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

J 2017

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 et. al.

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

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10611 Plant sciences, botany

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

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

Abstract

V originále

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

Citovat

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, 2017, vol. 18, May, p. nestránkováno, 15 pp. ISSN 1474-760X. Available from: https://dx.doi.org/10.1186/s13059-017-1209-z.

@article{1395011,
   author = {Rabanal, Fernando A. and Mandáková, Terezie and SotoandJimenez, Luz M. and Greenhalgh, Robert and Parrott, David L. and Lutzmayer, Stefan and Steffen, Joshua G. and Nizhynska, Viktoria and Mott, Richard and Lysák, Martin and Clark, Richar M. and Nordborg, Magnus},
   article_location = {LONDON},
   article_number = {May},
   doi = {http://dx.doi.org/10.1186/s13059-017-1209-z},
   keywords = {Ribosomes; rRNA genes; Transcription; Epistasis; Dominance},
   language = {eng},
   issn = {1474-760X},
   journal = {GENOME BIOLOGY},
   title = {Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana},
   url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1209-z},
   volume = {18},
   year = {2017}
}

TY  - JOUR
ID  - 1395011
AU  - 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
PY  - 2017
TI  - Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana
JF  - GENOME BIOLOGY
VL  - 18
IS  - May
SP  - nestránkováno
EP  - nestránkováno
PB  - BIOMED CENTRAL LTD
SN  - 1474760X
KW  - Ribosomes
KW  - rRNA genes
KW  - Transcription
KW  - Epistasis
KW  - Dominance
UR  - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1209-z
L2  - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1209-z
N2  - 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.
ER  -

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. \textit{GENOME BIOLOGY}. LONDON: BIOMED CENTRAL LTD, 2017, vol.~18, May, p.~nestránkováno, 15 pp. ISSN~1474-760X. Available from: https://dx.doi.org/10.1186/s13059-017-1209-z.

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