Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
05 04 2019
05 04 2019
Historique:
received:
29
07
2018
accepted:
15
03
2019
entrez:
7
4
2019
pubmed:
7
4
2019
medline:
10
5
2019
Statut:
epublish
Résumé
Charting a temporal path in gene networks requires linking early transcription factor (TF)-triggered events to downstream effects. We scale-up a cell-based TF-perturbation assay to identify direct regulated targets of 33 nitrogen (N)-early response TFs encompassing 88% of N-responsive Arabidopsis genes. We uncover a duality where each TF is an inducer and repressor, and in vitro cis-motifs are typically specific to regulation directionality. Validated TF-targets (71,836) are used to refine precision of a time-inferred root network, connecting 145 N-responsive TFs and 311 targets. These data are used to chart network paths from direct TF
Identifiants
pubmed: 30952851
doi: 10.1038/s41467-019-09522-1
pii: 10.1038/s41467-019-09522-1
pmc: PMC6451032
doi:
Substances chimiques
Arabidopsis Proteins
0
Basic-Leucine Zipper Transcription Factors
0
CRF4 protein, Arabidopsis
0
TGA1 protein, Arabidopsis
0
Transcription Factors
0
Nitrogen
N762921K75
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1569Subventions
Organisme : NIGMS NIH HHS
ID : F32 GM116347
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM032877
Pays : United States
Références
PLoS Comput Biol. 2013;9(8):e1003118
pubmed: 23950696
BMC Bioinformatics. 2010 Apr 01;11:165
pubmed: 20356413
Nat Commun. 2013;4:1713
pubmed: 23591880
Methods Mol Biol. 2015;1284:123-38
pubmed: 25757770
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Int J Mol Sci. 2018 Oct 27;19(11):
pubmed: 30373239
Plant Signal Behav. 2014;9(3):e28501
pubmed: 24642706
Nature. 2018 Nov;563(7730):259-264
pubmed: 30356219
Mol Syst Biol. 2015 Nov 17;11(11):839
pubmed: 26577401
Trends Plant Sci. 2015 Oct;20(10):664-675
pubmed: 26440435
Adv Biochem Eng Biotechnol. 2007;104:65-85
pubmed: 17290819
J Biotechnol. 2007 Jan 10;127(3):335-47
pubmed: 16959350
Nature. 2012 Apr 11;484(7393):251-5
pubmed: 22498630
Nature. 1997 Apr 24;386(6627):855-8
pubmed: 9126747
Cell. 2014 Jan 30;156(3):577-89
pubmed: 24485461
Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5136-41
pubmed: 12702751
Methods. 1999 Nov;19(3):425-33
pubmed: 10579938
Nat Methods. 2017 Aug;14(8):819-825
pubmed: 28650476
Trends Plant Sci. 2001 Jun;6(6):262-7
pubmed: 11378468
BMC Genomics. 2016 Feb 03;17:92
pubmed: 26843062
J Cell Sci. 2005 Nov 1;118(Pt 21):4947-57
pubmed: 16254242
Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10371-6
pubmed: 24958886
Plant J. 1997 Mar;11(3):605-12
pubmed: 9107046
Genome Biol. 2014;15(12):550
pubmed: 25516281
Plant J. 2009 Feb;57(3):426-35
pubmed: 18826430
Cell Rep. 2014 Sep 25;8(6):2015-2030
pubmed: 25220462
Nat Commun. 2015 Feb 27;6:6274
pubmed: 25723764
Science. 1999 Jan 15;283(5400):381-7
pubmed: 9888852
PLoS Comput Biol. 2013;9(11):e1003361
pubmed: 24278007
Nature. 2012 Sep 6;489(7414):91-100
pubmed: 22955619
Cell. 2014 Sep 11;158(6):1431-1443
pubmed: 25215497
Nat Rev Genet. 2017 Aug;18(8):457-472
pubmed: 28529337
Nucleic Acids Res. 2017 Jul 27;45(13):e119
pubmed: 28591841
Plant J. 2014 Oct;80(1):1-13
pubmed: 25039575
Science. 2011 Jul 29;333(6042):601-7
pubmed: 21798944
Nat Commun. 2018 Apr 10;9(1):1376
pubmed: 29636481
Genome Biol. 2010;11(12):R123
pubmed: 21182762
Science. 1999 Oct 15;286(5439):509-12
pubmed: 10521342
Trends Genet. 2014 Jun;30(6):211-9
pubmed: 24774859
Nat Genet. 2005 Apr;37(4):382-90
pubmed: 15778709
PLoS Biol. 2007 Jan;5(1):e8
pubmed: 17214507
Cell Rep. 2014 Jul 24;8(2):622-32
pubmed: 25043187
Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2367-72
pubmed: 24477691
Nucleic Acids Res. 2018 Jan 4;46(D1):D260-D266
pubmed: 29140473
Cell. 2008 Jun 13;133(6):1106-17
pubmed: 18555785
Dev Cell. 2016 Dec 5;39(5):585-596
pubmed: 27923776
Plant Cell. 2009 Nov;21(11):3567-84
pubmed: 19933203
Biochim Biophys Acta Gene Regul Mech. 2017 Jan;1860(1):75-83
pubmed: 27546191
Nat Methods. 2012 Jul 15;9(8):796-804
pubmed: 22796662
Cell. 2016 Sep 8;166(6):1598
pubmed: 27610578
Mol Cells. 2008 Jun 30;25(4):559-65
pubmed: 18587275
Trends Genet. 2015 Sep;31(9):509-15
pubmed: 26072453
Sci Signal. 2016 Oct 25;9(451):rs13
pubmed: 27811143
Genome Biol. 2013 Apr 25;14(4):R36
pubmed: 23618408
Cell. 2009 Apr 3;137(1):172-81
pubmed: 19327819
J Mol Biol. 1999 Apr 23;288(1):13-20
pubmed: 10329122
Plant Cell. 2017 Jan;29(1):20-38
pubmed: 28011690
Mol Biotechnol. 2011 Jun;48(2):109-15
pubmed: 21104043
Science. 2016 Nov 4;354(6312):
pubmed: 27811239
Plant Cell. 2014 Dec;26(12):4656-79
pubmed: 25549671
Nucleic Acids Res. 2007;35(19):6663-71
pubmed: 17913740
Nucleic Acids Res. 2017 Jul 3;45(W1):W122-W129
pubmed: 28472432
Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6494-6499
pubmed: 29769331
Plant J. 2017 Oct;92(2):305-316
pubmed: 28771873
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
pubmed: 19458158
Mol Plant. 2013 May;6(3):978-80
pubmed: 23335732
Plant Cell. 2008 Sep;20(9):2324-38
pubmed: 18796637
Nature. 2004 Sep 2;431(7004):99-104
pubmed: 15343339