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.

Základní údaje

Originální název

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

Autoři

RABANAL, Fernando A. (40 Rakousko), Terezie MANDÁKOVÁ (203 Česká republika, domácí), Luz M. SOTO-JIMENEZ (40 Rakousko), Robert GREENHALGH (840 Spojené státy), David L. PARROTT (840 Spojené státy), Stefan LUTZMAYER (40 Rakousko), Joshua G. STEFFEN (840 Spojené státy), Viktoria NIZHYNSKA (40 Rakousko), Richard MOTT (826 Velká Británie a Severní Irsko), Martin LYSÁK (203 Česká republika, garant, domácí), Richar M. CLARK (840 Spojené státy) a Magnus NORDBORG (40 Rakousko)

Vydání

GENOME BIOLOGY, LONDON, BIOMED CENTRAL LTD, 2017, 1474-760X

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10611 Plant sciences, botany

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 13.214

Kód RIV

RIV/00216224:14740/17:00095154

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1186/s13059-017-1209-z

UT WoS

000400331100001

Klíčová slova anglicky

Ribosomes; rRNA genes; Transcription; Epistasis; Dominance

Štítky

OA, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 23. 3. 2018 15:28, Mgr. Pavla Foltynová, Ph.D.

Anotace

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.

Návaznosti

GBP501/12/G090, projekt VaV

Název: 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 a Magnus NORDBORG. Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana. GENOME BIOLOGY. LONDON: BIOMED CENTRAL LTD, 2017, roč. 18, May, s. nestránkováno, 15 s. ISSN 1474-760X. Dostupné z: 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 a Magnus NORDBORG. Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana. \textit{GENOME BIOLOGY}. LONDON: BIOMED CENTRAL LTD, 2017, roč.~18, May, s.~nestránkováno, 15 s. ISSN~1474-760X. Dostupné z: https://dx.doi.org/10.1186/s13059-017-1209-z.

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