Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA339647 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Arabidopsis De-etiolated 1 Represses Photomorphogenesis by Positively Regulating Phytochrome Interacting Factors in the Dark
| PRJNA259643 | ENA
Project description:Seedling photomorphogenesis is a sophisticated developmental process that is controlled by both the transcriptional and posttranscriptional regulation of gene expression. Here, we identify an Arabidopsis noncoding RNA, designated HIDDEN TREASURE 1 (HID1), as a new factor promoting photomorphogenesisin continuous red light (cR). We show that HID1 acts through PHYTOCHROME-INTERACTING FACTOR 3 (PIF3), a bHLH transcription factor known to be a key repressor of photomorphogenesis.
2014-07-01 | GSE57806 | GEO
Project description:Splicing factor SRSF1 promotes breast cancer progression via regulating alternative splicing
| PRJNA684349 | ENA
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 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:Two Arabidopsis thaliana splicing factor [AtU2AF65 isoforms (AtU2AF65a and AtU2AF65b)] mutants displayed the opposite flowering phenotypes. To assay the RNA processing including alternative splicing and pre-mRNA splicing of target genes of this protein in Arabidopsis, the 7-day seedlings (shoot apices) of wild type atu2af65a and atu2af65b mutants were used for RNA-Seq.
2023-05-01 | E-MTAB-12648 | biostudies-arrayexpress
Project description:Light is a pivotal signal for plants’ growth and survival. The promptly responses are required and achieving by sophisticated transcriptomic adjustments, the promptly translation enhancement, and effective protein surveillance. However, the global role of alternative splicing regulations in response to the light is unknown. Through global surveys of alternative splicing profile and frequency calculation for individual events normalized to transcriptomic changes, we identify nearly half of transcript present at this stage are alternatively spliced. Through the unbiased event comparison in D and L4h mRNA, we reveal a clear impact of splicing control on 2,961 genes during early photomorphogenesis. Intron retention is the most frequently event under controls of light as discovered in other developmental tissues and stages of Arabidopsis. Cryptic exon is the most abundant event preserved only in the dark-grown Arabidopsis. Genes underlying the splicing and transcriptional control mostly not overlapped indicate the distinct impacts of two regulatory mechanisms. Through confirmation with a homemade microarray for their responsiveness of light, we conclude 1,792 genes as biological validated candidates. Through functional study for genes underlying light-mediated splicing controls, we explore new light-signaling components which mainly responsive in isoform abundance but steady state mRNA. Among examination both positive (RPR39, KH-RBP, RRM and RRC1) and negative (PIF4, AMI1, DNAJ, UKL3, TF-IIs-like, and ubknown-Golgi protein) factors are controlled by splicing. Through predictions for example isoform structures, PIF4-IR4, AMI1-IR7-IR8, and DNAJ-IR1 both possess PTC and possibly produce truncated coding protein. PIF4-IR4 becomes best illustration for the dysfunction for the negative regulator by light. Above PTC+ isoforms together with one third of retained introns translate that evident for NMD-insensitive retained introns and supplements for protein levels. The event identities and cis-motif signatures associated with light regulations confirm a given uniqueness for the gene expression regulation during Arabidopsis photomorphogenesis. mRNA and polysome-associated mRNA of 4 days old Arabidopsis seedling grown under the dark or with 4 h light-treatment were isolated and the transcriptome and splicing events profiles were surveyed by mRNAseq. Independent 3 biological replicates of dark and L4h mRNA were applied for two-color-microarray using custom designed alternative-splicing array from Agilent Technologies.
2015-07-26 | E-GEOD-49408 | biostudies-arrayexpress
Project description:Light is a pivotal signal for plants’ growth and survival. The promptly responses are required and achieving by sophisticated transcriptomic adjustments, the promptly translation enhancement, and effective protein surveillance. However, the global role of alternative splicing regulations in response to the light is unknown. Through global surveys of alternative splicing profile and frequency calculation for individual events normalized to transcriptomic changes, we identify nearly half of transcript present at this stage are alternatively spliced. Through the unbiased event comparison in D and L4h mRNA, we reveal a clear impact of splicing control on 2,961 genes during early photomorphogenesis. Intron retention is the most frequently event under controls of light as discovered in other developmental tissues and stages of Arabidopsis. Cryptic exon is the most abundant event preserved only in the dark-grown Arabidopsis. Genes underlying the splicing and transcriptional control mostly not overlapped indicate the distinct impacts of two regulatory mechanisms. Through confirmation with a homemade microarray for their responsiveness of light, we conclude 1,792 genes as biological validated candidates. Through functional study for genes underlying light-mediated splicing controls, we explore new light-signaling components which mainly responsive in isoform abundance but steady state mRNA. Among examination both positive (RPR39, KH-RBP, RRM and RRC1) and negative (PIF4, AMI1, DNAJ, UKL3, TF-IIs-like, and ubknown-Golgi protein) factors are controlled by splicing. Through predictions for example isoform structures, PIF4-IR4, AMI1-IR7-IR8, and DNAJ-IR1 both possess PTC and possibly produce truncated coding protein. PIF4-IR4 becomes best illustration for the dysfunction for the negative regulator by light. Above PTC+ isoforms together with one third of retained introns translate that evident for NMD-insensitive retained introns and supplements for protein levels. The event identities and cis-motif signatures associated with light regulations confirm a given uniqueness for the gene expression regulation during Arabidopsis photomorphogenesis. mRNA and polysome-associated mRNA of 4 days old Arabidopsis seedling grown under the dark or with 4 h light-treatment were isolated and the transcriptome and splicing events profiles were surveyed by mRNAseq. Independent 3 biological replicates of dark and L4h mRNA were applied for two-color-microarray using custom designed alternative-splicing array from Agilent Technologies.
2015-07-26 | E-GEOD-49407 | biostudies-arrayexpress
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
Project description:This study aims to identify in planta transcripts physically associated with alternative splicing regulator SR45. Interactions of SR45 with both RNAs and proteins are crucial for regulating RNA processing. However, in vivo RNA targets of SR45 are currently unclear. Using RNA immunoprecipitation followed by high-throughput sequencing, we identified over 4000 Arabidopsis thaliana RNAs that directly or indirectly associate with SR45, designated as SR45-associated RNAs
2015-05-12 | E-MTAB-4283 | biostudies-arrayexpress