Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana

Abstract

Floral homeotic transcription factors (TFs) act in a combinatorial manner to specify the organ identities in the flower. However, the architecture and the function of the gene regulatory network (GRN) controlling floral organ specification is still poorly understood. In particular, the interconnections of homeotic TFs, microRNAs (miRNAs) and other factors controlling organ initiation and growth have not been studied systematically so far. Here, using a combination of genome-wide TF binding, mRNA and miRNA expression data, we reconstruct the dynamic GRN controlling floral meristem development and organ differentiation. We identify prevalent feed-forward loops (FFLs) mediated by floral homeotic TFs and miRNAs that regulate common targets. Experimental validation of a coherent FFL shows that petal size is controlled by the SEPALLATA3-regulated miR319/TCP4 module. We further show that combinatorial DNA-binding of homeotic factors and selected other TFs is predictive of organ-specific patterns of gene expression. Our results provide a valuable resource for studying molecular regulatory processes underlying floral organ specification in plants.

Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks

“…From the CNSs present in the 12 rosids species associated with duster-specific copies in the 500bp upstream of genes, we found 67 duster-specific sequences. Among them, 42 are target genes of floral regulators according to Chen et al [39] and 18 of these display a colocalization of Duster-specific regions with a highly conserved CNSs and a TFBS (Table 4). T 1 G 2 5 3 8 0 A P 3 ; P I S O C 1 A T 1 G 4 9 7 6 0 A G L -1 5 A T 1 G 7 5 1 1 0 G L 1 A T 2 G 0 5 9 2 0 A G L -1 5 ; P I F 4 S O C 1 A T 2 G 3 0 4 0 0 A G L -1 5 A T 2 G 3 0 9 7 0 A G L -1 5 ; A P 1 ; S E P 3 A T 2 G 3 3 7 5 0 S E P 3 S O C 1 A T 2 G 4 1 3 7 0 A G L -1 5 ; A P 1 ; A P 3 ; P I A T 3 G 0 2 0 4 0 A P 3 ; A G L -1 5 ; P I S O C 1 A T 3 G 1 4 1 7 2 A G L -1 5 A T 3 G 1 9 1 7 0 A G L -1 5 ; P I F 4 ; P I F 3 ; P I ; A P 3 S O C 1 A T 4 G 0 0 8 1 0 P I F S O C 1 A T 4 G 3 2 6 8 0 F Y 3 S O C 1 A T 4 G 3 7 2 6 0 S E P 3 S O C 1 A T 5 G 0 3 6 8 0 A P 1 ; S E P 3 ; F L M ; P I F 4 A T 5 G 1 3 9 9 0 P I F 4 Using the MEME Suite we identified 10 of them with a sequence corresponding to a binding motif of the SOC1 TF.…”

ChIP-Hub: an Integrative Platform for Exploring Plant Regulome

“…The final meta-network consisted of regulatory relationships among 97 master TFs, 125 miRNAs and 447 common target TFs ( Supplementary Fig. 6a and Supplementary Table 2 ), covering nearly two-thirds of the predicted FFLs involved in flower development 13 ( Supplementary Fig. 6b,c ).…”

“…Integrative analysis of TF-bound genomic regions and target genes revealed potential TF co-associations ( Supplementary Figs. 4 and 5 ) and comprehensive miRNA-mediated feed-forward loops 13 (FFLs; Supplementary Fig. 6 ).…”

Co-expression clustering across flower development identifies modules for diverse floral forms inAchimenes(Gesneriaceae)

“…The role of TCP4 been characterized in Arabidopsis for its role in petal growth, showing restricted expression to the developing petal tissue (Nag, King & Jack, 2009). More recent work using gene regulatory networks in Arabidopsis has shown that petal size is controlled by a SEPALLATA3-regulated miR319/TCP4 module (Chen et al, 2018). Outside of Arabidopsis, TCP4 was also implicated for a having a role in the development of the petal spur in Aquilegia (Yant et al, 2015).…”