An SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE214299 | GEO | 2022/11/09
REPOSITORIES: GEO
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Project description:Purpose: The goals of this study are to compare the transcriptome profiling and alternative splicing (AS) profiling between Col-0 wild type and SFPS knockout mutant (sfps-2) through RNA-seq to determine the molecular mechanisms of how splicing factor SFPS regulates photomorphogenesis in Arabidopsis. Results: Using an optimized data analysis workflow, we mapped about 100 million sequence reads per sample to the Arabidopsis genome (TAIR10) and identified 1495 differentially expressed genes between Col-0 and mutant dark samples; 1361 differentially expressed genes between Col-0 and mutant red light treated samples; 4291 differentially expressed genes between Col-0 dark and red light treated samples; and 4479 differentially expressed genes between mutant dark and red light treated samples. Except for gene expression, we also discovered 788 differentially spliced bins between Col-0 and mutant dark samples; 827 differentially spliced bins between Col-0 and mutant red light treated samples; 610 differentially spliced bins between Col-0 dark and red light treated samples; and 405 differentially spliced bins between mutant dark and red light treated samples. Altered splicing of 9 genes was confirmed with qRT-PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of SFPS mutant transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show that SFPS regulates photomorphogenesis in Arabidopisis through regulating the splicing activity of light signaling genes, which helps us.
2017-08-10 | GSE85883 | GEO
Project description:We report the application of illumina high throughput RNA sequencing for rrc1-3 mutants in both light and dark conditions(three replicates under each condition) in Arabidopsis. By obtaining over 100 million reads (150bp paired_end) for each rRNA depleted lib, we compared the transcriptome profile between rrc1-3 mutant and Col-0 wild type light and dark conditions. We find that genome wide spliciing activities are general defective in rrc1-3 mutant comparing to Col-0 wild type, which indicates the importance of post-transcriptional processing on gene expression regulation. In addition, the sequencing data also indicates light signal probably regulates both splicing cascade and transcriptional cascade to control the downstream gene expression.
2019-09-25 | GSE114995 | GEO
Project description:Light signals perceived by a group of photoreceptors have profound effects on the physiology, growth, and development of plants. The red/far-red light-absorbing phytochromes (phys) modulate these aspects by intricately regulating gene expression at multiple levels. Here, we report the identification and functional characterization of an RNA-binding splicing factor, SWAP1 (SUPPRESSOR-OF-WHITE-APRICOT/SURP RNA-BINDING DOMAIN-CONTAINING PROTEIN1). Loss-of-function swap1-1 mutant is hyposensitive to red light and exhibits a day length-independent early flowering phenotype. SWAP1 physically interacts with two other splicing factors, (SFPS) SPLICING FACTOR FOR PHYTOCHROME SIGNALING and (RRC1) REDUCED RED LIGHT RESPONSES IN CRY1CRY2 BACKGROUND 1 in a light-independent manner and forms a ternary complex. In addition, SWAP1 physically interacts with photoactivated phyB and colocalizes with nuclear phyB photobodies. Phenotypic analyses show that the swap1sfps, swap1rrc1, and sfpsrrc1 double mutants display hypocotyl lengths similar to that of the respective single mutants under red light, suggesting that they function in the same genetic pathway. The swap1sfps double and swap1sfpsrrc1 triple mutants display pleiotropic phenotypes, including sterility at the adult stage. Deep RNA sequencing (RNA-seq) analyses show that SWAP1 regulates the gene expression and pre-messenger RNA (mRNA) alternative splicing of a large number of genes, including those involved in plant responses to light signaling. A comparative analysis of alternative splicing among single, double, and triple mutants showed that all three splicing factors coordinately regulate the alternative splicing of a subset of genes. Our study uncovered the function of a splicing factor that modulates light-regulated alternative splicing by interacting with photoactivated phyB and other splicing factors.
