Sequencing of mRNA with N6-methyladenosine (m6A) modification in AML cells upon ALKBH5 knockdown or overexpression
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE134763 | GEO | 2020/05/26
REPOSITORIES: GEO
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Project description:Recent advances in pancreatic differentiation from human pluripotent stem cells (hPSCs) hold great potentials for disease modeling and regenerative medicine, and more precise control over the dynamic differentiation process is critical. N6-methyladenosine (m6A) is the most prevalent internal messenger RNA (mRNA) modification, while the roles of m6A mark in pancreatic differentiation and development remain elusive. In addition, ALKBH5 is a major mRNA m6A demethylase and its role in pancreatic differentiation has not been reported. Here, we firstly studied mRNA m6A dynamics during pancreatic differentiation from hPSCs. Next, using the CRISPR-based genome editing tool, we generated ALKBH5 knockout hPSC lines and found that ALKBH5 plays important roles in pancreatic specification. After that, we conducted a series of functional and mechanistic studies, and demonstrated that ALKBH5 modulated many important genes involved in pancreatic differentiation. Collectively, our findings identified ALKBH5 as an essential regulator of human pancreatic differentiation and highlighted that m6A modification presents a new layer of regulation at epitranscriptome levels during cell-fate specification.
2022-06-13 | GSE163963 | GEO
Project description:N6-methyladenosine (m6A) is important for RNA metabolism including stability and translation of messenger RNA (mRNA). Recent studies indicate that m6A-methylated RNA can modulate dynamic chromatin accessibility and gene transcription, while the potential link of chromatin to mRNA m6A remains largely unknown. We found that targeted inhibition of bromodomain-containing protein 4 (BRD4) by siRNA or a small compound inhibitor (JQ1) significantly decreases mRNA m6A levels and suppresses the malignancy of breast cancer (BC) cells via increased expression of ALKBH5, a demethylase for mRNA methylation. Mechanistically, inhibition of BRD4 increases the mRNA stability of ALKBH5 via enhanced binding between ALKBH5 3’UTR with RNA-binding protein RALY. Further, BRD4 serves as a scaffold for ubiquitin enzymes TRIM21 and ALKBH5, resulting in the ubiquitination and degradation of ALKBH5 protein. JQ1-increased ALKBH5 then demethylates mRNA of ESPL1, a critical oncogenic driver for breast cancer, and reduces binding between ESPL1 mRNA and m6A reader IGF2BP3, leading to decay of ESPL1 mRNA. Animal and clinical studies confirm a critical role of the BRD4/ALKBH5/ESPL1 pathway in BC progression. Overall, our study sheds light on another layer of gene regulation involving crosstalks between histone modification and RNA methylation.
2021-12-11 | GSE190541 | GEO
Project description:Senescent foamy macrophages are the key pathogenic drivers of atherosclerosis (AS) progression and plaque stability. The RNA N6-methyladenosine (m6A) modification plays an important role in the development of various diseases. However, its role in foamy macrophage aging during AS is still not clarified. To assess m6A methylation levels and m6A modifying enzyme profiles, the infiltrated macrophages were sorted using CD68+ magnetic beads from plaque tissues of patients with AS and high-fat diet feeding Apoe-/- mice. The ALKBH5f/f, Lyz2Cre, Apoe-/- mice were constructed to observe senescent macrophage infiltrated in plaques and AS progression. The RNA-seq, MeRIP, RIP and dual luciferase assays were performed to explore the mechanisms of ALKBH5-mediated formation of senescent macrophage. Downregulated m6A methylation levels and upregulated ALKBH5 expression were observed in aortic plaques and infiltrated macrophages from AS patients and mice. Compared with control mice, ALKBH5f/f, Lyz2Cre, Apoe-/- mice decreased AS plaques and enhanced plaque stability by suppressing senescence of foamy macrophages and senescence-associated secretory phenotypes. In addition, the data of the RNA-seq, MeRIP, RIP and dual luciferase assays showed that ALKBH5 deletion reduced the mRNA level of CC chemokine ligand 5 (CCL5) by increased m6A methylation in macrophages. Actinomycin D assay indicated ALBH5 knockout destroyed stability of Ccl5 mRNA. Mechanismly, ALKBH5 promotes senescent macrophage formation by CCL5/CC chemokine receptor 5 (CCR5)/mTORC1/autophagy signaling. And ALKBH5 induced macrophage derived CCL5 recruits increasingly CD8+IFNγ+ T cells by CCL5-CCR5 axis. Furthermore, the application of ALKBH5 inhibitor IOX-1 and CCR5 monoclonal antibody Adaptavir are potential clinical interventions for the inhibition of senescent macrophage formation and AS progress. Myeloid ALKBH5 deletion mitigates AS progression by suppressing the formation of senescent macrophages and the recruitment of CD8+IFNγ+ T cells. These findings favour the ALKBH5/CCL5/CCR5 signaling as novel targets for atherosclerosis therapy.
