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

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 Lavarenne J. auteur aut IRD Gonin M. auteur aut IRD Guyomarc'h S. auteur aut IRD Rouster J. auteur aut IRD Champion Antony auteur aut IRD Sallaud C. auteur aut IRD Laplaze Laurent auteur aut IRD Gantet Pascal auteur aut IRD Lucas Mikaël auteur aut IRD text journalArticle eng text/pdf born digital access 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. specialized rice root biology meristem development gene regulation transcriptome analysis systems biology 076 020 Plant Journal 100 5 954-968 2019 0960-7412 https://www.documentation.ird.fr/hor/fdi:010077032 10.1111/tpj.14487 0960-7412 [F B010077032] https://www.documentation.ird.fr/hor/fdi:010077032 https://www.documentation.ird.fr/intranet/publi/depot/2020-11-19/010077032.pdf Accès réservé (Intranet de l'IRD) IRD - Base Horizon / Pleins textes 2019-11-05 2020-11-24 fdi:010077032 fre