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Project description:We analyzed transcriptome-wide gene expression and AS changes in etiolated Arabidopsis seedlings exposed to red, blue, and white light. Our study revealed that different types of light signals trigger rapid AS responses of numerous genes, including splicing factors and other functional groups. Among these candidates was RRC1, which was previously shown to function in PHYB signaling. The light signaling phenotype of an rrc1 mutant could only be complemented with the splicing variant being up-regulated upon light exposure, indicating a self-reinforcing circuit. Finally, we provide evidence that light-regulated AS can occur in a phytochrome-independent manner and is closely intertwined with the plantâ??s energy status. Analysis of alternative splicing patterns of dark-grown Arabidopsis seedlings exposed for 1 or 6 hours to white, blue, or red light, or kept in darkness; all samples in duplicates
2016-10-23 | E-GEOD-70575 | biostudies-arrayexpress
Project description:We analyzed transcriptome-wide gene expression and AS changes in etiolated Arabidopsis seedlings exposed to red, blue, and white light. Our study revealed that different types of light signals trigger rapid AS responses of numerous genes, including splicing factors and other functional groups. Among these candidates was RRC1, which was previously shown to function in PHYB signaling. The light signaling phenotype of an rrc1 mutant could only be complemented with the splicing variant being up-regulated upon light exposure, indicating a self-reinforcing circuit. Finally, we provide evidence that light-regulated AS can occur in a phytochrome-independent manner and is closely intertwined with the plant’s energy status.
2016-10-23 | GSE70575 | GEO
Project description:rs09-01_det1 - photomorphogenesis - - Identification of the genes deregulated in det1-1 when seedlings grow in light or in dark (dark increase morphological differences between det1-1 and wild-type) - Expression profile of seedlings grown in dark then exposed to light - etiolated seedlings (5days) are briefly exposed to light to induce developmental transition between skoto- and photomorphogenesis without visible change in plant morphology and differences between col0 and the mutant det1-1 grown in light or in dark Keywords: treatment variations
2010-05-01 | GSE19843 | GEO
Project description:Expression data from Arabidopsis thaliana under dark and far-red light
2015-06-01 | E-GEOD-30712 | ExpressionAtlas
Project description:Light and brassinosteroids (BRs) have been proved to be crucial in regulating plant growth and development, however, the mechanism of how they synergistically function is still largely unknown. To explore the underlying mechanisms in photomorphogenesis, genome-wide analyses were carried out through examining the gene expressions of the dark-grown WT or BR biosynthesis-defective mutant det2 seedlings in presence of light stimuli, or exogenous Brassinolide (BL). Results showed that BR deficiency stimulates, while BL treatment suppresses, the expressions of light responsive genes and photomorphogenesis, revealing the negative effects of BR in photomorphogenesis. This is consistent with that genes involved in cell wall modification and cellular metabolism were specifically modulated by BL during dark-light transition, and altered expressions of genes related to energy utilization. Further analysis revealed that hormone biosynthesis and signaling related genes, especially those of auxin, were altered under BL treatment or light stimuli, indicating that BR may modulate photomorphogenesis through synergetic regulation with other hormones. Additionally, suppressed ubiquitin-cycle pathway during light-dark transition hinted the presence of a complicated network among light, hormone and protein degradation. The study provides the direct evidence of BR effects in photomorphogenesis and identified the genes involved in BR and light signaling pathway, which will help to elucidate the molecular mechanism of plant photomorphogenesis.
2010-02-10 | GSE14788 | GEO
Project description:rs09-01_det1 - photomorphogenesis - - Identification of the genes deregulated in det1-1 when seedlings grow in light or in dark (dark increase morphological differences between det1-1 and wild-type) - Expression profile of seedlings grown in dark then exposed to light - etiolated seedlings (5days) are briefly exposed to light to induce developmental transition between skoto- and photomorphogenesis without visible change in plant morphology and differences between col0 and the mutant det1-1 grown in light or in dark Keywords: treatment variations 6 dye-swap - CATMA arrays
2010-04-30 | E-GEOD-19843 | biostudies-arrayexpress
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