Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana

• Published in: Genome Biology Vol. 18; no. 1; p. 75
• Main Authors: Rabanal, Fernando A, Mandáková, Terezie, Soto-Jiménez, Luz M, Greenhalgh, Robert, Parrott, David L, Lutzmayer, Stefan, Steffen, Joshua G, Nizhynska, Viktoria, Mott, Richard, Lysak, Martin A, Clark, Richard M, Nordborg, Magnus
• Format: Journal Article
• Language: English
• Published: England BioMed Central 03.05.2017; BMC
• Subjects: Alleles; Arabidopsis - genetics; Arabidopsis thaliana; Bioinformatics; Chromosomes; Cloning; Deoxyribonucleic acid; DNA; DNA methylation; Dominance; Epistasis; Epistasis, Genetic; Gene clusters; Gene Expression Regulation, Plant; Gene mapping; Gene polymorphism; Genes; Genomes; Genomics; Haplotypes; Multigene Family; Plant biology; Population; Ribosomal DNA; Ribosomal subunits; Ribosomes; RNA polymerase; RNA processing; RNA, Ribosomal - genetics; rRNA 45S; rRNA genes; Transcription; Dominance; Epistasis; Transcription; Ribosomes; rRNA genes
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-017-1209-z

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. 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. By 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). We 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.