Transcriptome analysis of alternative splicing under ABA exposure in osfkbp20-1b mutant compared to wild-type (ZH11) of rice
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Japonica Group
PROVIDER: GSE197599 | GEO | 2023/04/24
REPOSITORIES: GEO
Similar Datasets
Project description:Abscisic acid (ABA) plays a key role in plant development and responses to abiotic stress. A wide number of regulatory mechanisms on ABA perception and signaling are known, including transcriptional regulation and post-translational regulations; however, less to know about the post-transcriptional regulations. In this work, we have found that SKIP, a splicing factor in spliceosome, positively regulates ABA signal transduction. Mutation of SKIP, skip-1, confers ABA insensitive phenotype in seed germination, root growth, and ABA-responsive gene expression. Transformation of SKIP genomic DNA to skip-1 is able to recover its defects. SKIP binds to the pre-mRNA of genes in ABA signaling, such as PYL8, to regulate their splicing. The alternative splicing of PYL7, PYL8, ABF2, and ABI5 in ABA pathway is disrupted by skip-1, reducing the mRNA levels of them. The abnormal splicing of PP2Cs activates their transcription by skip-1, suggesting there is a feedback regulation for PP2Cs caused by skip-1. The down-regulation of PYL ABA receptors, ABF2 and ABI5 ABA response transcription factors, and the up-regulation of PP2Cs through alternative splicing reduce the plant responses to ABA in skip-1. SKIP is required for ABA-mediated genome-wide alternative splicing. ABA treatment enhances the novel splicing events in WT genome-widely. The novel alternative splicing events are increased by skip-1 in the absence and present of ABA. Our results first reveal a principle on how a splicing factor affects the ABA signaling.
2023-02-02 | GSE144823 | GEO
Project description:B-1b cells are known to produce higher IgM level compared to B-1a cells. This study aims to identify differentially expressed genes and pathways that might enrich in B-1b cells and contribute to higher IgM production.
2022-06-30 | GSE207011 | GEO
Project description:Nuclear-localized RNA binding proteins are involved in various aspects of RNA metabolism, which in turn modulates gene expression. However, the functions of nuclear-localized RNA binding proteins in plants are poorly understood. Here we report the functions of two proteins containing RNA recognition motifs, At RZ-1B and At RZ-1C, in Arabidopsis. At RZ-1B and At RZ-1C were localized to nuclear speckles and interacted with a spectrum of serine/arginine-rich (SR) proteins through their C-termini. At RZ-1C preferentially bound to purine-rich RNA sequences in vitro through its N-terminal RNA recognition motif. Disrupting the RNA-binding activity of At RZ-1C with SR proteins through over-expression of the C-terminus of At RZ-1C conferred defective phenotypes similar to those observed in At rz-1b/At rz-1c double mutants, including delayed seed germination, reduced stature, and serrated leaves. Loss of function of At RZ-1B and At RZ-1C was accompanied by defective splicing of many genes and global perturbation of gene expression. In addition, we found that At RZ-1C directly targeted FLC, promoting efficient splicing of FLC introns and likely also repressing FLC transcription. Our findings highlight the critical role of At RZ-1B/1C in regulating RNA splicing, gene expression, and many key aspects of plant development via interaction with proteins including SR proteins. mRNA-seq to look at the transcriptome and splicing differences between wild type and At rz-1b At rz-1c mutant of Arabidopsis thaliana
2015-12-15 | E-GEOD-75959 | biostudies-arrayexpress
Project description:We analyzed alternative splicing with Shh medulloblastoma. This dataset contains bam files of whole genome sequencing from 4 cases. Genomic DNA was isolated from both tumor and matched control specimens. We performed whole genome sequence on Illumina Hiseq.
| EGAS00001003220 | EGA
Project description:We report the results of scRNA sequencing of parental and mIDH2R140Q TF-1 cell lines following exposure to PBS (control) and IL-1B. We obtained 1 million cells of each cell line for each condition and incubated them with either PBS or IL-1B. Following treatment, cells were processed using previously described inDrop protocols (Wolock et al., 2019 Cell Reports). Samples were split into 3,000 single-cell transcriptomes and one library per sample was prepared and sequenced on NextSeq 500. Data was prepared for analysis as described in our methods and gene expression was normalized and quantified. Gene set enrichment, differential gene expression and UMAP visualization was performe dusing SEurat 3.0. Ultimately, we compared the cellular response of parental and mIDH2 cells to IL-1B and our results indicate that mIDH2 cells have augmented expression of NF-κB target transcripts . This component of our study demonstrates a dynamic response of both cell lines to IL-1B with an exaggerated response seen in mIDH2 cells.
