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

RABANAL, Fernando A., Terezie MANDÁKOVÁ, Luz M. SOTO-JIMENEZ, Robert GREENHALGH, David L. PARROTT, Stefan LUTZMAYER, Joshua G. STEFFEN, Viktoria NIZHYNSKA, Richard MOTT, Martin LYSÁK, Richar M. CLARK and Magnus NORDBORG. Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana. GENOME BIOLOGY. LONDON: BIOMED CENTRAL LTD, vol. 18, May, p. nestránkováno, 15 pp. ISSN 1474-760X. doi:10.1186/s13059-017-1209-z. 2017.

Basic information

• Original name: Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana
• Authors: RABANAL, Fernando A. (40 Austria), Terezie MANDÁKOVÁ (203 Czech Republic, belonging to the institution), Luz M. SOTO-JIMENEZ (40 Austria), Robert GREENHALGH (840 United States of America), David L. PARROTT (840 United States of America), Stefan LUTZMAYER (40 Austria), Joshua G. STEFFEN (840 United States of America), Viktoria NIZHYNSKA (40 Austria), Richard MOTT (826 United Kingdom of Great Britain and Northern Ireland), Martin LYSÁK (203 Czech Republic, guarantor, belonging to the institution), Richar M. CLARK (840 United States of America) and Magnus NORDBORG (40 Austria).
• Edition: GENOME BIOLOGY, LONDON, BIOMED CENTRAL LTD, 2017, 1474-760X.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10611 Plant sciences, botany
• Country of publisher: United Kingdom of Great Britain and Northern Ireland
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 13.214
• RIV identification code: RIV/00216224:14740/17:00095154
• Organization unit: Central European Institute of Technology
• Doi: http://dx.doi.org/10.1186/s13059-017-1209-z
• UT WoS: 000400331100001
• Keywords in English: Ribosomes; rRNA genes; Transcription; Epistasis; Dominance
• Tags: OA, rivok
• Tags: International impact, Reviewed

Abstract

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.

Links

• GBP501/12/G090, research and development project: Name: Evoluce a funkce komplexních genomů rostlin