Ontology highlight
ABSTRACT:
PROVIDER: PRJNA975320 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24693228_1.fastq.gz | Fastqsanger.gz | |||
| SRR24693228_2.fastq.gz | Fastqsanger.gz | |||
| SRR24693229_1.fastq.gz | Fastqsanger.gz | |||
| SRR24693229_2.fastq.gz | Fastqsanger.gz | |||
| SRR24693230_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
Project description:Snhg18 regulates Yap subcellular localization to maintain bone homeostasis
| PXD064764 |
Project description:ASD gene Bcl11a regulates subcellular RNA localization, associative circuitry, and social behavior
| PRJNA870113 | ENA
Project description:Alternative Splicing regulation protein subcellular localization
| PRJNA481540 | ENA
Project description:The regulation of flowering time to synchronise with external environmental signals is critical to plant reproductive success and agricultural productivity. Previously, we used CRISPR-Cas9 gene editing to show the INHIBITOR OF GROWTH 2 gene (MtING2) promotes flowering and growth in the model temperate legume Medicago truncatula, especially under inductive vernalized long days. A second ING gene, MtING1, did not appear to regulate flowering. To further dissect the genetic function of the two ING genes in flowering and growth, we cross-pollinated selected Mting1 and Mting2 single mutants to create two different double mutants; Mting1-7 Mting2-2 double knockout mutant and Mting1-1 Mting2-11 double PHD finger mutant. The growth and flowering of these mutants was assessed in vernalized long-day conditions. We also used fluorescence confocal microscopy and in vitro protein biophysical analysis to investigate the subcellular localization and oligomerization of the proteins. Finally we carried out gene expression analysis by both RNA-seq and RT-qPCR to determine how the two genes affect transcript accumulation to influence flowering.
2025-04-09 | GSE277907 | GEO
Project description:Translation initiation is a rate-limiting step in protein synthesis. The eukaryotic translation initiation factor 4E (eIF4E) plays an essential role in the translation initiation process. However, how eIF4E-dependent translation initiation regulates plant growth and development remains not fully understood. In this study, we have found that Arabidopsis eIF4E proteins distribute both in the nucleus and cytoplasm, and only cytoplasmic eIF4E is implicated in the control of flowering time. Results of profiling the genome-wide translation by Ribo-tag sequencing further reveal that eIF4E may regulate plant flowering by affecting homeostatic translation of flowering-time genes, including the Central Oscillator Genes (COGs). Consistent with the hypothesis that transcription-translation feedback loop is the core mechanism to drive the oscillation of circadian clock, we show that the eIF4E-dependent translation modulates the rhythmic oscillation of protein abundance of the clock-related genes (CCGs). Together, our study provides mechanistic insights into how the protein translation regulates multiple developmental processed in Arabidopsis including circadian clock and photoperiodic flowering.
2023-10-25 | GSE245858 | GEO
Project description:In the preimplantation mouse embryo TEAD4 is critical to establishing the trophectoderm (TE)-specific transcriptional program and segregating TE from the inner cell mass (ICM). However, TEAD4 is expressed both in the TE and the ICM. Thus, differential function of TEAD4 rather than expression itself regulates specification of the first two cell lineages. We used ChIP-seq to define genome-wide TEAD4 target genes and asked how transcription of TEAD4 target genes is specifically maintained in the TE. Our analyses revealed an evolutionarily conserved mechanism, in which lack of nuclear localization of TEAD4 impairs the TE-specific transcriptional program in inner blastomeres, thereby allowing their maturation towards the ICM lineage. Restoration of TEAD4 nuclear localization maintains the TE-specific transcriptional program in the inner blastomeres and prevents segregation of the TE and ICM lineages and blastocyst formation. We propose that altered subcellular localization of TEAD4 in blastomeres dictates first mammalian cell fate specification. ChIPseq profiles of TEAD4, IgG, Input in Mouse trophoblast stem cells using Illumina HiSeq 2000 and Illumina Genome Analyzer IIx
2012-04-18 | E-GEOD-37350 | biostudies-arrayexpress
Project description:Altered Subcellular Localization of Transcription Factor TEAD4 Regulates First Mammalian Cell Lineage Commitment
| PRJNA159725 | ENA
Project description:Parallel RNA silencing pathways regulate gene expression in plants, either by transcriptional gene silencing via RNA-dependent DNA methylation (RdDM), or by post-transcriptional silencing targeting mRNAs. Both pathways rely on distinct Dicer-like proteins to cleave double-stranded RNA into small-interfering RNAs. Experiments to determine the subcellular localization of Dicer-like proteins in Arabidopsis revealed that DCL4 is predominantly expressed as a transcriptional start site isoform that encodes a cytoplasmic protein. A second, longer DCL4 transcript isoform encodes a nuclear-localization signal and its expression is repressed by DNA methylation. Consequently this isoform is induced when promoter methylation decreases due to infection with a bacterial pathogen or during silique development. Nuclear DCL4 produces unique populations of small RNAs, called DCL4NLS isoform-dependent siRNAs (disiRNAs), which function via a post-transcriptional silencing effector, but whose precursors are generated by the RdDM pathway. Arabidopsis cells can thus respond to genome methylation changes by modulating DCL4 localization, which in turn recruits PTGS factors to reinforce RNA silencing.
2016-11-14 | GSE74731 | GEO
Project description:The autonomous flowering pathway promotes flowering in rapid-flowering accessions of Arabidopsis thaliana by reducing the expression of the key flowering repressor gene FLC. Although previous studies identified several autonomous pathway components, little is known about how these components cooperate in the regulation of flowering time. Here, we identified an autonomous pathway complex (APC) composed of three known autonomous pathway components (FLD, LD, and SDG26) and three previously uncharacterized components (EFL2, EFL4, and APRF1). Loss-of-function mutations of all of these components result in increased FLC expression and delayed flowering. The late-flowering phenotype is independent of photoperiod and can be overcome by vernalization, supporting the inference that the complex regulates flowering time specifically through the autonomous pathway. Our ChIP-seq analyses indicated that the APC components are required for the suppression of the histone modifications (H3Ac, H3K4me3, and H3K36me3) associated with the activation of gene expression and for the promotion of the histone modification (H3K27me3) associated with the repression of gene expression at FLC. We also found that the C-terminal coiled-coil domain of SDG26 binds to DNA in vitro and that the DNA-binding ability mediates the association of SDG26 with FLC chromatin in vivo. These results reveal the molecular basis of the autonomous pathway.
2022-06-25 | GSE193251 | GEO
Project description:The distribution of RNA in human embryonic stem cells (hESC) and the function of RNA localization in maintaining hESC pluripotency and differentiation are currently unknown. Here, by isolating five subcellular components of hESCs and differentiated cells, we uncovered the global subcellular RNA localization in hESC. For protein-coding mRNA, different transcripts of the same gene exhibit an “isoform switch” between subcellular components, which is regulated by localization cis-elements in their variable regions. For noncoding RNA, multiple sequence features such as polyA tail, length, and GC content jointly regulate their subcellular localization. In addition, we found that some developmental genes can be transcribed in advance and confined to chromatin in undifferentiated hESCs. Finally, we revealed significant changes in overall RNA distribution, mapped RNA dynamic localization atlas, and characterized different dynamic RNA localization patterns during hESC differentiation into mesoderm. The multiple RNA localization patterns we revealed will provide some new enlightenment for hESC stemness maintenance and differentiation.
2023-12-22 | GSE206328 | GEO