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

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Authors

RABANAL Fernando A. MANDÁKOVÁ Terezie SOTO-JIMENEZ Luz M. GREENHALGH Robert PARROTT David L. LUTZMAYER Stefan STEFFEN Joshua G. NIZHYNSKA Viktoria MOTT Richard LYSÁK Martin CLARK Richar M. NORDBORG Magnus

Year of publication 2017
Type Article in Periodical
Magazine / Source GENOME BIOLOGY
MU Faculty or unit

Central European Institute of Technology

Citation
Web https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1209-z
Doi http://dx.doi.org/10.1186/s13059-017-1209-z
Field Genetics and molecular biology
Keywords Ribosomes; rRNA genes; Transcription; Epistasis; Dominance
Description Background: 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. Results: 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). Conclusions: 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.
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