Variation of 45S rDNA intergenic spacers in Arabidopsis
thaliana

J 2016

Variation of 45S rDNA intergenic spacers in Arabidopsis thaliana

HAVLOVÁ, Kateřina, Martina DVOŘÁČKOVÁ, Ramon PEIRO, David ABIA, Iva MOZGOVÁ et. al.

Základní údaje

Originální název

Variation of 45S rDNA intergenic spacers in Arabidopsis thaliana

Autoři

HAVLOVÁ, Kateřina (203 Česká republika, domácí), Martina DVOŘÁČKOVÁ (203 Česká republika, domácí), Ramon PEIRO (724 Španělsko), David ABIA (724 Španělsko), Iva MOZGOVÁ (203 Česká republika, domácí), Lenka VANSÁČOVÁ (703 Slovensko, domácí), Crisanto GUTIERREZ (724 Španělsko) a Jiří FAJKUS (203 Česká republika, garant, domácí)

Vydání

Plant Molecular Biology, Dordrecht, Springer, 2016, 0167-4412

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Odkazy

Full Text

Impakt faktor

Impact factor: 3.356

Kód RIV

RIV/00216224:14740/16:00088684

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1007/s11103-016-0524-1

UT WoS

000387114900005

Klíčová slova anglicky

Arabidopsis thaliana; Chromatin assembly factor; Nucleolus organizer region; 45S ribosomal DNA; Intergenic spacer; rDNA rearrangements

Štítky

rivok

Změněno: 20. 1. 2020 16:56, Mgr. Marie Šípková, DiS.

Anotace

V originále

Approximately seven hundred 45S rRNA genes (rDNA) in the Arabidopsis thaliana genome are organised in two 4 Mbp-long arrays of tandem repeats arranged in head-to-tail fashion separated by an intergenic spacer (IGS). These arrays make up 5 % of the A. thaliana genome. IGS are rapidly evolving sequences and frequent rearrangements inside the rDNA loci have generated considerable interspecific and even intra-individual variability which allows to distinguish among otherwise highly conserved rRNA genes. The IGS has not been comprehensively described despite its potential importance in regulation of rDNA transcription and replication. Here we describe the detailed sequence variation in the complete IGS of A. thaliana WT plants and provide the reference/consensus IGS sequence, as well as genomic DNA analysis. We further investigate mutants dysfunctional in chromatin assembly factor-1 (CAF-1) (fas1 and fas2 mutants), which are known to have a reduced number of rDNA copies, and plant lines with restored CAF-1 function (segregated from a fas1xfas2 genetic background) showing major rDNA rearrangements. The systematic rDNA loss in CAF-1 mutants leads to the decreased variability of the IGS and to the occurrence of distinct IGS variants. We present for the first time a comprehensive and representative set of complete IGS sequences, obtained by conventional cloning and by Pacific Biosciences sequencing. Our data expands the knowledge of the A. thaliana IGS sequence arrangement and variability, which has not been available in full and in detail until now. This is also the first study combining IGS sequencing data with RFLP analysis of genomic DNA.

Návaznosti

GJ16-04166Y, projekt VaV

Název: Chromatin asociované faktory podílející se na regulaci 45SrDNA v Arabidopsis

Investor: Grantová agentura ČR, Chromatin asociované faktory podílející se na regulaci 45SrDNA v Arabidopsis

LH15189, projekt VaV

Název: Struktura a dynamika 45S rDNA lokusů v Arabidopsis thaliana

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Struktura a dynamika 45S rDNA lokusů v Arabidopsis thaliana

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

HAVLOVÁ, Kateřina, Martina DVOŘÁČKOVÁ, Ramon PEIRO, David ABIA, Iva MOZGOVÁ, Lenka VANSÁČOVÁ, Crisanto GUTIERREZ a Jiří FAJKUS. Variation of 45S rDNA intergenic spacers in Arabidopsis thaliana. Plant Molecular Biology. Dordrecht: Springer, 2016, roč. 92, 4-5, s. 457-471. ISSN 0167-4412. Dostupné z: https://dx.doi.org/10.1007/s11103-016-0524-1.

