Inference of the gene regulatory network acting downstream of CROWN ROOTLESS 1 in rice reveals a regulatory cascade linking genes involved in auxin signaling, crown root initiation, and root meristem specification and maintenance.
Gene Expression Profiling
Gene Expression Regulation, Plant
/ drug effects
Gene Ontology
Gene Regulatory Networks
/ drug effects
Genes, Homeobox
Indoleacetic Acids
/ metabolism
Meristem
/ genetics
Oryza
/ genetics
Plant Proteins
/ metabolism
Plant Roots
/ drug effects
Plants, Genetically Modified
Promoter Regions, Genetic
Protein Domains
/ genetics
Signal Transduction
/ drug effects
Transcription Factors
/ genetics
Transcriptome
gene regulation
meristem development
rice
root biology
systems biology
transcriptome analysis
Journal
The Plant journal : for cell and molecular biology
ISSN: 1365-313X
Titre abrégé: Plant J
Pays: England
ID NLM: 9207397
Informations de publication
Date de publication:
12 2019
12 2019
Historique:
received:
16
04
2019
revised:
16
07
2019
accepted:
17
07
2019
pubmed:
2
8
2019
medline:
31
7
2020
entrez:
2
8
2019
Statut:
ppublish
Résumé
Crown roots (CRs) are essential components of the rice root system. Several genes involved in CR initiation or development have been identified but our knowledge about how they organize to form a gene regulatory network (GRN) is still limited. To characterize the regulatory cascades acting during CR formation, we used a systems biology approach to infer the GRN controlling CR formation downstream of CROWN ROOTLESS 1 (CRL1), coding for an ASL (asymmetric leaves-2-like)/LBD (LOB domain) transcription factor necessary for CR initiation. A time-series transcriptomic dataset was generated after synchronized induction of CR formation by dexamethasone-mediated expression of CRL1 expression in a crl1 mutant background. This time series revealed three different genome expression phases during the early steps of CR formation and was further exploited to infer a GRN using a dedicated algorithm. The predicted GRN was confronted with experimental data and 72% of the inferred links were validated. Interestingly, this network revealed a regulatory cascade linking CRL1 to other genes involved in CR initiation, root meristem specification and maintenance, such as QUIESCENT-CENTER-SPECIFIC HOMEOBOX, and in auxin signalling. This predicted regulatory cascade was validated in vivo using transient activation assays. Thus, the CRL1-dependant GRN reflects major gene regulation events at play during CR formation and constitutes a valuable source of discovery to better understand this developmental process.
Substances chimiques
Indoleacetic Acids
0
Plant Proteins
0
Transcription Factors
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
954-968Informations de copyright
© 2019 The Authors The Plant Journal © 2019 John Wiley & Sons Ltd.
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