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Light releases the TCP4-SAUR16/50 transcription module from the repression of PIF3 to facilitate cotyledon opening during de-etiolation [RNA-seq]

ABSTRACT: Etiolated Arabidopsis seedlings open their cotyledons and halt rapid elongation of hypocotyl when exposed to light (de-etiolation). Major light responsive components in this process have been identified and signaling pathways revealed, yet how the organ-specific light responses are achieved remains unknown. Here we report that a developmental regulator TCP4 (TEOSINTE BRANCHED1, CYCLOIDEA, and PCF) participates in photomorphogenesis and facilitates light-induced cotyledon-opening. We demonstrate that TCP4-like transcriptional factors, which predominantly express in cotyledons of both light and dark seedlings, activate SAUR16 and SAUR50 in response to light. Light repressor PIF3 (or PIFs, phytochrome-interacting factors), which accumulates in etiolated seedlings and rapidly declines upon light exposure, inhibits TCP4 promoter-binding and prevents activation of SAUR16/50 in darkness. Our study reveals how an interplay between light responsive factors and developmental regulators leads to signal-dependent and tissue-specific regulation of gene expressions, which ultimately resulted in organ-specific light responses during de-etiolation.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE115584 | GEO | 2019/03/28

REPOSITORIES: GEO

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Light releases the TCP4-SAUR16/50 transcription module from the repression of PIF3 to facilitate cotyledon opening during de-etiolation [ChIP-Seq]

Project description:Etiolated Arabidopsis seedlings open their cotyledons and halt rapid elongation of hypocotyl when exposed to light (de-etiolation). Major light responsive components in this process have been identified and signaling pathways revealed, yet how the organ-specific light responses are achieved remains unknown. Here we report that a developmental regulator TCP4 (TEOSINTE BRANCHED1, CYCLOIDEA, and PCF) participates in photomorphogenesis and facilitates light-induced cotyledon-opening. We demonstrate that TCP4-like transcriptional factors, which predominantly express in cotyledons of both light and dark seedlings, activate SAUR16 and SAUR50 in response to light. Light repressor PIF3 (or PIFs, phytochrome-interacting factors), which accumulates in etiolated seedlings and rapidly declines upon light exposure, inhibits TCP4 promoter-binding and prevents activation of SAUR16/50 in darkness. Our study reveals how an interplay between light responsive factors and developmental regulators leads to signal-dependent and tissue-specific regulation of gene expressions, which ultimately resulted in organ-specific light responses during de-etiolation.

2019-03-28 | GSE115358 | GEO

Tissue specific light response during Arabidopsis de-etiolation

Project description:The time between seed germination and the development of the first true leaves is crucial for plants success. Depending on the environmental light conditions a plant must decide which developmental program to use. If light is limited, the seedling will use etiolated growth characterized by an elongated hypocotyl and tightly-closed, underdeveloped cotyledons, thus allowing it to reach a light source as quickly as possible. In contrast, seedlings that are grown in unlimited light will use de-etiolation growth, that is characterized by inhibited hypocotyl growth and unhooked, unfolded and fully expanded cotyledons. These seedlings become photosynthetic and increase their chances for reproduction. Interestingly, the outcome of the light signal varies between the seedling’s different organs, e.g. hypocotyl growth is inhibited by light whereas cotyledon expansion is induced. Separating the cotyledons and hypocotyls of de-etiolated seedlings during their first 12 hours of white light exposure, enabled us to perform individual transcriptome analyses of each organ and to examine what causes this variation in light responsiveness.

2020-04-20 | GSE132861 | GEO

Dynamic changes of Arabidopsis cis-NAT pairs during de-etiolation

Project description:We systematically identified long noncoding natural antisense transcripts (lncNATs), defined as lncRNAs transcribed from the opposite DNA strand of coding or noncoding genes. We identified in total 37,238 sense-antisense transcript pairs and found 70% mRNAs are associated with antisense transcripts in Arabidopsis. To investigate the role of NATs in response to white light treatment, we designed an Agilent custom array, ATH NAT array, and analyzed WT seedlings grown in the dark (0h) and seedlings undergoing de-etiolation in continuous white light for 1h and 6h. To obtain information on organ-specific transcriptome profiles, we further dissected seedlings into cotyledons, hypocotyls and roots. We examined the abundance of NATs in etiolated seedlings and seedlings undergoing de-etiolation in continuous white light for 1/6h. Seedlings were further dissected into cotyledons, hypocotyls and roots. RNAs from 3 biological replicates of each of the 3 organs were separately hybridized to ATH NAT arrays to profile light-regulated NAT pairs.

