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Photomorphogenesis of Arabidopsis seedlings is accompanied by complex alternative splicing alterations

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE70575 | GEO | 2016/10/23

SECONDARY ACCESSION(S): PRJNA289063

REPOSITORIES: GEO

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Photomorphogenesis of Arabidopsis seedlings is accompanied by complex alternative splicing alterations

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

RRC1 is required for epidermal phyB siganling by maintaining the circadian rhythm by suppressing the alternative splicing of core clock genes.

Project description:Purpose : The goal of this study is to identify transcriptome changes induced by rrc1 mutation under red light. We compared the transcriptome of MLB (ML1pro::phyB-GFP/phyB-9) with EMS27 grown either in darkness or continuous red light to investigate the genes that the expression and the splicing patterns are regulated by epidermal phyB and/or RRC1. The transcriptome of Col-0 and rrc1-689 was further compared to enlarge the list of putative splicing targets of RRC1. Methods : Seedlings grown under either monochromatic red light (19 μmol/m2s) or darkness for 60 hours on 1/2 MS agar plates were sampled. Total RNAs were extracted using the Spectrum Plant Total RNA Extraction Kit (Sigma-Aldrich). RNA libraries were generated and sequenced on the Illumina NextSeq 500 platform. The analysis was performed with three biological replicates. Roughly 90% of the sequencing reads were mapped to specific loci on the Arabidopsis TAIR10 reference genome using the TopHat pipeline. Mapped sequencing files were further processed with Aspli1.9 R package for Differentially Expressed Gene (DEG) analysis and Differentially Spliced Gene (DSG) analysis.

2023-03-01 | GSE199039 | GEO

Coordinated regulation of pre-mRNA splicing by the SFPS-RRC1 complex to promote photomorphogenesis in Arabidopsis

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

Transcriptome analysis of gene expression divergence in BBX11 mutation in red light

Project description:phytochrome B (phyB) acts as the red light photoreceptor and negatively regulates the growth-promoting factor PHYTOCHROME INTERACTING 4 (PIF4) through a direct physical interaction, which in turn changes the expression of a large number of genes. phyB-PIF4 module regulates a variety of biological and developmental processes in plants. In this study, we demonstrate that B-BOX PROTEIN 11 (BBX11) physically interacts with both phyB and PIF4. BBX11 negatively regulates PIF4 accumulation as well as its biochemical activity, consequently leading to the repression of PIF4-controlled genes' expression and promotion of photomorphogenesis in the prolonged red light. This study reveals a regulatory mechanism that mediates red light signal transduction and sheds a light on phyB-PIF4 module in promoting red light-dependent photomorphognenesis.

2022-11-02 | GSE166109 | GEO

Arabidopsis De-etiolated 1 Represses Photomorphogenesis by Positively Regulating Phytochrome Interacting Factors in the Dark

Project description:Arabidopsis seedlings undergo photomorphogenic development even in darkness when the function of De-etiolated 1 (DET1), a repressor of photomorphogenesis, is disrupted. Our results indicate that DET1 directly interacts with a group of transcription factors known as the phytochrome-interacting factors (PIFs). Furthermore, our results suggest that DET1 positively regulates PIF protein levels primarily by stabilizing PIF proteins in the dark. Genomic analysis also revealed that DET1 may control the expression of light-regulated genes to mediate photomorphogenesis partially through PIFs.

2015-03-19 | GSE60835 | GEO

Genome-wide identification of microRNAs and their targets involved in the phyB-mediated light signaling pathway in rice

Project description:Phytochrome B (phyB), one member of phytochrome family in rice, plays important roles in regulating a range of developmental processes, and stress responses. However, little information about the mechanism involved in phyB-mediated light signaling pathway has been reported in rice. Another, it has been well-known that microRNAs (miRNAs) perform important roles in plant development and stress responses. Thus it is intriguing to explore the role of miRNAs in phyB-mediated light signaling pathway in rice. In this study, comparative high-throughput sequencing and degradome analysis were adopted to identify candidate miRNAs and their targets that participate in phyB-mediated light signaling pathway. A total of 838 known miRNAs, 663 novel miRNAs and 1,957 target genes were identified from wild-type (WT) and phyB mutant. Among them, 135 miRNAs showed differential expression, suggesting that the expressions of these miRNAs are under the control of phyB. In addition, 32 out of the 135 differentially expressed miRNAs were detected to slice 70 genes in rice genome. Analysis of these target genes showed that members of various transcription factor families constitute the largest proportion, indicating miRNAs are probably involved in phyB-mediated light signaling pathway mainly via regulating the expression of transcription factors. This study presented a comprehensive expression analysis of miRNAs and their targets that might be involved in phyB-mediated light signaling pathway for the first time. The results provide new clues for functional characterization of miRNAs in phyB-mediated light signaling pathway, which would be helpful in comprehensively uncovering molecular mechanism of phytochrome-mediated photomorphogenesis and stress responses in plant. Examination of miRNA profiles in wild type (WT) and phyB mutant at four-leaf stage by deep sequencing using Illumina Hiseq2500.

2015-01-01 | E-GEOD-62334 | biostudies-arrayexpress

photomorphogenesis-Expression profile of DET1-1 mutant during photomorphogenesis

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

Genome-wide identification of microRNAs and their targets involved in the phyB-mediated light signaling pathway in rice

2015-01-01 | GSE62334 | GEO

Arabidopsis De-etiolated 1 Represses Photomorphogenesis by Positively Regulating Phytochrome Interacting Factors in the Dark

2015-03-19 | E-GEOD-60835 | biostudies-arrayexpress

Analyses of phyB-regulated genes by RNA-seq

Project description:The phytochrome family consists of five numbers (phyA-phyE) in Arabidopsis, of which phyB is the best characterized and shown to play a major role in mediating red light inhibition of hypocotyl elongation. In order to reveal the molecular basis for phyB-mediated red light signaling to promote photomorphogenesis, we analyzed the gene expression profile of red light-grown WT and phyB mutant seedlings by high throughput sequencing.

2020-07-25 | GSE101875 | GEO

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