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Coordinated regulation of Arabidopsis microRNA biogenesis and red light signaling through Dicer-like 1 and phytochrome-interacting factor 4

ABSTRACT: Coordinated regulation of Arabidopsis microRNA biogenesis and red light signaling through Dicer-like 1 and phytochrome-interacting factor 4

PROVIDER: PRJNA429462 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6458655.fastq.gz	Fastqsanger.gz
	SRR6458656.fastq.gz	Fastqsanger.gz
	SRR6458657.fastq.gz	Fastqsanger.gz
	SRR6794834.fastq.gz	Fastqsanger.gz
	SRR6794835.fastq.gz	Fastqsanger.gz

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Coordinated regulation of Arabidopsis microRNA biogenesis and red light signaling through Dicer-like 1 and phytochrome-interacting factor 4

Project description:Light and microRNAs (miRNAs) are key external and internal signals for plant development respectively. However the relationship between light signaling and miRNA biogenesis pathways remains unknown. Here we found that miRNA processer DCL1/HYL1 interacts with a basic helix–loop–helix (bHLH) transcription factor, phytochrome-interacting factor 4 (PIF4), which mediates the destabilization of DCL1 during dark-red light transition. PIF4 acts as a transcription factor for some miRNA genes and is necessary for the proper accumulation of miRNAs. DCL1/HYL1 and mature miRNAs play roles in the regulation of plant hypocotyl growth. These results uncovered a previously unknown crosstalk between miRNA biogenesis and red light signaling through the PIF4-dependent regulation of miRNA transcription and processing to affect red light-directed plant photomorhogenesis.

2018-02-27 | GSE109038 | GEO

Coordinated regulation of Arabidopsis microRNA biogenesis and red light signaling through Dicer-like 1 and phytochrome-interacting factor 4.

Project description:Light and microRNAs (miRNAs) are key external and internal signals for plant development, respectively. However, the relationship between the light signaling and miRNA biogenesis pathways remains unknown. Here we found that miRNA processer proteins DCL1 and HYL1 interact with a basic helix-loop-helix (bHLH) transcription factor, phytochrome-interacting factor 4 (PIF4), which mediates the destabilization of DCL1 during dark-to-red-light transition. PIF4 acts as a transcription factor for some miRNA genes and is necessary for the proper accumulation of miRNAs. DCL1, HYL1, and mature miRNAs play roles in the regulation of plant hypocotyl growth. These results uncovered a previously unknown crosstalk between miRNA biogenesis and red light signaling through the PIF4-dependent regulation of miRNA transcription and processing to affect red-light-directed plant photomorphogenesis.

| S-EPMC5862502 | biostudies-literature

Phytochrome Interacting Factors 4 and 5

Project description:This SuperSeries is composed of the following subset Series: GSE35057: Phytochrome Interacting Factor 4 and 5 regulate different set of genes in high and low red/far-red light GSE35059: ChIP-Seq analysis of Phytochrome Interacting Factor 5 DNA binding in low R/FR condition Refer to individual Series

2012-05-02 | E-GEOD-35062 | biostudies-arrayexpress

Phytochrome Interacting Factors 4 and 5

Project description:Phytochrome Interacting Factors 4 and 5

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PHYTOCHROME INTERACTING FACTORs trigger environmentally responsive chromatin dynamics

Project description:PHYTOCHROME INTERACTING FACTORs trigger environmentally responsive chromatin dynamics

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DICER-interacting partners in juvenile mouse testes

Project description:DICER has a well-characterized role in the processing of microRNAs (miRNAs) and small interfering RNAs (siRNA) that are important for post-transcriptional gene regulation. Emerging evidence suggests that DICER also has several non-canonical functions beyond miRNA/siRNA biogenesis, for example in transcriptional gene silencing at the chromatin level, as well as in RNA degradation and maintenance of genomic integrity. We have shown that the function of DICER in germ cells is essential for normal spermatogenesis; male mice lacking DICER in postnatal male germ cells are infertile due to severe defects in haploid differentiation. To better understand the function of DICER in male germ cells, we immunoprecipitated DICER from juvenile mouse testes and performed mass spectrometric analysis to identify DICER-interacting proteins.

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Phytochrome Interacting Factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light.

Project description:Phytochromes are red/far red photosensors regulating numerous developmental programs in plants. Among them phytochrome A (phyA) is essential to enable seedling de-etiolation in continuous far-red (FR) light a condition mimicking the environment under a dense canopy. The ecological relevance of this response is demonstrated by the high mortality rate of phyA mutants germinating in deep vegetational shade. phyA signaling involves a direct interaction of the photoreceptor with members of the bHLH transcription factor family, PIF1 and PIF3 (Phytochrome Interacting Factor). Here we investigated the involvement of PIF4 and PIF5 in phyA signaling and found that they redundantly control de-etiolation in FR light. The pif4pif5 double mutant is hypersensitive to low fluence rates of FR light. This phenotype is dependent on FR light perception by phyA but does not rely on alterations of the phyA level. Our microarrays analysis shows that PIF4 and PIF5 are part of an inhibitory mechanism repressing the expression of some light-responsive genes in the dark and are also needed for full expression of several growth-related genes in the light. Unlike PIF1 and PIF3, PIF4 and PIF5 are not degraded in response to FR light indicating that they are light-regulated by a different mechanism. Our genetic analysis suggests that this is achieved through the sequestration of these PIFs by the closely related bHLH transcription factor HFR1 (long Hypocotyl in FR light).

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ChIP-Seq analysis of Phytochrome Interacting Factor 5 DNA binding in low R/FR condition

Project description:Phytochrome Interacting Factor 5 plays an important role in adaptive responses of plants to shaded environment collectively called shade avoidance syndrome. PIF 5 belongs to the bHLH transcription factor family and regulated gene expression in a low R/FR dependent fashion. In this experiment we investigate PIF5-DNA-binding genome wide to generate a candidate list of genes, which are directly regulated by PIF5. ChIP-Seq sample of whole seedlings treated with low R/FR light

2012-05-02 | E-GEOD-35059 | biostudies-arrayexpress

Gene expression in the rcb (regulator for chloroplast biogenesis) mutant in red light conditions

Project description:The regulator for chloroplast biogenesis (rcb) mutant was identified as a mutant defective in phytochrome-mediated chloroplast biogenesis. The rcb mutant has long hypocotyl and albino phenotypes. RCB initiates chloroplast biogenesis in the nucleus by promoting the degradation of the master repressors for chloroplast biogenesis, the PIFs (Phytochrome Interacting Factors). To understand how RCB regulates the expression of PIF-regulated genes, we performed genome-wide expression analysis of RCB-dependent genes using a rcb-10 null allele.

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Transcription profiling of Arabidopsis thaliana phytochrome interacting factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light.

2009-09-17 | E-GEOD-16333 | biostudies-arrayexpress