Abstract
RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2. The data revealed that the majority of the genome exists in a heterochromatic state defined by inaccessible chromatin that is marked by H3K9me2 and H3K27me2 but that lacks RdDM. The minority of the genome marked by RdDM was predominantly near genes, and its overall chromatin structure appeared more similar to euchromatin than to heterochromatin. These and other data indicate that the densely staining chromatin defined as heterochromatin differs fundamentally from RdDM-targeted chromatin. We propose that small interfering RNAs perform a specialized role in repressing transposons in accessible chromatin environments and that the bulk of heterochromatin is incompatible with small RNA production.
Highlights
Eukaryotic genomes typically contain a large fraction of repetitive DNA that appears to be dispensable, at least in terms of supporting the production of proteins
MEDIATOR OF PARAMUTATION1 (MOP1) is an RNA-dependent RNA polymerase (RdRP) homologous to Arabidopsis RDR2, which is a key factor in Arabidopsis RNA-directed DNA methylation (RdDM) because of its role in the synthesis of 24-nucleotide siRNAs
The maize genome encodes nine putative RdRPs, including one (GRMZMG481730) with 35% amino acid identify to MOP1, but MOP1 alone is required for accumulation of the vast majority of 24-nucleotide siRNAs and for DNA methylation at specific loci in maize, as evidenced by small RNA sequencing and RNA and DNA gel blots in wild-type and mop1 mutant plants (Lisch et al, 2002; Woodhouse et al, 2006; Nobuta et al, 2008)
Summary
Eukaryotic genomes typically contain a large fraction of repetitive DNA that appears to be dispensable, at least in terms of supporting the production of proteins. The abundance of the transposons and tandem repeats that make up this repetitive DNA is highly variable between species and even between populations within a single species, as illustrated by studies in maize (Zea mays) (Tenaillon et al, 2011; Kanizay et al, 2013). Repetitive regions of the genomes were identified early on by their dense staining, both by light and electron microscopy. These regions were not just condensed during cell division but remained so in interphase cells. Similar to knobs in maize, the repeat-rich centromeric regions of many other organisms, including Drosophila melanogaster, mouse, and Arabidopsis thaliana, form visible heterochromatic structures called
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
