Ontology highlight
ABSTRACT:
PROVIDER: PRJNA213870 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Alternative splicing fine-tunes transcriptome and translatome in photomorphogenic Arabidopsis [array]
| PRJNA213909 | ENA
Project description:RNA-Seq analyses of GSC line NSC11 after 2Gy irradiation in the transcriptome and the translatome to evaluate radiation-induced changes in alternative splicing.
2018-02-14 | GSE94693 | GEO
Project description:Introns are removed by the spliceosome, a large complex composed of five ribonucleoprotein subcomplexes (U snRNP). In metazoans, the U1 snRNP, which binds to 5’ splice sites, also fulfills regulatory roles in splice site selection and possesses non-splicing related functions. Here, we show that an Arabidopsis U1 snRNP subunit, LUC7, affects constitutive and alternative splicing. Interestingly, LUC7 specifically promotes splicing of a subset of terminal introns. Splicing of LUC7-dependent terminal introns is a prerequisite for nuclear export and can be modulated by stress. Globally, intron retention under stress conditions occurs preferentially among first and terminal introns, uncovering an unknown bias for splicing regulation in Arabidopsis. Taken together, our study reveals that the Arabidopsis U1 snRNP is important for alternative splicing and removal of terminal introns and it suggests that Arabidopsis terminal introns fine-tune gene expression under stress conditions.
2017-05-24 | GSE98779 | GEO
Project description:Wild-type and RBMX-overexpressed HEK293 cells where profiled at the transcriptome and translatome levels through polysomal profiling. Paired-end RNA-seq libraries were built and sequenced on an Illumina HiSeq 2000 machine to allow for accurate gene expression quantification and alternative splicing isoforms detection.
2019-12-01 | GSE68990 | GEO
Project description:We generated a global analysis of Rbfox2 splicing regulation combined with a highly specific, single nucleotide-resolution Rbfox2 RNA binding map. We found that Rbfox2 regulates the splicing and expression of many previously unknown targets, and particularly a number of RNA binding proteins (RBPs), by modulating alternative splicing coupled-NMD. Based on our observations of RBP-Rbfox2 co-regulation with a polarity predicted by Rbfox2 binding, we propose a model whereby Rbfox2 tunes autoregulatory splicing events to control RBP expression levels and in turn alter their respective splicing networks. iCLIP for epitope-tagged Rbfox2 and control untagged Rbfox2; RNAseq of control and Rbfox2 knockdown in mouse embryonic stem cells
2014-03-17 | E-GEOD-54794 | biostudies-arrayexpress
Project description:Light, an important environmental factor regulates most of plant physiology and development. In the photomorphogenic stage, light globally enhances translation status in de-etiolating Arabidopsis seedlings. More than 1500 genes showed increased translation but not transcription in this developmental process. This implies these mRNAs are translationally repressed in dark-grown seedlings. Through transcriptome and translatome comparisons, we revealed that p-bodies attenuate the translation of mRNAs in the etiolated seedlings. We found hundreds of mRNAs accumulated and also increased translation for thousands of genes in dark-grown dcp5-1, including genes known to regulate the transition from skotomorphogenesis to photomorphogenesis. Our data reports p-bodies regulate both RNA stability and attenuation of translation for specific mRNAs in the dark.
2019-06-20 | GSE107892 | GEO
Project description:au13-12_polysome - transcriptome and translatome of arabidopsis wt seeds according to dormancy - Identification of transcripts that are differentially abundant (transcriptome) and transcripts that are addressed to translation (translatome) in imbibed Arabidopsis seeds in relation with dormancy. During imbibition of seeds (16h and 24h in darkness at 25°C, dormant and non-dormant seeds), transcriptome analysis is done on total RNA and translatome analysis on polysomal RNA. - At harvest seeds are dormant. They stay dormant if they are stored at -20°C (D) and become non-dormant (ND) if they are stored 3 weeks at +20°C. Arabidopsis dormant seeds do not germinate at 25°C in darkness while non-dormant seeds do. Total RNA and polysomal RNA (polysomal fractions purified on sucrose gradients) were extracted from imbibed seeds for 16h or 24h at 25°C in darkness (3 biological replicates). Transcriptome and translatome are compared for Dormant vs Non-Dormant for 16h and 24 imbibition. In silico comparison will allow to compare transcriptome and translatome for each point and type of seeds and to compare the time points (16 vs 24h) for each type of sample. 12 dye-swap - time course
2014-09-27 | E-GEOD-61809 | biostudies-arrayexpress
Project description:We analyze the effect of a double deletion mutant for alternative-splicing regulators nsra and nsrb (Nuclear Speckle RNA binding proteins), on the Arabidopsis thaliana transcriptome.
2018-07-12 | GSE116923 | GEO
Project description:We analyze the effect of a double deletion mutant for alternative-splicing regulators nsra and nsrb (Nuclear Speckle RNA binding proteins), on the Arabidopsis thaliana transcriptome.
2016-01-01 | GSE65717 | GEO
Project description:Alternative splicing (AS) is an important component of RNA processing controlled by cis- and trans-acting component. Here we investigate modes and mechanisms of AS co-regulation by MBNL1 and RBFOX1. We generated two cell models (human and mouse) whereby the expression of both RBPs can be independently modulated and utilize these cell lines to perform RNAseq and transcriptome wide alternative splicing analysis. Categorization of alternative splicing outcomes of the impacts of RBFOX1 expression on MBNL1 splicing revealed a common co-regulatory mode whereby RBFOX1 buffers MBNL1 dose-dependent splicing regulation by reducing the total range of exon inclusion induced. Overall, our studies define a conserved co-regulatory mechanism through which RBFOX1 and MBNL1 can fine-tune and provide redundancy for AS outcomes.
2021-03-25 | GSE169518 | GEO