Abstract
BackgroundRibosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. In Arabidopsis thaliana, 45S rRNA genes are found in two large ribosomal DNA (rDNA) clusters and little is known about the contribution of each to the overall transcription pattern in the species.ResultsBy taking advantage of genome sequencing data from the 1001 Genomes Consortium, we characterize rRNA gene sequence variation within and among accessions. Notably, variation is not restricted to the pre-rRNA sequences removed during processing, but it is also present within the highly conserved ribosomal subunits. Through linkage mapping we assign these variants to a particular rDNA cluster unambiguously and use them as reporters of rDNA cluster-specific expression. We demonstrate that rDNA cluster-usage varies greatly among accessions and that rDNA cluster-specific expression and silencing is controlled via genetic interactions between entire rDNA cluster haplotypes (alleles).ConclusionsWe show that rRNA gene cluster expression is controlled via complex epistatic and allelic interactions between rDNA haplotypes that apparently regulate the entire rRNA gene cluster. Furthermore, the sequence polymorphism we discovered implies that the pool of rRNA in a cell may be heterogeneous, which could have functional consequences.
Highlights
Ribosomal RNA accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time
Sequence variation in Ribosomal RNA (rRNA) genes within and between individuals Monitoring expression of particular rRNA genes is difficult because all copies are extremely similar due to concerted evolution, an evolutionary process that promotes homogeneity among the many rRNA gene repeats
In order to assign them to ribosomal DNA (rDNA) clusters, we used the multi-parent advanced generation inter-cross (MAGIC) population: a set of recombinant inbred lines derived from intercrossing a genetically heterogeneous stock of 19 worldwide accessions [47]
Summary
Ribosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. Because of the requirement for large quantities of rRNA, hundreds to thousands of 45S rRNA genes are tandemly arrayed head-to-tail in large ribosomal DNA (rDNA) clusters that, when expressed, form nucleolus organizer regions (NORs) [8,9,10,11] (Fig. 1a). RRNA accounts for the majority of the RNA in a eukaryotic cell, only a subset of the rRNA genes appear to be active at any given time: the others are silenced by repressive chromatin modifications [5, 12,13,14]. Many model organisms, such as Rabanal et al Genome Biology (2017) 18:75
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