DRNA sequencing of Drosophila FBL KD
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ABSTRACT:
PROVIDER: PRJEB45722 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The goal of this study is to compare NGS-derived wild-type Raw264.7 transcriptome profiling (RNA-seq) to NGS-derived Fibrillarin knockdown (Fbl+/-) Raw264.7 RNA-seq. The mRNA profiles of wild-type Raw264.7 and Fbl+/− Raw264.7 were generated by deep sequencing, in duplicate, using illumina NovaSeq 6000.
2022-04-05 | GSE185660 | GEO
Project description:We combined high-resolution tiling microarrays and 5'-end RNA sequencing to obtain a genome-wide map of transcription start sites (TSSs) for Shewanella oneidensis MR-1. To test the reliability of these TSSs, we compared our result to those from differential RNA sequencing (dRNA-seq), which discriminates primary and processed ends of transcripts. We found that our identified TSSs tend to have significantly more mapped reads in the TEX(+) sample than the TEX(-) sample. Overall, the dRNA-seq results support the validity of our predictions for TSS. S. oneidensis MR-1 was grown to mid-log phase in Luria-Bertani broth (LB) or defined lactate minimal medium, and total RNA was isolated and used for differential RNA-sequencing (dRNA-seq) by next-generation sequencing, which is used to verify genome-wide transcription start sites. For dRNA-seq, total RNA was partially treated with Terminator Exonuclease (TEX) to digest processed RNA and thereby enrich for primary transcript ends.
2014-06-12 | E-GEOD-58292 | biostudies-arrayexpress
Project description:Pluripotent stem cells have been shown to have unique nuclear properties, e.g., hyperdynamic chromatin and large, condensed nucleoli. However, the contribution of the latter unique nucleolar character to pluripotency has not been well understood. Here, we show fibrillarin (FBL), a critical methyltransferase for ribosomal RNA (rRNA) processing in nucleoli, as one of the proteins highly expressed in pluripotent embryonic stem (ES) cells. Stable expression of FBL in ES cells prolonged the pluripotent state of mouse ES cells cultured in the absence of leukemia inhibitory factor (LIF). Analyses using deletion mutants and a point mutant revealed that the methyltransferase activity of FBL regulates stem cell pluripotency. Knock down of this gene led to significant delays in rRNA processing, growth inhibition, and apoptosis in mouse ES cells. Interestingly, both partial knock down of FBL and treatment with actinomycin D, an inhibitor for rRNA synthesis, induced the expression of differentiation markers in the presence of LIF and promoted stem cell differentiation into neuronal lineages. Moreover, we identified p53 signaling as the regulatory pathway for pluripotency and differentiation of ES cells. These results suggest that proper activity of rRNA production in nucleoli is a novel factor for the regulation of pluripotency and differentiation ability of ES cells. Tc-inducible FBL-knock down ES cells were cultured for 2 days with or without Tc in the presence of LIF. These 2 conditions were analysed transcription profile.
2014-08-01 | E-GEOD-51139 | biostudies-arrayexpress
Project description:2′-O-Methylation is prominent in ribosome RNA catalyzed by Fibrillarin (FBL). However, the stoichiometry of 2′-O-methylation at base resolution in the internal mRNA and its functions remain to be explored. Here, we firstly investigate the effect of the 2′-O-methylation on the mRNA stability and expression at a genome-wide scale. Combined with Nanopore sequencing and a machine learning strategy, we identified thousands of RNA methylation sites in mRNA and rRNA at base resolution. The mRNA half-life profiling of FBL deficient cells established a direct effect of RNA methylation and FBL binding on the mRNA stability. We further determined the RNA methylation on the expression levels and tested the post-transcriptional effect of elevated FBL mediated 2′-O-Methylation in mRNA within the prostate cancer model. Besides the role of the translational regulation of FBL in rRNA, elevated FBL promotes cancer progress by stabilizing the mRNA through RNA binding and 2′-O-Methylation. Our results reveal a novel mechanism that FBL regulates the 2′-O-methylation and turnover of mRNA at whole transcriptome levels.
2024-06-20 | GSE208837 | GEO
Project description:We performed CLASH for 15.5K and FBL in HEK293T cells which overexpressed 15.5K and FBL, respectively.
