Identification of a Bipartite Jasmonate-Responsive Promoter Element in the <i>Catharanthus roseus ORCA3</i> Transcription Factor Gene That Interacts Specifically with AT-Hook DNA-Binding Proteins

Endt, Débora Vom; Silva, Marina Soares e; Kijne, Jan W.; Pasquali, Giancarlo; Memelink, Johan

doi:10.1104/pp.107.096115

Cited by 114 publications

(78 citation statements)

References 27 publications

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“…6D; Supplemental Table S3). The ATACAT motif is similar to the AT-hook containing TF 20 (AHL20) (PCC distance = 0.24) (Methods), which has been implicated in the regulation of plant defense response (Vom Endt et al 2007;Lu et al 2010). In contrast to ATACAT motif, the G-box (CACGTG) showed a nucleosome-depleted pattern both in control and COR samples (normalized NOC = −0.49 in control and −0.46 in COR) ( Fig.…”

Section: Influence Of Environmental Condition On Nucleosome Occupancymentioning

confidence: 99%

Determinants of nucleosome positioning and their influence on plant gene expression

et al. 2015

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Nucleosome positioning influences the access of transcription factors (TFs) to their binding sites and gene expression. Studies in plant, animal, and fungal models demonstrate similar nucleosome positioning patterns along genes and correlations between occupancy and expression. However, the relationships among nucleosome positioning, cis-regulatory element accessibility, and gene expression in plants remain undefined. Here we showed that plant nucleosome depletion occurs on specific 6-mer motifs and this sequence-specific nucleosome depletion is predictive of expression levels. Nucleosome-depleted regions in Arabidopsis thaliana tend to have higher G/C content, unlike yeast, and are centered on specific G/C-rich 6-mers, suggesting that intrinsic sequence properties, such as G/C content, cannot fully explain plant nucleosome positioning. These 6-mer motif sites showed higher DNase I hypersensitivity and are flanked by strongly phased nucleosomes, consistent with known TF binding sites. Intriguingly, this 6-mer-specific nucleosome depletion pattern occurs not only in promoter but also in genic regions and is significantly correlated with higher gene expression level, a phenomenon also found in rice but not in yeast. Among the 6-mer motifs enriched in genes responsive to treatment with the defense hormone jasmonate, there are no significant changes in nucleosome occupancy, suggesting that these sites are potentially preconditioned to enable rapid response without changing chromatin state significantly. Our study provides a global assessment of the joint contribution of nucleosome occupancy and motif sequences that are likely cis-elements to the control of gene expression in plants. Our findings pave the way for further understanding the impact of chromatin state on plant transcriptional regulatory circuits.

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Section: Influence Of Environmental Condition On Nucleosome Occupancymentioning

confidence: 99%

Determinants of nucleosome positioning and their influence on plant gene expression

et al. 2015

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“…Several AT-hook DNA binding proteins with a similar domain organization to BAF1 have been described in plants. They were mainly identified by yeast onehybrid or activation-tagging screens and have been implicated in jasmonate signaling, gibberellin biosynthesis, senescence, and hypocotyl elongation (Vom Endt et al, 2007;Lim et al, 2007;Matsushita et al, 2007;Street et al, 2008). Recently GIANT KILLER (GIK), another AT-hook transcriptional regulator, was identified as a target of the floral homeotic protein AGAMOUS.…”

Section: Baf1 Reveals a New Function And Properties Of At-hook Dna Bimentioning

confidence: 99%

BARREN STALK FASTIGIATE1 Is an AT-Hook Protein Required for the Formation of Maize Ears

et al. 2011

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Ears are the seed-bearing inflorescences of maize (Zea mays) plants and represent a crucial component of maize yield. The first step in the formation of ears is the initiation of axillary meristems in the axils of developing leaves. In the classic maize mutant barren stalk fastigiate1 (baf1), first discovered in the 1950s, ears either do not form or, if they do, are partially fused to the main stalk. We positionally cloned Baf1 and found that it encodes a transcriptional regulator containing an AT-hook DNA binding motif. Single coorthologs of Baf1 are found in syntenic regions of brachypodium (Brachypodium distachyon), rice (Oryza sativa), and sorghum (Sorghum bicolor), suggesting that the gene is likely present in all cereal species. Proteinprotein interaction assays suggest that BAF1 is capable of forming homodimers and heterodimers with other members of the AT-hook family. Another transcriptional regulator required for ear initiation is the basic helix-loop-helix protein BARREN STALK1 (BA1). Genetic and expression analyses suggest that Baf1 is required to reach a threshold level of Ba1 expression for the initiation of maize ears. We propose that Baf1 functions in the demarcation of a boundary region essential for the specification of a stem cell niche.

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“…Accumulating evidence also reveals that plant AT-hook DNA-binding proteins play crucial roles in governing growth, development, and differentiation, such as gibberellin (GA) homeostasis (10), jasmonate signaling (11), leaf longevity (12), photomorphogenesis (13,14), flowering (14) and reproductive organ patterning and differentiation (15). There is further evidence that AT-hook proteins regulate expression levels of target genes by binding to the cis-element on the target promoters (10,11,15,16). These results suggest that AT-hook DNA-binding proteins play diverse functional roles via transcriptional regulation of target genes during the plant life cycle.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of AHL homologous genes encoding AT-hook motif nuclear localized protein in rice

Kim¹,

Oh²,

Park³

et al. 2011

BMB Reports

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The AT-hook motif is a small DNA-binding protein motif that has been found in the high mobility group of non-histone chromosomal proteins. The Arabidopsis genome contains 29 genes encoding the AT-hook motif DNA-binding protein (AHL). Recent studies of Arabidopsis genes (AtAHLs) have revealed that they might play diverse functional roles during plant growth and development. In this report, we mined 20 AHL genes (OsAHLs) from the rice genome database using AtAHL genes as queries and characterized their molecular features. A phylogenetic tree revealed that OsAHL proteins can be classified into 2 evolutionary clades. Tissue expression pattern analysis revealed that all of the OsAHL genes might be functionally expressed genes with 3 distinct expression patterns. Nuclear localization analysis using transgenic Arabidopsis showed that several OsAHL proteins are exclusively localized in the nucleus, indicating that they may act as architectural transcription factors to regulate expression of their target genes during plant growth and development. [BMB reports 2011; 44(10): 680-685]

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Identification of a Bipartite Jasmonate-Responsive Promoter Element in the Catharanthus roseus ORCA3 Transcription Factor Gene That Interacts Specifically with AT-Hook DNA-Binding Proteins

Cited by 114 publications

References 27 publications

Determinants of nucleosome positioning and their influence on plant gene expression

Determinants of nucleosome positioning and their influence on plant gene expression

BARREN STALK FASTIGIATE1 Is an AT-Hook Protein Required for the Formation of Maize Ears

Comprehensive analysis of AHL homologous genes encoding AT-hook motif nuclear localized protein in rice

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