Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana
| Autor: | Richard M. Clark, Richard Mott, Viktoria Nizhynska, Magnus Nordborg, Robert Greenhalgh, Joshua G. Steffen, Terezie Mandáková, Luz Mayela Soto-Jiménez, David Lee Parrott, Martin A. Lysak, Stefan Lutzmayer, Fernando A. Rabanal |
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| Rok vydání: | 2017 |
| Předmět: |
0106 biological sciences
0301 basic medicine lcsh:QH426-470 Arabidopsis Genomics Biology 01 natural sciences Ribosome 03 medical and health sciences Gene Expression Regulation Plant 28S ribosomal RNA Gene cluster rRNA genes lcsh:QH301-705.5 Gene Ribosomal DNA Alleles Dominance Genetics Research Epistasis Genetic Ribosomal RNA lcsh:Genetics 030104 developmental biology lcsh:Biology (General) Haplotypes RNA Ribosomal Multigene Family Epistasis Ribosomes Transcription Functional genomics 010606 plant biology & botany |
| Zdroj: | Genome Biology Genome Biology, Vol 18, Iss 1, Pp 1-15 (2017) |
| ISSN: | 1474-760X |
| DOI: | 10.1186/s13059-017-1209-z |
| Popis: | 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. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1209-z) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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