In eukaryotes, 45S rRNA genes are arranged in tandem arrays in copy numbers ranging from several hundred to several thousand in plants. Although it is clear that not all copies are transcribed under normal growth conditions, the molecular basis controlling the expression of specific sets of rRNA genes remains unclear. Here, we report four major rRNA gene variants in Arabidopsis thaliana. Interestingly, while transcription of one of these rRNA variants is induced, the others are either repressed or remain unaltered in A. thaliana plants with a disrupted nucleolin-like protein gene (Atnuc-L1). Remarkably, the most highly represented rRNA gene variant, which is inactive in WT plants, is reactivated in Atnuc-L1 mutants. We show that accumulated pre–rRNAs originate from RNA Pol I transcription and are processed accurately. Moreover, we show that disruption of the AtNUC-L1 gene induces loss of symmetrical DNA methylation without affecting histone epigenetic marks at rRNA genes. Collectively, these data reveal a novel mechanism for rRNA gene transcriptional regulation in which the nucleolin protein plays a major role in controlling active and repressed rRNA gene variants in Arabidopsis.
Chromatin remodeling plays a central role in controlling gene expression in all eukaryotic organisms. Chromatin can be found in a repressive or transcriptionally inactive state (heterochromatin) or in a more permissive or transcriptionally active state (euchromatin). The building block of chromatin is the nucleosome, which consists of four histones, H2A, H2B, H3, and H4, surrounded by 147 base pairs of DNA. In addition, a linker histone H1 directs the path of DNA between adjacent nucleosomes to form the chromatin fiber. Chromatin compaction also depends on DNA methylation and on a number of histone modifications, including methylation and acetylation of histone tails. However, other non-histone proteins are required to direct chromatin structure and remodeling. Nucleolin is a major nucleolar protein involved not only in rRNA transcription and processing of 45S pre–rRNA transcribed by RNA Pol I, but also in the control of RNA pol II transcription in the nucleoplasm. Through genetic, molecular, and immunocytological approaches, we studied the role of this protein in vivo in controlling rRNA chromatin structure and the expression of hundreds of clustered rRNA genes using the model plant Arabidopsis thaliana.