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Lavarenne J., Gonin M., Guyomarc'h S., Rouster J., Champion Antony, Sallaud C., Laplaze Laurent, Gantet Pascal, Lucas Mikaël. (2019). 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. Plant Journal, [Early access], [15 p.]. ISSN 0960-7412

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Lien direct chez l'éditeur doi:10.1111/tpj.14487

Titre
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
Année de publication2019
Type de documentArticle référencé dans le Web of Science WOS:000487894200001
AuteursLavarenne J., Gonin M., Guyomarc'h S., Rouster J., Champion Antony, Sallaud C., Laplaze Laurent, Gantet Pascal, Lucas Mikaël.
SourcePlant Journal, 2019, [Early access], p. [15 p.]. p. [15 p.] ISSN 0960-7412
RésuméCrown 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.
Plan de classementSciences du monde végétal [076] ; Sciences fondamentales / Techniques d'analyse et de recherche [020]
LocalisationFonds IRD [F B010077032]
Identifiant IRDfdi:010077032
Lien permanenthttp://www.documentation.ird.fr/hor/fdi:010077032

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