TY - JOUR
T1 - Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors
AU - Ding, Pingtao
AU - Sakai, Toshiyuki
AU - Shrestha, Ram Krishna
AU - Perez, Nicolas Manosalva
AU - Guo, Wenbin
AU - Ngou, Bruno Pok Man
AU - He, Shengbo
AU - Liu, Chang
AU - Feng, Xiaoqi
AU - Zhang, Runxuan
AU - Vandepoele, Klaas
AU - MacLean, Dan
AU - Jones, Jonathan D. G.
N1 - We thank the Gatsby Foundation (United Kingdom) for funding to the JDGJ laboratory. PD acknowledges support from the European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodowska-Curie Actions (grant agreement: 656243) and a Future Leader Fellowship from the Biotechnology and Biological Sciences Research Council (BBSRC) (grant agreement: BB/R012172/1). TS, RKS, DM and JDGJ were supported by the Gatsby Foundation funding to the Sainsbury Laboratory. NMP and KV were supported by a BOF grant from Ghent University (grant agreement: BOF24Y2019001901). WG and RZ were supported by Scottish Government Rural and Environment Science and Analytical Services division (RESAS), and RZ also acknowledge the support from a BBSRC Bioinformatics and Biological Resources Fund (grant agreement: BB/S020160/1). BN was supported by the Norwich Research Park (NRP) Biosciences Doctoral Training Partnership (DTP) funded by BBSRC (grant agreement: BB/M011216/1). SH and XF were supported by a BBSRC Responsive Mode grant (grant agreement: BB/S009620/1) and a European Research Council Starting grant ‘SexMeth’ (grant agreement: 804981). CL was supported by Deutsche Forschungsgemeinschaft (grant agreement: LI 2862/4)
© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: [email protected].
PY - 2021/12/4
Y1 - 2021/12/4
N2 - Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defense genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, and by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems.
AB - Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defense genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, and by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems.
KW - ATAC-seq and RNA-seq
KW - cell surface immune receptors
KW - chromatin accessibility
KW - gene regulatory network
KW - intracellular immune receptors
KW - plant innate immunity
KW - PRR and NLR
KW - transcriptional regulation
U2 - 10.1093/jxb/erab373
DO - 10.1093/jxb/erab373
M3 - Article
C2 - 34387350
SN - 0022-0957
VL - 72
SP - 7927
EP - 7941
JO - Journal of Experimental Botany
JF - Journal of Experimental Botany
IS - 22
ER -