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Cited by 37Chromosomal and Genetic VariationsPlant Molecular Biology ResearchGenomics and Chromatin Dynamics

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

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Rabanal, Fernando A., Mandáková, Terezie, Soto-Jiménez, Luz M., Greenhalgh, Robert, Parrott, David L., Lutzmayer, Stefan, Steffen, Joshua G., Nizhynska, Viktoria +4 more·2017·Genome Biology
DOI 10.1186/s13059-017-1209-zPMC PMC5414317
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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.

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Authors
Rabanal, F. A., Mandáková, T., Soto-Jiménez, L. M., Greenhalgh, R., Parrott, D. L., Lutzmayer, S., Steffen, J. G., Nizhynska, V., Mott, R., Lysak, M. A., Clark, R. M., & Nordborg, M.
Affiliations
  • Gregor Mendel Institute of Molecular Plant Biology (AT)
  • Central European Institute of Technology (CZ)
  • University of Utah (US)
  • Colby–Sawyer College (US)
  • University College London (GB)
Corresponding author
  • Rabanal, Fernando A.
  • Nordborg, Magnus
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2017-05-03
Volume
18
Issue
1
Pages
75-75
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-017-1209-z
PMC
PMC5414317
OpenAlex
W2608005343
Cited by
37
References
0
Citations by year
2026: 2 · 2024: 3 · 2023: 7 · 2022: 3 · 2021: 10 · 2020: 5 · 2019: 4 · 2018: 3
FWCI
3.23
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • UCL Discovery (University College London) (submittedVersion)
Funders
  • European Research Council (288962)
  • National Human Genome Research Institute (P50 HG002790)
  • National Institute of General Medical Sciences (T32 GM07464)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
ribosomal DNA, 45S rRNA, epistasis, allelic interaction, rRNA gene expression, sequence variation, linkage mapping, Arabidopsis thaliana
MeSH terms
Alleles, Epistasis, Genetic, Multigene Family, Haplotypes, RNA, Ribosomal, Arabidopsis, Gene Expression Regulation, Plant

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