Bidirectional promoters in seed development and related hormone/stress responses

Kourmpetli, Sofia; Lee, Kate D; Hemsley, R. J.; Rossignol, Pascale; Papageorgiou, Thaleia; Drea, Sinéad

doi:10.1186/1471-2229-13-187

Cited by 20 publications

(14 citation statements)

References 81 publications

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“…S5A) (23). Our initial approach was to assign only the nearest TSS as a target of the peak, but we expanded our analysis to include all TSS within 1 kb of the peak, thus allowing more than one target per peak and the inclusion of bidirectional promoters (51,52). This inclusive target list identified 2,327 TSS within 1 kb of the peaks in LL and 2,459 TSS in LD conditions (Dataset S4).…”

Section: Countmentioning

confidence: 99%

Genome-wide identification of CCA1 targets uncovers an expanded clock network inArabidopsis

Nagel

Doherty

Pruneda‐Paz

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

235

279

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The circadian clock in Arabidopsis exerts a critical role in timing multiple biological processes and stress responses through the regulation of up to 80% of the transcriptome. As a key component of the clock, the Myb-like transcription factor CIRCADIAN CLOCK ASSOCIATED1 (CCA1) is able to initiate and set the phase of clockcontrolled rhythms and has been shown to regulate gene expression by binding directly to the evening element (EE) motif found in target gene promoters. However, the precise molecular mechanisms underlying clock regulation of the rhythmic transcriptome, specifically how clock components connect to clock output pathways, is poorly understood. In this study, using ChIP followed by deep sequencing of CCA1 in constant light (LL) and diel (LD) conditions, more than 1,000 genomic regions occupied by CCA1 were identified. CCA1 targets are enriched for a myriad of biological processes and stress responses, providing direct links to clock-controlled pathways and suggesting that CCA1 plays an important role in regulating a large subset of the rhythmic transcriptome. Although many of these target genes are evening expressed and contain the EE motif, a significant subset is morning phased and enriched for previously unrecognized motifs associated with CCA1 function. Furthermore, this work revealed several CCA1 targets that do not cycle in either LL or LD conditions. Together, our results emphasize an expanded role for the clock in regulating a diverse category of genes and key pathways in Arabidopsis and provide a comprehensive resource for future functional studies.genome-wide | circadian clock | clock-controlled outputs | transcriptional regulation I n anticipation of the daily changes in light and temperature, the plant's internal circadian clock regulates a large portion of the transcriptome, nearly 80% in rice, poplar, and Arabidopsis (1, 2). The clock provides temporal coordination of multiple biological functions to ensure optimal efficiency. For example, before dawn, photosynthetic transcripts accumulate in anticipation of the expected sunlight. Even when shifted to constant light (LL) and temperature, in the absence of day/night cues, transcripts associated with photosynthesis are still up-regulated before the subjective day (1-4). Not only are light-and energyrelated activities restricted to particular times, but other aspects of plant growth, including water use, hormone activity, UVB response, and low-temperature response, show this gating effect (5-9). This temporal partitioning of biological responses ultimately provides an optimal integration of the plant's organismal functions with the environment.The circadian clock in plants involves a posttranscriptional component and a well-studied transcriptional-translation feedback regulation between the Myb-like transcription factors CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) and a member of the PSEUDO RESPONSE REGULATOR (PRR) family, TIMING OF CAB2 EXPRESSION 1 (TOC1) (10-16). Together these three components contribute t...

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Section: Countmentioning

confidence: 99%

Genome-wide identification of CCA1 targets uncovers an expanded clock network inArabidopsis

Nagel

Doherty

Pruneda‐Paz

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

235

279

View full text Add to dashboard Cite

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“…Similarly, plant BDPs function in the regulation of important agricultural traits131415161718. The transcription of bidirectional protein-coding gene pairs arranged with in a head-to-head orientation is controlled by bidirectional promoters (BDPs), which have been intensively investigated in eukaryotic genomes, ranging from yeast1920, Drosophila 21, and humans522 to plants2324.…”

mentioning

confidence: 99%

Functional characterization of open chromatin in bidirectional promoters of rice

Fang

Wang

et al. 2016

Sci Rep

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Bidirectional gene pairs tend to be highly coregulated and function in similar biological processes in eukaryotic genomes. Structural features and functional consequences of bidirectional promoters (BDPs) have received considerable attention among diverse species. However, the underlying mechanisms responsible for the bidirectional transcription and coexpression of BDPs remain poorly understood in plants. In this study, we integrated DNase-seq, RNA-seq, ChIP-seq and MNase-seq data and investigated the effect of physical DNase I hypersensitive site (DHS) positions on the transcription of rice BDPs. We found that the physical position of a DHS relative to the TSS of bidirectional gene pairs can affect the expression of the corresponding genes: the closer a DHS is to the TSS, the higher is the expression level of the genes. Most importantly, we observed that the distribution of DHSs plays a significant role in the regulation of transcription and the coexpression of gene pairs, which are possibly mediated by orchestrating the positioning of histone marks and canonical nucleosomes around BDPs. Our results demonstrate that the combined actions of chromatin structures with DHSs, which contain functional cis-elements for interaction with transcriptional machinery, may play an important role in the regulation of the bidirectional transcription or coexpression in rice BDPs. Our findings may help to enhance the understanding of DHSs in the regulation of bidirectional gene pairs.

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“…These results suggested that Pxy promoter sequence is activated during infection. Bidirectional promoters are known to be regulated in specific tissues at particular developmental stage or triggered during stress of hormonal stimulation 8,44 . www.nature.com/scientificreports www.nature.com/scientificreports/ In synthetic biology and genetic engineering, the strength of the promoter is crucial to drive the expression of the heterologous protein.…”

Section: Discussionmentioning

confidence: 99%

Functional characterization of an inducible bidirectional promoter from Fusarium oxysporum f. sp. cubense

Dash

Gurdaswani

D’Souza

et al. 2020

Sci Rep

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Bidirectional promoters (BDPs) are regulatory DNA sequences (~1000 bp long) intervening two genes arranged on opposite strands with their 5′ ends in close proximity. these genes are mostly co-expressed; but, instances of anti-correlation and independent transcription have been observed. In fungal systems, BDPs have shown to provide an improved genetic circuit by assembling and regulating transcription of different genes of a common metabolic pathway. We have identified an intergenic region (1063 bp) from the genome of Fusarium oxysporum f. sp. cubense (Foc), a banana root pathogen. this intergenic region regulates the expression of a gene pair required for the breakdown of hemicellulose. For characterization, it was cloned into pCSN44 vector backbone between two reporter genes, namely β-glucuronidase (GUS) and enhanced green fluorescent protein (EGFP). The newly formed vector was transformed into Foc and tested for its bidirectional expression activity. Using histochemical staining and fluorescence microscopy, the kinetics for both, GUS and EGFP expression were tested under different growth conditions respectively. The activity was differentially regulated by inducers such as xylan, arabinogalactan and pectin. This is the first report on the isolation of the intergenic region with inducible bidirectional promoter activity from Fusarium. characterization of such BDPs will find applications in genetic engineering, metabolic engineering and synthetic biology using fungal systems.

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Bidirectional promoters in seed development and related hormone/stress responses

Cited by 20 publications

References 81 publications

Genome-wide identification of CCA1 targets uncovers an expanded clock network inArabidopsis

Genome-wide identification of CCA1 targets uncovers an expanded clock network inArabidopsis

Functional characterization of open chromatin in bidirectional promoters of rice

Functional characterization of an inducible bidirectional promoter from Fusarium oxysporum f. sp. cubense

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