@article{fdi:010077032,
  title = {{I}nference 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},
  author = {{L}avarenne, {J}. and {G}onin, {M}. and {G}uyomarc'h, {S}. and {R}ouster, {J}. and {C}hampion, {A}ntony and {S}allaud, {C}. and {L}aplaze, {L}aurent and {G}antet, {P}ascal and {L}ucas, {M}ika{\¨e}l},
  editor = {},
  language = {{ENG}},
  abstract = {{C}rown roots ({CR}s) are essential components of the rice root system. {S}everal 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. {T}o 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 ({CRL}1), 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 {CRL}1 expression in a crl1 mutant background. {T}his 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. {T}he predicted {GRN} was confronted with experimental data and 72% of the inferred links were validated. {I}nterestingly, this network revealed a regulatory cascade linking {CRL}1 to other genes involved in {CR} initiation, root meristem specification and maintenance, such as {QUIESCENT}-{CENTER}-{SPECIFIC} {HOMEOBOX}, and in auxin signalling. {T}his predicted regulatory cascade was validated in vivo using transient activation assays. {T}hus, the {CRL}1-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.},
  keywords = {rice ; root biology ; meristem development ; gene regulation ; transcriptome ; analysis ; systems biology},
  booktitle = {},
  journal = {{P}lant {J}ournal},
  volume = {100},
  numero = {5},
  pages = {954--968},
  ISSN = {0960-7412},
  year = {2019},
  DOI = {10.1111/tpj.14487},
  URL = {https://www.documentation.ird.fr/hor/fdi:010077032},
}