2013-12-23 | E-GEOD-49382 | biostudies-arrayexpress

Dynamic changes of Arabidopsis cis-NAT pairs during de-etiolation

2013-12-23 | GSE49382 | GEO

Arabidopsis SAURs Are Critical for Differential Light Regulation of the Development of Various Organs

Project description:During de-etiolation of Arabidopsis seedlings, light promotes the expansion of cotyledons but inhibits the elongation of hypocotyls. The mechanism of this differential regulation of cell enlargement is unclear. Our organ-specific transcriptomic analysis identified 32 Small Auxin Up RNA (SAUR) genes whose transcripts were light-induced in cotyledons and/or repressed in hypocotyls. We therefore named these SAURs as lirSAURs. Both overexpression and mutation analyses demonstrated that lirSAURs could promote cotyledon expansion and opening and enhance hypocotyl elongation, possibly by inhibiting phosphatase activity of PP2C-Ds. Light reduced auxin levels to down-regulate the expression of lirSAURs in hypocotyls. Further, phytochrome-interacting factors (PIFs) were shown

2016-05-03 | GSE79576 | GEO

Ethylene-independent Promotion of Photomorphogenesis by Cytokinin Requires a Functional Cytokinin and Light Signaling Pathway.

Project description:The transition of skotomorphogenesis to photomorphogenesis is induced by the perception of light and is characterized by the inhibition of hypocotyl elongation and opening of cotyledons. Although it is known that the plant hormone cytokinin, when applied in high concentrations, inhibits hypocotyl elongation in the dark-grown Arabidopsis plants, it is unclear to what extent this response is the result of cytokinin alone or cytokinin-induced ethylene production. We show that treatment of etiolated seedlings in presence of ethylene inhibitors (eg. AgNO3) or treatment of the ethylene-resistant mutant ein2, resulted in a significant inhibition of hypocotyl elongation. This indicates that cytokinin induced de-etiolation is largely independent of ethylene and suggests a close connection between the cytokinin two component system and the light singalling networks. We show that this cytokinin signal is mainly mediated through the cytokinin receptor ARIBIDOPSIS HISTIDIN KINASE 3 (AHK3) and the ARABIDOPSIS RESPONSE REGULATORS 1 (ARR1) in combination with ARR12. Interestingly, mutation of COP1, DET1 and CIN4/COP10 renders plants insensitive to cytokinin and these factors are indispensable for the transcriptional response during cytokinin induced de-etiolation which indicates that a functional light signaling pathway is essential for this cytokinin response. In addition, the cytokinin effect on hypocotyl elongation is highly dependent on the ambient light conditions where higher light intensities causes a switch in the response to CK from an inhibitor to a promoter of hypocotyl elongation.

2018-10-01 | GSE108912 | GEO

CsBRC1 inhibits axillary bud outgrowth by repressing auxin efflux carriers CsPIN1b and CsPIN3 and in response to shade in cucumber

