Abiotic stress-mediated modulation of the chromatin landscape
in Arabidopsis thaliana

J 2020

Abiotic stress-mediated modulation of the chromatin landscape in Arabidopsis thaliana

RAXWAL, Vivek Kumar, S. GHOSH, S. SINGH, S. KATIYAR-AGARWAL, S. GOEL et. al.

Základní údaje

Originální název

Abiotic stress-mediated modulation of the chromatin landscape in Arabidopsis thaliana

Autoři

RAXWAL, Vivek Kumar (356 Indie, garant, domácí), S. GHOSH, S. SINGH, S. KATIYAR-AGARWAL, S. GOEL, A. JAGANNATH, A. KUMAR, V. SCARIA a M. AGARWAL

Vydání

Journal of Experimental Botany, Oxford, OXFORD UNIV PRESS, 2020, 0022-0957

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: 6.992

Kód RIV

RIV/00216224:14740/20:00114766

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1093/jxb/eraa286

UT WoS

000573252000014

Klíčová slova anglicky

Abiotic stress; Arabidopsis; chromatin landscape; DNase-seq; FAIRE-seq; open chromatin; transcription

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 11. 3. 2021 19:22, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

Limited information is available on abiotic stress-mediated alterations of chromatin conformation influencing gene expression in plants. In order to characterize the effect of abiotic stresses on changes in chromatin conformation, we employed FAIRE-seq (formaldehyde-assisted isolation of regulatory element sequencing) and DNase-seq to isolate accessible regions of chromatin from Arabidopsis thaliana seedlings exposed to either heat, cold, salt, or drought stress. Approximately 25% of regions in the Arabidopsis genome were captured as open chromatin, the majority of which included promoters and exons. A large proportion of chromatin regions apparently did not change their conformation in response to any of the four stresses. Digital footprints present within these regions had differential enrichment of motifs for binding of 43 different transcription factors. Further, in contrast to drought and salt stress, both high and low temperature treatments resulted in increased accessibility of the chromatin. Also, pseudogenes attained increased chromatin accessibility in response to cold and drought stresses. The highly accessible and inaccessible chromatin regions of seedlings exposed to drought stress correlated with the Ser/Thr protein kinases (MLK1 and MLK2)-mediated reduction and increase in H3 phosphorylation (H3T3Ph), respectively. The presented results provide a deeper understanding of abiotic stress-mediated chromatin modulation in plants.

Návaznosti

EF15_003/0000479, projekt VaV

Název: Regulace rostlinné meiózy

GA16-18578S, projekt VaV

Název: Funkce UPF1 helikázy v procesech odehrávajících se v buněčném jádře

Investor: Grantová agentura ČR, Funkce UPF1 helikázy v procesech odehrávajících se v buněčném jádře

Citovat

RAXWAL, Vivek Kumar, S. GHOSH, S. SINGH, S. KATIYAR-AGARWAL, S. GOEL, A. JAGANNATH, A. KUMAR, V. SCARIA a M. AGARWAL. Abiotic stress-mediated modulation of the chromatin landscape in Arabidopsis thaliana. Journal of Experimental Botany. Oxford: OXFORD UNIV PRESS, 2020, roč. 71, č. 17, s. 5280-5293. ISSN 0022-0957. Dostupné z: https://dx.doi.org/10.1093/jxb/eraa286.

@article{1751479,
   author = {Raxwal, Vivek Kumar and Ghosh, S. and Singh, S. and KatiyarandAgarwal, S. and Goel, S. and Jagannath, A. and Kumar, A. and Scaria, V. and Agarwal, M.},
   article_location = {Oxford},
   article_number = {17},
   doi = {http://dx.doi.org/10.1093/jxb/eraa286},
   keywords = {Abiotic stress; Arabidopsis; chromatin landscape; DNase-seq; FAIRE-seq; open chromatin; transcription},
   language = {eng},
   issn = {0022-0957},
   journal = {Journal of Experimental Botany},
   title = {Abiotic stress-mediated modulation of the chromatin landscape in Arabidopsis thaliana},
   url = {https://academic.oup.com/jxb/article/71/17/5280/5856113},
   volume = {71},
   year = {2020}
}

TY  - JOUR
ID  - 1751479
AU  - Raxwal, Vivek Kumar - Ghosh, S. - Singh, S. - Katiyar-Agarwal, S. - Goel, S. - Jagannath, A. - Kumar, A. - Scaria, V. - Agarwal, M.
PY  - 2020
TI  - Abiotic stress-mediated modulation of the chromatin landscape in Arabidopsis thaliana
JF  - Journal of Experimental Botany
VL  - 71
IS  - 17
SP  - 5280-5293
EP  - 5280-5293
PB  - OXFORD UNIV PRESS
SN  - 00220957
KW  - Abiotic stress
KW  - Arabidopsis
KW  - chromatin landscape
KW  - DNase-seq
KW  - FAIRE-seq
KW  - open chromatin
KW  - transcription
UR  - https://academic.oup.com/jxb/article/71/17/5280/5856113
N2  - Limited information is available on abiotic stress-mediated alterations of chromatin conformation influencing gene expression in plants. In order to characterize the effect of abiotic stresses on changes in chromatin conformation, we employed FAIRE-seq (formaldehyde-assisted isolation of regulatory element sequencing) and DNase-seq to isolate accessible regions of chromatin from Arabidopsis thaliana seedlings exposed to either heat, cold, salt, or drought stress. Approximately 25% of regions in the Arabidopsis genome were captured as open chromatin, the majority of which included promoters and exons. A large proportion of chromatin regions apparently did not change their conformation in response to any of the four stresses. Digital footprints present within these regions had differential enrichment of motifs for binding of 43 different transcription factors. Further, in contrast to drought and salt stress, both high and low temperature treatments resulted in increased accessibility of the chromatin. Also, pseudogenes attained increased chromatin accessibility in response to cold and drought stresses. The highly accessible and inaccessible chromatin regions of seedlings exposed to drought stress correlated with the Ser/Thr protein kinases (MLK1 and MLK2)-mediated reduction and increase in H3 phosphorylation (H3T3Ph), respectively. The presented results provide a deeper understanding of abiotic stress-mediated chromatin modulation in plants.
ER  -

RAXWAL, Vivek Kumar, S. GHOSH, S. SINGH, S. KATIYAR-AGARWAL, S. GOEL, A. JAGANNATH, A. KUMAR, V. SCARIA a M. AGARWAL. Abiotic stress-mediated modulation of the chromatin landscape in Arabidopsis thaliana. \textit{Journal of Experimental Botany}. Oxford: OXFORD UNIV PRESS, 2020, roč.~71, č.~17, s.~5280-5293. ISSN~0022-0957. Dostupné z: https://dx.doi.org/10.1093/jxb/eraa286.

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