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Chimeric activators and repressors define HY5 activity and a feedback control mechanism in Arabidopsis (HY5_ChIPseq)

ABSTRACT: Chimeric activators and repressors define HY5 activity and a feedback control mechanism in Arabidopsis (HY5_ChIPseq)

PROVIDER: PRJNA549284 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10811456.fastq.gz	Fastqsanger.gz
	SRR10811457.fastq.gz	Fastqsanger.gz
	SRR10811458.fastq.gz	Fastqsanger.gz
	SRR10811459.fastq.gz	Fastqsanger.gz
	SRR9312922.fastq.gz	Fastqsanger.gz

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Chimeric activators and repressors define HY5 activity and a feedback control mechanism in Arabidopsis (HY5_RNAseq)

Project description:Chimeric activators and repressors define HY5 activity and a feedback control mechanism in Arabidopsis (HY5_RNAseq)

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Chimeric activators and repressors define HY5 activity and a feedback control mechanism in Arabidopsis (HY5_ChIPseq)

Project description:Transcription regulation requires many protein interactions on chromatin, and only a subset of transcription factors have well-defined activation or repression domains. The Arabidopsis transcription factor HY5 controls critical growth-related gene expression programs during plant development, but it’s primary activity in regulating transcription remains unclear. To address this question, we generated constitutive repressor and activator HY5 fusion proteins to direct the expression of HY5 target genes. We used RNA-seq, ChIP-seq, and multiple phenotypes to demonstrate that HY5 depends on accessory factors to promote transcription and identify high confidence direct targets of HY5. We suggest that this strategy can be used broadly to define the transcription regulation activity and direct targets of transcription factors. Interestingly, this approach also revealed a mechanism by which HY5 promotes the accumulation of its own negative regulators. We show that HY5 directly regulates components of the COP1 E3-ubiquitin ligase complex, and by uncoupling this feedback loop we can induce partial de-etiolation in the dark. This provides a system by which plants can quickly repress growth upon light exposure. Lastly, we show that modulating this system can generate significant phenotypic diversity and provide proof of concept that these fusion proteins can modulate growth in tomato, opening a novel path toward selecting desirable traits in crop species.

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Project description:Despite growing knowledge of the functions of individual human transcriptional effector domains, much less is understood about how multiple effector domains within the same protein combine to regulate gene expression. Here, we measure transcriptional activity for 8,400 effector domain combinations by recruiting them to reporter genes in human cells. In our assay, weak and moderate activation domains synergize to drive strong gene expression, while combining strong activators often results in weaker activation. In contrast, repressors combine linearly and produce full gene silencing, and repressor domains often overpower activation domains. We use this information to build a synthetic transcription factor whose function can be tuned between repression and activation independent of recruitment to target genes by using a small molecule drug. Altogether, we outline the basic principles of how effector domains combine to regulate gene expression and demonstrate their value in building precise and flexible synthetic biology tools.

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ELONGATED HYPOCOTYL (HY5) AND HY5 HOMOLOG (HYH) maintain shade avoidance suppression in sunlight

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Project description:Gene expression profiles between wild type (WT) and hy5 were compared to know HY5-targets.

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