Project description:Shoot branching is an important agronomic trait that directly determines plant architecture and affects crop productivity. To promote crop yield and quality, axillary branches need to be manually removed during cucumber production for fresh market and thus are undesirable. Auxin is well known as the primary signal imposing for apical dominance and acts as a repressor for branching outside of the lateral buds. The TEOSINTE BRANCHED1/CYCLOIDEA /PCF (TCP) family gene BRANCHED1 (BRC1) has been shown to be the central integrator for multiple environmental and developmental factors that functions locally to inhibit shoot branching. However, no direct link has been reported between auxin and BRC1. Here, we find that cucumber BRANCHED1 (CsBRC1) is expressed in the axillary buds and displays higher expression level in cultivated cucumber than its wild ancestor. Knockdown of CsBRC1 by RNAi leads to increased bud outgrowth and reduced auxin accumulation in buds. We further show that CsBRC1 directly binds to two auxin efflux carriers PIN-FORMED (CsPIN1b and CsPIN3) and negatively regulates their expression. Ectopic expression of CsPIN1b or CsPIN3 driven by CsBRC1 promoter results in increased shoot branching. Moreover, shade induces the expression of CsBRC1 in cultivated cucumber, but not in wild ancestor, which may be partly due to the addition of two light response elements in the CsBRC1 promoter of cultivated cucumber. Therefore, our data suggest the formation of a regulatory pathway of shade-CsBRC1-auxin transport in suppressing lateral bud outgrowth during cucumber domestication.

2020-04-13 | GSE123949 | GEO

Transcriptome Analyses of Two Hybrid Citrus Cultivars in Seedlings Etiolation

Project description:Citrus species are among the most important fruit crops. However, gene regulation and signaling pathways related to etiolation in this crop remain unknown. Using Illumina sequencing technology, modification of global gene expression in two hybrid citrus cultivars—Huangguogan and Shiranuhi, respectively—were investigated. More than 834.16 million clean reads and 125.12 Gb of RNA-seq data were obtained, more than 91.37% reads had a quality score of Q30 (sequencing error rate, 0.1%). 124,952 unigenes were finally generated with a mean length of 1,189 bp. Of these unigenes, 98,904 (79.15%), 105,408 (84.35%), 42,016 (33.62%), 78,872 (63.12%), 72,068 (57.67%), 72,464 (57.99%), 72464 (57.99%) and 46,308 (37.06%) had been annotated in NR, NT, KO, SwissProt, PFAM, GO and KOG databases, respectively. Further, we identified 604 differentially expressed genes (DEGs) in multicoloured and etiolated seedlings of Shiranuhi, including 180 up-regulated genes and 424 down-regulated genes. While in Huangguogan, we found 1,035 DEGs, 271 of which were increasing and the others were decreasing. 7 DEGs were commonly up-regulated, and 59 DEGs down-regulated in multicoloured and etiolated seedlings of these two cultivars, suggesting that some genes play fundamental roles in two hybrid citrus seedlings during etiolation. Functional classification of the DEGs in two cultivars using GO term indicated that biological process, cellular component and molecular function were three major groups. Our study is the first to provide the transcriptome sequence resource for seedlings etiolation of Shiranuhi and Huangguogan, and advance our knowledge of the genes involved in the complex regulatory networks of seedling etiolation.

2017-06-13 | GSE90935 | GEO

The roles of red light and phytochrome A/B in photomorphogenesis

Project description:Analysis of etiolated seedlings exposed for 1hr to red light. Phytochromes are red/far-red light receptors, palying important roles in photomorphogenesis. Results suggest that red light and phytochromes regulate a set of genes' expression in seedlings.

2021-03-01 | GSE111380 | GEO

The soil emergence-related transcription factor PIF3 regulates root penetration by interacting with the receptor kinase FER

Project description:The cotyledons of etiolated seedlings from terrestrial flowering plants must emerge from the soil surface, while roots must penetrate the soil to ensure plant survival. We show here that the soil emergence related transcription factor PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) regulates root penetration via transducing external signals perceived by the receptor kinase FERONIA (FER) in Arabidopsis thaliana. The loss of FER function in the fer-4 mutant resulted in a severe defect in root penetration into hard soil or medium. Single-cell RNA-seq profiling of roots revealed a distinct cell clustering pattern, especially for root cap cells, and revealed PIF3 as a putative FER-regulated transcription factor. Biochemical, imaging, and genetic experiments confirmed that PIF3 is required for root soil penetration. Moreover, FER interacted with and stabilized PIF3, which then modulated the expression of mechanosensitive ion channels and the sloughing of outer cells in the root cap. We propose a novel mechanism of soil penetration by plant roots.

2023-12-31 | GSE225299 | GEO

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