Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis

Simonini, Sara; Bencivenga, Stefano; Trick, Martin; Østergaard, Lars

doi:10.1105/tpc.17.00389

Cited by 97 publications

(119 citation statements)

References 70 publications

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“…Redundant clusters of activator binding sites are thought to be common, and may contribute to robustness (Frankel et al, 2010;Hong, Hendrix, & Levine, 2008;Levine, 2010;Perry, Boettiger, Bothma, & Levine, 2010). Effects may be larger in other tissues, given the important functions of ARF repressors in fruits and roots (Marin et al, 2010;Sessions & Zambryski, 1995;Simonini, Bencivenga, Trick, & Østergaard, 2017;Simonini et al, 2016;Su et al, 2017). Alternatively, the sites may simply be nonfunctional, at least in A. thaliana.…”

Section: Discussionmentioning

confidence: 99%

Functional dissection of the ARGONAUTE7 promoter

et al. 2019

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ARGONAUTES are the central effector proteins of RNA silencing which bind target transcripts in a small RNA ‐guided manner. Arabidopsis thaliana has 10 ARGONAUTE ( AGO ) genes, with specialized roles in RNA ‐directed DNA methylation, post‐transcriptional gene silencing, and antiviral defense. To better understand specialization among AGO genes at the level of transcriptional regulation we tested a library of 1497 transcription factors for binding to the promoters of AGO 1 , AGO 10 , and AGO 7 using yeast 1‐hybrid assays. A ranked list of candidate DNA ‐binding TF s revealed binding of the AGO 7 promoter by a number of proteins in two families: the miR156‐regulated SPL family and the miR319‐regulated TCP family, both of which have roles in developmental timing and leaf morphology. Possible functions for SPL and TCP binding are unclear: we showed that these binding sites are not required for the polar expression pattern of AGO 7 , nor for the function of AGO 7 in leaf shape. Normal AGO 7 transcription levels and function appear to depend instead on an adjacent 124‐bp region. Progress in understanding the structure of this promoter may aid efforts to understand how the conserved AGO 7‐triggered TAS 3 pathway functions in timing and polarity.

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Section: Discussionmentioning

confidence: 99%

Functional dissection of the ARGONAUTE7 promoter

et al. 2019

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“…Another interesting phenomenon involving PPIs and hormones is the ability of a hormone to modify the physical interaction of proteins, which has been observed recently for auxin with ETT (an ARF member) (Simonini et al, 2016), as well as affecting the transcriptional output (Simonini et al, 2017). Since we recovered all the colonies that grew in our Y2H experiments, we had the entire dimer collection in yeast colonies.…”

Section: Inserting Hormones Into the Networkmentioning

confidence: 99%

An interaction map of transcription factors controlling gynoecium development in Arabidopsis

Herrera-Ubaldo

Campos

Luna-García

et al. 2018

Preprint

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Flowers are composed of different organs, whose identity is defined at the molecular by the combinatorial activity of transcription factors (TFs). MADS-box TFs interact forming complexes that have been schematized in the quartet model. The gynoecium is the female reproductive part in the flower, crucial for plant reproduction, and fruit and seed production.Once carpel identity is established, a gynoecium containing many tissues arises. Several TFs have been identified as regulators of gynoecium development, and some of these TFs form complexes. However, broad knowledge about the interactions among these TFs is still scarce. In this work, we used a systems biology approach to understand the formation of a complex reproductive unit as the gynoecium by mapping binary interactions between wellcharacterized TFs. We analyzed over 3500 combinations and detected more than 200 protein-protein interactions (PPIs), resulting in a process specific interaction map.Topological analyses suggest hidden functions and novel roles for many TFs. Furthermore, a relationship between TFs involved in auxin and cytokinin signaling pathways and other TFs was observed. We analyzed the network by combining PPI data, expression and genetic data, allowing us to dissect it into several dynamic spatio-temporal sub-networks related to gynoecium development subprocesses.Arabidopsis has been studied for more than 20 years (Roeder and Yanofsky, 2006;Alvarez-Buylla et al., 2010). The accepted model for floral organ formation relies on the combinatorial action of mostly MADS-box proteins, resulting in the specification of the four whorls of the flower: sepals, petals, stamens and carpels (Coen and Meyerowitz, 1991).At the molecular level, MADS-box transcription factors (TFs) form complexes in order to regulate gene expression. For the female reproductive organs, the C-class and E-class

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“…Redundant clusters of activator binding sites are thought to be common, and may contribute to robustness [59][60][61][62]. Effects may be larger in other tissues, given the important functions of ARF repressors in fruits and roots [63][64][65][66][67]. Alternatively, the sites may simply be nonfunctional, at least in A. thaliana.…”

Section: Tcpsmentioning

confidence: 99%

Functional dissection of theARGONAUTE7promoter

Hoyer

Pruneda‐Paz

Breton

et al. 2018

Preprint

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ARGONAUTES are the central effector proteins of RNA silencing which bind target transcripts in a small RNA-guided manner. Arabidopsis thaliana has ten ARGONAUTE (AGO) genes, with specialized roles in RNA-directed DNA methylation, post-transcriptional gene silencing, and antiviral defense. To better understand specialization among AGO genes at the level of transcriptional regulation we tested a library of 1497 transcription factors for binding to the promoters of AGO1, AGO10, and AGO7 using yeast 1-hybrid assays. A ranked list of candidate DNA-binding TFs revealed binding of the AGO7 promoter by a number of proteins in two families: the miR156-regulated SPL family and the miR319-regulated TCP family, both of which have roles in developmental timing and leaf morphology. Possible functions for SPL and TCP binding are unclear: we showed that these binding sites are not required for the polar expression pattern of AGO7, nor for the function of AGO7 in leaf shape. Normal AGO7 transcription levels and function appear to depend instead on an adjacent 124-bp region. Progress in understanding the structure of this promoter may aid efforts to understand how the conserved AGO7-triggered TAS3 pathway functions in timing and polarity.A total of 1497 TFs were tested for AGO promoter binding. This collection consisted mainly of 2/25 3/25 Figure 2. Identification of SPL11 binding sites. A. Sequence logo for SPL11 PWM, as downloaded from CisBP. Individual position weights can be interpreted as binding specificity contributions (changes in free energy, arbitrary units). B and C. Scores for SPL11 PWM at each position of the 1 kb region upstream of the annotated AGO7 transcription start site. D. Reporter activity (relative luminescence units normalized by A600) for SPL11 and pDEST22 (empty vector) tested in yeast against AGO7 promoter baits including several derivatives of the -531/-446 region. Modifications included one or two 4-bp deletions, 8 substitutions (TCCG/AAGG), and an unrelated 6-bp deletion; see Table 2, below. 4/25 6/25 8/25 Our truncation analysis provided preliminary evidence for two other functional regions of the AGO7 10/25 12/25 13/25

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Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis

Cited by 97 publications

References 70 publications

Functional dissection of the ARGONAUTE7 promoter

Functional dissection of the ARGONAUTE7 promoter

An interaction map of transcription factors controlling gynoecium development in Arabidopsis

Functional dissection of theARGONAUTE7promoter

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