Multimegabase Silencing in Nucleolar Dominance Involves siRNA-Directed DNA Methylation and Specific Methylcytosine-Binding Proteins

Abstract

In genetic hybrids, the silencing of nucleolar rRNA genes inherited from one progenitor is the epigenetic phenomenon known as nucleolar dominance. An RNAi knockdown screen identified the Arabidopsis de novo cytosine methyltransferase, DRM2 and the methylcytosine binding domain proteins, MBD6 and MBD10 as activities required for nucleolar dominance. MBD10 localizes throughout the nucleus, but MBD6 preferentially associates with silenced rRNA genes, and does so in a DRM2-dependent manner. DRM2 methylation is thought to be guided by siRNAs whose biogenesis requires RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3). Consistent with this hypothesis, knockdown of DCL3 or RDR2 disrupts nucleolar dominance. In genetic hybrids, the silencing of nucleolar rRNA genes inherited from one progenitor is the epigenetic phenomenon known as nucleolar dominance. An RNAi knockdown screen identified the Arabidopsis de novo cytosine methyltransferase, DRM2 and the methylcytosine binding domain proteins, MBD6 and MBD10 as activities required for nucleolar dominance. MBD10 localizes throughout the nucleus, but MBD6 preferentially associates with silenced rRNA genes, and does so in a DRM2-dependent manner. DRM2 methylation is thought to be guided by siRNAs whose biogenesis requires RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3). Consistent with this hypothesis, knockdown of DCL3 or RDR2 disrupts nucleolar dominance. Collectively, these results indicate that in addition to directing the silencing of retrotransposons and noncoding repeats, siRNAs specify de novo cytosine methylation patterns that are recognized by MBD6 and MBD10 in the large-scale silencing of rRNA gene loci.

Nucleoli: Composition, Function, and Dynamics

“…An RNAi approach has been used with Arabidopsis suecica, a hybrid of Arabidopsis and Arabidopsis arenosa, to determine factors involved in nucleolar dominance. This has shown the involvement of the histone deacetylases Histone Deacetylase1 and Histone Deacetylase6, the de novo DNA methyltransferase Domains Rearranged Methyltransferase2 (DRM2), and the methylcytosine binding domain proteins Methyl CpG Binding Domain6 (MBD6) and MBD10 (Preuss et al, 2008). Further confirmation that nucleolar dominance in plants involves RNA-directed DNA methylation was obtained by knockdown of RNA Dependent RNA Polymerase2, Dicer-like3, and DRM2, which disrupted the silencing of the Arabidopsisderived rRNA genes in A. suecica (Preuss et al, 2008).…”

Nucleolar Dominance of the Y Chromosome in Drosophila melanogaster

“…Specialized chromatin modification complexes that target rDNA genes have been described in budding yeast (Straight et al 1999), Arabidopsis Earley et al 2006;Preuss et al 2008), and in mammals (Murayama et al 2008). In Arabidopsis and mammals, these complexes reduce overall histone acetylation and direct histone methylation at lysine-9 of the histone H3 (H3K9me), leading to silencing of rDNA genes.…”

Selective nucleolus organizer inactivation in Arabidopsis is a chromosome position-effect phenomenon

“…One early hypothesis was that specific rRNA genes are selectively activated, based on transcription factor binding affinities (6). However, subsequent studies in plants and mammals revealed that specific rRNA genes are selectively silenced via changes in cytosine methylation and repressive histone modifications (7)(8)(9)(10)(11)(12)(13). Subtle sequence differences among rRNA genes have been proposed to influence nucleosome positioning, or base-pairing with noncoding RNAs, thereby inhibiting or enabling regulatory proteins that influence cytosine methylation and/or histone modification (11,(14)(15)(16).…”