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.

Basic information

Original name

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

Authors

RAXWAL, Vivek Kumar (356 India, guarantor, belonging to the institution), S. GHOSH, S. SINGH, S. KATIYAR-AGARWAL, S. GOEL, A. JAGANNATH, A. KUMAR, V. SCARIA and M. AGARWAL

Edition

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

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: 6.992

RIV identification code

RIV/00216224:14740/20:00114766

Organization unit

Central European Institute of Technology

DOI

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

UT WoS

000573252000014

Keywords in English

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

Abstract

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.

Links

EF15_003/0000479, research and development project

Name: Regulace rostlinné meiózy

GA16-18578S, research and development project

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

Investor: Czech Science Foundation

Citovat

RAXWAL, Vivek Kumar, S. GHOSH, S. SINGH, S. KATIYAR-AGARWAL, S. GOEL, A. JAGANNATH, A. KUMAR, V. SCARIA and M. AGARWAL. Abiotic stress-mediated modulation of the chromatin landscape in Arabidopsis thaliana. Journal of Experimental Botany. Oxford: OXFORD UNIV PRESS, 2020, vol. 71, No 17, p. 5280-5293. ISSN 0022-0957. Available from: 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 and M. AGARWAL. Abiotic stress-mediated modulation of the chromatin landscape in Arabidopsis thaliana. \textit{Journal of Experimental Botany}. Oxford: OXFORD UNIV PRESS, 2020, vol.~71, No~17, p.~5280-5293. ISSN~0022-0957. Available from: https://dx.doi.org/10.1093/jxb/eraa286.

Detailed Information on Publication Record