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Phase separation-competent FBL shapes nucleolar function and translation in leukemogenesis (RNA-Seq)

ABSTRACT: Exploring the mechanism of transformation and propagation of acute myeloid leukemia is still the key to solving its refractory and relapse-prone problems. Phase separation refers to the process of specific aggregation of biological macromolecules through multivalent binding, and then leads to the functional sectorization in cell. Despite the fact that phase separation has been related to the dysregulation of various cellular processes, its role in the malignant transformation and development of AML is still less characterized. Nucleolus, as a multilayer condensate formed by phase separation, is an important place for the initiation of ribosome formation, and its function is directly related to protein translation. High-resolution imaging and fluorescence recovery after photo-bleaching experiments decode the positive regulatory relationship between the phase separation of FBL and the structure and function of nucleoli. Here, we used polysome profiling coupled with RNA-seq to depict transcriptome of AML cells with or without FBL knockdown.

ORGANISM(S): Homo sapiens

PROVIDER: GSE222264 | GEO | 2024/03/04

REPOSITORIES: GEO

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Phase separation-competent FBL shapes nucleolar function and translation in leukemogenesis (rRNA 2'-O-me modification)

Project description:Exploring the mechanism of transformation and propagation of acute myeloid leukemia is still the key to solving its refractory and relapse-prone problems. Phase separation refers to the process of specific aggregation of biological macromolecules through multivalent binding, and then leads to the functional sectorization in cell. Despite the fact that phase separation has been related to the dysregulation of various cellular processes, its role in the malignant transformation and development of AML is still less characterized. Nucleolus, as a multilayer condensate formed by phase separation, is an important place for the initiation of ribosome formation, and its function is directly related to protein translation.High-resolution imaging and fluorescence recovery after photo-bleaching experiments decode the positive regulatory relationship between the phase separation of FBL and the structure and function of nucleoli. Here, we used RiboMeth-seq to examine rRNA 2’-O-me modification changes influenced by FBL knockdown in AML cells.

2024-03-04 | GSE222265 | GEO

Transcription profile of FBL-knock down ES cells

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

CLASH for 15.5K and FBL proteins in HEK293T cells

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

FBL promotes cancer cell resistance to DNA damage by transcriptionally regulating BRCA1 via YBX1

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

Transcription profile of FBL-knock down ES cells

2014-08-01 | GSE51139 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Fbl+/- Raw264.7 Transcriptomes

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

FBL promotes cancer cell proliferation and DNA damage repair via YBX1

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

Lactiplantibacillus plantarum strain:FBL-3a | isolate:FBL-3a | breed:prokaryote | cultivar:Lactobacillus plantarum

Project description:Lactiplantibacillus plantarum strain:FBL-3a | isolate:FBL-3a | breed:prokaryote | cultivar:Lactobacillus plantarum Genome sequencing and assembly

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Victoriomyces antarcticus strain:FBL 165

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Homodimer-mediated phosphorylation of C/EBPα-p42 S16 modulates acute myeloid leukaemia differentiation through liquid-liquid phase separation [ChIP-seq]

Project description:CCAAT/enhancer binding protein α (C/EBPα) regulates myeloid differentiation, and its dysregulation contributes to acute myeloid leukaemia (AML) progress. Clarifying its functional implementation mechanism is of great significance for its further clinical application. Here, we show that C/EBPα regulates AML cell differentiation through liquid-liquid phase separation (LLPS), which can be disrupted by C/EBPα-p30. Considering that C/EBPα-p30 inhibits the functions of C/EBPα through the LZ region, a small peptide TAT-LZ that could instantaneously interfere with the homodimerization of C/EBPα-p42 was constructed, and dynamic inhibition of C/EBPα phase separation was observed, demonstrating the importance of C/EBPα-p42 homodimers for its LLPS. Mechanistically, homodimerization of C/EBPα-p42 mediated its phosphorylation at the novel phosphorylation site S16, which promoted LLPS and subsequent AML cell differentiation. Finally, decreasing the endogenous C/EBPα-p30/C/EBPα-p42 ratio rescued the phase separation of C/EBPα in AML cells, which provided a new insight for the treatment of the AML.

2023-11-08 | GSE243423 | GEO

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