@article{1373248,
   author = {Havlová, Kateřina and Dvořáčková, Martina and Peiro, Ramon and Abia, David and Mozgová, Iva and Vansáčová, Lenka and Gutierrez, Crisanto and Fajkus, Jiří},
   article_location = {Dordrecht},
   article_number = {4-5},
   doi = {http://dx.doi.org/10.1007/s11103-016-0524-1},
   keywords = {Arabidopsis thaliana; Chromatin assembly factor; Nucleolus organizer region; 45S ribosomal DNA; Intergenic spacer; rDNA rearrangements},
   language = {eng},
   issn = {0167-4412},
   journal = {Plant Molecular Biology},
   title = {Variation of 45S rDNA intergenic spacers in Arabidopsis thaliana},
   url = {http://link.springer.com/article/10.1007%2Fs11103-016-0524-1},
   volume = {92},
   year = {2016}
}

TY  - JOUR
ID  - 1373248
AU  - Havlová, Kateřina - Dvořáčková, Martina - Peiro, Ramon - Abia, David - Mozgová, Iva - Vansáčová, Lenka - Gutierrez, Crisanto - Fajkus, Jiří
PY  - 2016
TI  - Variation of 45S rDNA intergenic spacers in Arabidopsis thaliana
JF  - Plant Molecular Biology
VL  - 92
IS  - 4-5
SP  - 457-471
EP  - 457-471
PB  - Springer
SN  - 01674412
KW  - Arabidopsis thaliana
KW  - Chromatin assembly factor
KW  - Nucleolus organizer region
KW  - 45S ribosomal DNA
KW  - Intergenic spacer
KW  - rDNA rearrangements
UR  - http://link.springer.com/article/10.1007%2Fs11103-016-0524-1
L2  - http://link.springer.com/article/10.1007%2Fs11103-016-0524-1
N2  - Approximately seven hundred 45S rRNA genes (rDNA) in the Arabidopsis thaliana genome are organised in two 4 Mbp-long arrays of tandem repeats arranged in head-to-tail fashion separated by an intergenic spacer (IGS). These arrays make up 5 % of the A. thaliana genome. IGS are rapidly evolving sequences and frequent rearrangements inside the rDNA loci have generated considerable interspecific and even intra-individual variability which allows to distinguish among otherwise highly conserved rRNA genes. The IGS has not been comprehensively described despite its potential importance in regulation of rDNA transcription and replication. Here we describe the detailed sequence variation in the complete IGS of A. thaliana WT plants and provide the reference/consensus IGS sequence, as well as genomic DNA analysis. We further investigate mutants dysfunctional in chromatin assembly factor-1 (CAF-1) (fas1 and fas2 mutants), which are known to have a reduced number of rDNA copies, and plant lines with restored CAF-1 function (segregated from a fas1xfas2 genetic background) showing major rDNA rearrangements. The systematic rDNA loss in CAF-1 mutants leads to the decreased variability of the IGS and to the occurrence of distinct IGS variants. We present for the first time a comprehensive and representative set of complete IGS sequences, obtained by conventional cloning and by Pacific Biosciences sequencing. Our data expands the knowledge of the A. thaliana IGS sequence arrangement and variability, which has not been available in full and in detail until now. This is also the first study combining IGS sequencing data with RFLP analysis of genomic DNA.
ER  -

HAVLOVÁ, Kateřina, Martina DVOŘÁČKOVÁ, Ramon PEIRO, David ABIA, Iva MOZGOVÁ, Lenka VANSÁČOVÁ, Crisanto GUTIERREZ a Jiří FAJKUS. Variation of 45S rDNA intergenic spacers in Arabidopsis thaliana. \textit{Plant Molecular Biology}. Dordrecht: Springer, 2016, roč.~92, 4-5, s.~457-471. ISSN~0167-4412. Dostupné z: https://dx.doi.org/10.1007/s11103-016-0524-1.

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