Abstract
Nucleolar dominance is an epigenetic phenomenon in plant and animal genetic hybrids that describes the expression of 45S ribosomal RNA genes (rRNA genes) inherited from only one progenitor due to the silencing of the other progenitor's rRNA genes. rRNA genes are tandemly arrayed at nucleolus organizer regions (NORs) that span millions of basepairs, thus gene silencing in nucleolar dominance occurs on a scale second only to X-chromosome inactivation in female mammals. In Arabidopsis suecica, the allotetraploid hybrid of A. thaliana and A. arenosa, the A. thaliana –derived rRNA genes are subjected to nucleolar dominance and are silenced via repressive chromatin modifications. However, the developmental stage at which nucleolar dominance is established in A. suecica is currently unknown. We show that nucleolar dominance is not apparent in seedling cotyledons formed during embryogenesis but becomes progressively established during early postembryonic development in tissues derived from both the shoot and root apical meristems. The progressive silencing of A. thaliana rRNA genes correlates with the transition of A. thaliana NORs from a decondensed euchromatic state associated with histone H3 that is trimethylated on lysine 4 (H3K4me3) to a highly condensed heterochromatic state in which the NORs are associated with H3K9me2 and 5-methylcytosine-enriched chromocenters. In RNAi-lines in which the histone deacetylases HDA6 and HDT1 are knocked down, the developmentally regulated condensation and inactivation of A. thaliana NORs is disrupted. Collectively, these data demonstrate that HDA6 and HDT1 function in the postembryonic establishment of nucleolar dominance, a process which recurs in each generation.
Highlights
Epigenetic phenomena reflect alternative gene expression states that are maintained through multiple rounds of mitosis, and sometimes through meiosis
An S1 nuclease protection assay using species-specific probes to detect transcripts from the A. thaliana or A. arenosa-derived rRNA genes that are present in the A. suecica genome revealed that rRNA genes of both progenitors are actively transcribed in cotyledons (Figure 1B), showing that nucleolar dominance does not occur in these organs
In total RNA isolated from the first four true leaves to emerge from the shoot apical meristem, transcripts from the A. arenosa-derived rRNA genes are abundant whereas A. thalianaderived rRNA genes are detected at much lower levels (Figure 1B), indicative of incomplete nucleolar dominance
Summary
Epigenetic phenomena reflect alternative gene expression states that are maintained through multiple rounds of mitosis, and sometimes through meiosis. The alternative expression states are not due to mutation or changes in gene sequence and are reversible to varying degrees [1,2]. One of the first epigenetic phenomena described was nucleolar dominance, initially known as differential amphiplasty [3]. Nucleolar dominance occurs in organisms as diverse as fruit flies, frogs, mammals and marine copepods [3,4,5,6,7]. Nucleolar dominance is typically studied in interspecific hybrids (hybrids formed between species within the same genus) and occurs independent of maternal or paternal effects, indicating that gametic imprinting is not key to the phenomenon. The direction of silencing is not random; instead, the same progenitor species’ rRNA genes are consistently silenced
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