2023-04-10 | GSE160636 | GEO
Project description:We combined high-resolution tiling microarrays and 5'-end RNA sequencing to obtain a genome-wide map of transcription start sites (TSSs) for Shewanella oneidensis MR-1. To test the reliability of these TSSs, we compared our result to those from differential RNA sequencing (dRNA-seq), which discriminates primary and processed ends of transcripts. We found that our identified TSSs tend to have significantly more mapped reads in the TEX(+) sample than the TEX(-) sample. Overall, the dRNA-seq results support the validity of our predictions for TSS.
2014-06-12 | GSE58292 | GEO
Project description:In order to study the molecular mechanism of FBL in cells, this project constructed the full length of FBL into the SFB (S-Flag-SBP tag) vector, and constructed a stable cell line overexpressing FBL. Affinity chromatography combined with LC-MS/MS technology to screen FBL interacting proteins.
2023-07-26 | PXD034434 | Pride
Project description:To further investigate the underlying function and molecular mechanism of FBL in DNA damage response, we conducted RNA sequencing analysis (RNA-seq) and detected the genome-wide transcriptomic changes in HCT116 cells and shFBL-HCT116 cells following MMC treatment. Together, these data indicate that the activation of the FBL/YBX1 signaling axis upon DNA damage regulates the transcriptional activation of genes directly involved in the repair of DNA DSBs, such as BRCA1 and contributes to promoting the resistance of cells to DNA-damaging agents.
2023-07-13 | GSE205366 | GEO
Project description:Pluripotent stem cells have been shown to have unique nuclear properties, e.g., hyperdynamic chromatin and large, condensed nucleoli. However, the contribution of the latter unique nucleolar character to pluripotency has not been well understood. Here, we show fibrillarin (FBL), a critical methyltransferase for ribosomal RNA (rRNA) processing in nucleoli, as one of the proteins highly expressed in pluripotent embryonic stem (ES) cells. Stable expression of FBL in ES cells prolonged the pluripotent state of mouse ES cells cultured in the absence of leukemia inhibitory factor (LIF). Analyses using deletion mutants and a point mutant revealed that the methyltransferase activity of FBL regulates stem cell pluripotency. Knock down of this gene led to significant delays in rRNA processing, growth inhibition, and apoptosis in mouse ES cells. Interestingly, both partial knock down of FBL and treatment with actinomycin D, an inhibitor for rRNA synthesis, induced the expression of differentiation markers in the presence of LIF and promoted stem cell differentiation into neuronal lineages. Moreover, we identified p53 signaling as the regulatory pathway for pluripotency and differentiation of ES cells. These results suggest that proper activity of rRNA production in nucleoli is a novel factor for the regulation of pluripotency and differentiation ability of ES cells.
2014-08-01 | GSE51139 | GEO
Project description:Translational regulation in adult regenerative tissue remains unclear. Planarians, renowned for remarkable cell turnover and tissue regeneration capabilities, are regenerative flatworms that provide an ideal model to address the gap in knowledge between translational control and cell turnover during adult tissue homeostasis and regeneration. Fibrillarin (FBL) is an RNA 2-O’-methyltransferase crucial for rRNA processing, playing a pivotal role in translational regulation. We explored this in planarian Schmidtea mediterranea and identified two FBL homologs: Smed-fbl-1 (fbl-1) and Smed-fbl-2 (fbl-2) are essential for homeostasis and regeneration, but have distinct roles. fbl-1 is enriched in neoblasts and essential for multiple progenitor cell differentiation. Conversely, fbl-2 is expressed in egr5+ epidermal progenitors, crucial for late-stage epidermal lineage specification. Knockdown (KD) of fbl-1 and fbl-2 resulted in different 2-O’-methylation patterns, suggesting their influence on specific mRNA translation during regeneration. Riboseq analysis revealed that fbl-1 KD reduced the translation of genes associated with alternative splicing, cell cycle, and DNA replication, while fbl-2 KD reduced the translation of genes related to protein stability. Interestingly, fbl-2+ cells spatially correlated with wnt-1+ cells, hinting at fbl-2’s role in its localization. Our study indicated that duplicate fbl genes may have a compensatory role in the development of specific cell lineages. This finding underscores the significance of rRNA modification in translation regulation during the maintenance and regeneration of adult tissues.
2024-11-13 | GSE255594 | GEO