Large tandem duplications affect gene expression, 3D
organization, and plant-pathogen response

J 2020

Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response

PICART-PICOLO, A.; S. GROB; N. PICAULT; Michal FRANEK; C. LLAURO et al.

Základní údaje

Originální název

Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response

Autoři

Vydání

Genome research, COLD SPRING HARBOR, COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2020, 1088-9051

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 9.043

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/20:00114759

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

RIBOSOMAL-RNA GENES; SISTER-CHROMATID EXCHANGE; COPY NUMBER VARIATION; ARABIDOPSIS-THALIANA; DOSAGE CONTROL; REVEALS; NUCLEOLUS; DOMAINS; TRANSCRIPTION; MECHANISMS

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 11. 3. 2021 17:54, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

Rapid plant genome evolution is crucial to adapt to environmental changes. Chromosomal rearrangements and gene copy number variation (CNV) are two important tools for genome evolution and sources for the creation of new genes. However, their emergence takes many generations. In this study, we show that in Arabidopsis thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the genome structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. Our data suggest that these TDDOs appeared within a few generations, leading to the duplication of hundreds of genes. By subsequently focusing on a line only containing 20% of rRNA gene copies (20rDNA line), we investigated the impact of TDDOs on 3D genome organization, gene expression, and cytosine methylation. We found that duplicated genes often accumulate more transcripts. Among them, several are involved in plant-pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and discuss their potential implications for the evolution of plant genomes.

Návaznosti

EF16_026/0008446, projekt VaV

Název: Integrace signálu a epigenetické reprogramování pro produktivitu rostlin

GJ19-11880Y, projekt VaV

Název: Chromatinové prostředí indukované genotoxickými látkami

Investor: Grantová agentura ČR, Chromatinové prostředí indukované genotoxickými látkami

LTC18048, projekt VaV

Název: Prostorové uspořádání významných jaderných domén a jejich proteinových složek

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Prostorové uspořádání významných jaderných domén a jejich proteinových složek, INTER-COST

Citovat

PICART-PICOLO, A.; S. GROB; N. PICAULT; Michal FRANEK; C. LLAURO; T. HALTER; T.R. MAIER; E. JOBET; J. DESCOMBIN; P.P. ZHANG; V. PARAMASIVAN; T.J. BAUM; L. NAVARRO; Martina DVOŘÁČKOVÁ; M. MIROUZE a F. PONTVIANNE. Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response. Genome research. COLD SPRING HARBOR: COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2020, roč. 30, č. 11, s. 1583-1592. ISSN 1088-9051. Dostupné z: https://doi.org/10.1101/gr.261586.120.

@article{1749406,
   author = {PicartandPicolo, A. and Grob, S. and Picault, N. and Franek, Michal and Llauro, C. and Halter, T. and Maier, T.R. and Jobet, E. and Descombin, J. and Zhang, P.P. and Paramasivan, V. and Baum, T.J. and Navarro, L. and Dvořáčková, Martina and Mirouze, M. and Pontvianne, F.},
   article_location = {COLD SPRING HARBOR},
   article_number = {11},
   doi = {https://doi.org/10.1101/gr.261586.120},
   keywords = {RIBOSOMAL-RNA GENES; SISTER-CHROMATID EXCHANGE; COPY NUMBER VARIATION; ARABIDOPSIS-THALIANA; DOSAGE CONTROL; REVEALS; NUCLEOLUS; DOMAINS; TRANSCRIPTION; MECHANISMS},
   language = {eng},
   issn = {1088-9051},
   journal = {Genome research},
   title = {Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response},
   url = {https://genome.cshlp.org/content/30/11/1583},
   volume = {30},
   year = {2020}
}

TY  - JOUR
ID  - 1749406
AU  - Picart-Picolo, A. - Grob, S. - Picault, N. - Franek, Michal - Llauro, C. - Halter, T. - Maier, T.R. - Jobet, E. - Descombin, J. - Zhang, P.P. - Paramasivan, V. - Baum, T.J. - Navarro, L. - Dvořáčková, Martina - Mirouze, M. - Pontvianne, F.
PY  - 2020
TI  - Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response
JF  - Genome research
VL  - 30
IS  - 11
SP  - 1583-1592
EP  - 1583-1592
PB  - COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
SN  - 10889051
KW  - RIBOSOMAL-RNA GENES
KW  - SISTER-CHROMATID EXCHANGE
KW  - COPY NUMBER VARIATION
KW  - ARABIDOPSIS-THALIANA
KW  - DOSAGE CONTROL
KW  - REVEALS
KW  - NUCLEOLUS
KW  - DOMAINS
KW  - TRANSCRIPTION
KW  - MECHANISMS
UR  - https://genome.cshlp.org/content/30/11/1583
N2  - Rapid plant genome evolution is crucial to adapt to environmental changes. Chromosomal rearrangements and gene copy number variation (CNV) are two important tools for genome evolution and sources for the creation of new genes. However, their emergence takes many generations. In this study, we show that in Arabidopsis thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the genome structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. Our data suggest that these TDDOs appeared within a few generations, leading to the duplication of hundreds of genes. By subsequently focusing on a line only containing 20% of rRNA gene copies (20rDNA line), we investigated the impact of TDDOs on 3D genome organization, gene expression, and cytosine methylation. We found that duplicated genes often accumulate more transcripts. Among them, several are involved in plant-pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and discuss their potential implications for the evolution of plant genomes.
ER  -

PICART-PICOLO, A.; S. GROB; N. PICAULT; Michal FRANEK; C. LLAURO; T. HALTER; T.R. MAIER; E. JOBET; J. DESCOMBIN; P.P. ZHANG; V. PARAMASIVAN; T.J. BAUM; L. NAVARRO; Martina DVOŘÁČKOVÁ; M. MIROUZE a F. PONTVIANNE. Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response. \textit{Genome research}. COLD SPRING HARBOR: COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2020, roč.~30, č.~11, s.~1583-1592. ISSN~1088-9051. Dostupné z: https://doi.org/10.1101/gr.261586.120.

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