epigenetic silencing. However, the repetitive nature of transposons and the fact that they generate large insertion/deletion polymorphisms among genotypes has led to difficulties in monitoring the link between transposon polymorphism and DNA methylation variation. Daron and Slotkin describe a new tool to study the interactions between transposon methylation and transposon insertions using whole-genome bisulfite sequencing datasets [3]. This type of analysis is expected to be very useful in documenting the role of genetic and epigenetic variation in DNA methylation among individuals of the same species.
The RNA-dependent DNA methylation (RdDM) pathway is crucial for maintenance of CHH methylation and requires the plant-specific RNA polymerases IV and V (Pol IV and V, respectively). Pol IV generates precursor transcripts of 24-nt small RNAs (sRNAs) that target scaffold transcripts from Pol V by sequence complementarity and recruit the domains rearranged methyltransferase 2 [4]. A rather unexpected link between RdDM and the chromatin remodeling factor PICKLE (PKL) is revealed by Zhang and colleagues, who report that PKL is required for the accumulation of transcripts generated by Pol V and for the positioning of Pol V-stabilized nucleosomes at a subset of RdDM target loci [5]. These findings link nucleosome positioning with the initiation of RdDM, consistent with the previously proposed role of SWI/SNF chromatin remodeling complexes in establishing positioned nucleosomes on specific loci primed for RdDM [6]. It is well established that PKL regulates plant development and, in particular, regulates the access of Polycomb-group proteins to its targets [7]. Likewise, SWI/SNF complexes have well-described roles in plant development [7], extended by the study of Benhamed and colleagues in this issue showing that the SWI/SNF complex core subunit BAF60 regulates access of the Phytochrome Interacting Factor 4 (PIF4) to nucleosome-free regions [8]. The dual functional role of chromatin-remodeling factors in regulating plant development and RdDM suggests that both processes are more closely connected than is widely appreciated.
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