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TERMINAL FLOWER 1 (TFL1) is a key regulator of Arabidopsis plant architecture that responds to developmental and environmental signals to control flowering time and the fate of shoot meristems. TFL1 expression is dynamic, being found in all shoot meristems, but not in floral meristems, with the level and distribution changing throughout development. Using a variety of experimental approaches we have analysed the TFL1 promoter to elucidate its functional structure. TFL1 expression is based on distinct cis-regulatory regions, the most important being located 3' of the coding sequence. Our results indicate that TFL1 expression in the shoot apical versus lateral inflorescence meristems is controlled through distinct cis-regulatory elements, suggesting that different signals control expression in these meristem types. Moreover, we identified a cis-regulatory region necessary for TFL1 expression in the vegetative shoot and required for a wild-type flowering time, supporting that TFL1 expression in the vegetative meristem controls flowering time. Our study provides a model for the functional organisation of TFL1 cis-regulatory regions, contributing to our understanding of how developmental pathways are integrated at the genomic level of a key regulator to control plant architecture., This work was supported by a Joint Project Grant from the Royal Society [ESEP/JP 15057] to D.B. and F.M. The laboratory of F.M. was funded by grants from the Spanish Ministerio de Ciencia e Innovacion [BIO2009-10876 and CSD2007-00057], the Spanish Ministerio de Economia y Competitividad [BFU2012-38929] and from the Generalitat Valenciana [ACOMP09-083 and ACOMP2012-099]. Work in the Y.H. lab was supported by the Plant Genome Research Program from the National Science Foundation [NSF-PGRP-IOS-1339388]. P.F.-N. was supported by a fellowship from the I3P Program of Consejo Superior de Investigaciones Cientificas.