2021-11-05 | GSE187777 | GEO
Project description:Differentiating erythroid cells execute a unique gene expression program that insures synthesis of the appropriate proteome at each stage of maturation. Standard expression microarrays provide important insight into erythroid gene expression, but cannot detect qualitative changes in transcript structure, mediated by RNA processing, that alter structure and function of encoded proteins. We analyzed stage-specific changes in the late erythroid transcriptome via use of high resolution microarrays that detect altered expression of individual exons. Ten differentiation-associated changes in erythroblast splicing patterns were identified, including the previously known activation of protein 4.1R exon 16 splicing. Six new alternative splicing switches involving enhanced inclusion of internal cassette exons were discovered, as well as three changes in use of alternative first exons. All of these erythroid stage-specific splicing events represent activated inclusion of authentic annotated exons, suggesting they represent an active regulatory process rather than a general loss of splicing fidelity. The observation that three of the regulated transcripts encode RNA binding proteins (SNRP70, HNRPLL, MBNL2) may indicate significant changes in the RNA processing machinery of late erythroblasts. Together these results support the existence of a regulated alternative pre-mRNA splicing program that is critical for late erythroid differentiation. Keywords: Time course; Splicing-sensitive microarray For Exon array hybridizations: 3 biological replicates of day 7, 2 biological replicates of day 10, 3 biological replicates of day 14; For HJAY array hybridizations: 5 biological replicates each were analyzed from day 7 and day 14. One day 14 replicate was deemed an outlier and removed from subsequent analyses.
2010-05-16 | E-GEOD-14588 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE23513: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (HJAY) GSE23514: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (Exon array) Refer to individual Series
2010-09-01 | E-GEOD-23522 | biostudies-arrayexpress
Project description: Not available
| S-EPMC2810302 | biostudies-literature
Project description:Nuclear-localized RNA binding proteins are involved in various aspects of RNA metabolism, which in turn modulates gene expression. However, the functions of nuclear-localized RNA binding proteins in plants are poorly understood. Here we report the functions of two proteins containing RNA recognition motifs, At RZ-1B and At RZ-1C, in Arabidopsis. At RZ-1B and At RZ-1C were localized to nuclear speckles and interacted with a spectrum of serine/arginine-rich (SR) proteins through their C-termini. At RZ-1C preferentially bound to purine-rich RNA sequences in vitro through its N-terminal RNA recognition motif. Disrupting the RNA-binding activity of At RZ-1C with SR proteins through over-expression of the C-terminus of At RZ-1C conferred defective phenotypes similar to those observed in At rz-1b/At rz-1c double mutants, including delayed seed germination, reduced stature, and serrated leaves. Loss of function of At RZ-1B and At RZ-1C was accompanied by defective splicing of many genes and global perturbation of gene expression. In addition, we found that At RZ-1C directly targeted FLC, promoting efficient splicing of FLC introns and likely also repressing FLC transcription. Our findings highlight the critical role of At RZ-1B/1C in regulating RNA splicing, gene expression, and many key aspects of plant development via interaction with proteins including SR proteins.
2015-12-15 | GSE75959 | GEO
Project description:Growth Factor Independence-1B (Gfi-1B) is a transcriptional repressor essential for erythropoiesis and megakaryopoiesis. Targeted gene disruption of Gfi-1B in mice leads to embryonic lethality due to failure to produce definitive erythrocytes, hindering the study of Gfi-1B function in adult hematopoiesis. We here show that, in humans, Gfi-1B controls the development of erythrocytes and megakaryocytes by regulating the proliferation and differentiation of bipotent erythro-megakaryocytic progenitors (MEP). We further identify in this cell population the type III transforming growth factor-? receptor gene, TGFBR3, as a direct target of Gfi-1B. Knock down of Gfi-1B results in altered TGF? signaling as shown by the increase in Smad2 phosphorylation and its inability to associate to the Transcription Intermediary Factor 1? (TIF1?). Because Smad2/TIF1? complex is known to specifically regulate erythroid differentiation, we propose that, by repressing the transforming growth factor-? receptor III (T?R?II) expression, Gfi-1B favors the Smad2/TIF1? interaction downstream of TGF? signaling, allowing immature progenitors to differentiate toward the erythroid lineage.
2010-04-19 | E-MEXP-2560 | biostudies-arrayexpress