2025-01-01 | GSE249354 | GEO
Project description:Sequencing of mRNA with N6-methyladenosine (m6A) modification in AML cells upon ALKBH5 knockdown or overexpression
| PRJNA556354 | ENA
Project description:N6-methyladenosine (m6A) is the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Here we report ALKBH5 as a new mammalian demethylase that oxidatively removes the m6A modification in mRNA in vitro and inside cells. This demethylation activity of ALKBH5 significantly affects mRNA export and RNA metabolism as well as the assembly of mRNA processing factors in nuclear speckles. Alkbh5-deficient male mice are characterized by impaired fertility resulting from apoptosis that affects meiotic metaphase-stage spermatocytes. In accordance with this defect, we have identified in mouse testes 1552 differentially expressed genes which cover broad functional categories and include spermatogenesis-related mRNAs involved in the p53 functional interaction network. We show that Alkbh5-deficiency impacts the expression levels of some of these mRNAs, supporting the observed phenotype. The discovery of this new RNA demethylase strongly suggests that the reversible m6A modification plays fundamental and broad functions in mammalian cells. RNA-seq in two cell types
2013-02-15 | E-GEOD-40132 | biostudies-arrayexpress
Project description:Through m6A mRNA-profiling, we aim to characterize the m6A mRNA changes in the liver between Alkbh5flox/flox and Alkbh5-HKO mice.
2025-02-27 | GSE227175 | GEO
Project description:Recent advances in pancreatic differentiation from human pluripotent stem cells (hPSCs) hold great potentials for disease modeling and regenerative medicine, and more precise control over the dynamic differentiation process is critical. N6-methyladenosine (m6A) is the most prevalent internal messenger RNA (mRNA) modification, while the roles of m6A mark in pancreatic differentiation and development remain elusive. In addition, ALKBH5 is a major mRNA m6A demethylase and its role in pancreatic differentiation has not been reported. Here, we firstly studied mRNA m6A dynamics during pancreatic differentiation from hPSCs. Next, using the CRISPR-based genome editing tool, we generated ALKBH5 knockout hPSC lines and found that ALKBH5 plays important roles in pancreatic specification. After that, we conducted a series of functional and mechanistic studies, and demonstrated that ALKBH5 modulated many important genes involved in pancreatic differentiation. Collectively, our findings identified ALKBH5 as an essential regulator of human pancreatic differentiation and highlighted that m6A modification presents a new layer of regulation at epitranscriptome levels during cell-fate specification.
2022-06-13 | GSE163945 | GEO
Project description:Faithful genome integrity maintenance plays an essential role in cell survival. Here, we identify the RNA demethylase ALKBH5 as a key regulator that protects cells from DNA damage and apoptosis during reactive oxygen species (ROS)-induced stress. We find that ROS significantly induces global mRNA N6-methyladenosine (m6A) levels by modulating ALKBH5 post-translational modifications (PTMs), leading to the rapid and efficient induction of thousands of genes involved in a variety of biological processes including DNA damage repair. Mechanistically, ROS promotes ALKBH5 SUMOylation through activating ERK/JNK signaling, leading to inhibition of ALKBH5 m6A demethylase activity by blocking substrate accessibility. Moreover, ERK/JNK/ALKBH5-PTMs/m6A axis is activated by ROS in hematopoietic stem/progenitor cells (HSPCs) in vivo in mice, suggesting a physiological role of this molecular pathway in the maintenance of genome stability in HSPCs. Together, our study uncovers a molecular mechanism involving ALKBH5 PTMs and increased mRNA m6A levels that protect genomic integrity of cells in response to ROS.
2021-04-29 | GSE144620 | GEO
Project description:To identify the potential mRNA targets of FTO inhibitor, we conducted m6A-seq with mRNA samples enriched from AML cells upon DMSO and FB23-2 (FTO inhibitor) treatment
2019-04-29 | GSE103496 | GEO
Project description:N6-methyladenosine (m6A) is the most abundant internal modification in the messenger RNA (mRNA) of all higher eukaryotes. This modification has been shown to be reversible in mammals; it is installed by a methyltransferase heterodimer complex of METTL3 and METTL14 bound with WTAP, and reversed by iron(II)- and α-ketoglutarate-dependent demethylases FTO and ALKBH5. This modification exhibits significant functional roles in various biological processes. The m6A modification as a RNA mark is recognized by reader proteins, such as YTH domain family proteins and HNRNPA2B1; m6A can also act as a structure switch to affect RNA-protein interactions for biological regulation. In Arabidopsis thaliana, the methyltransferase subunit MTA (the plant orthologue of human METTL3, encoded by At4g10760) was well characterized and FIP37 (the plant orthologue of human WTAP) was first identified as the interacting partner of MTA. Here we report the discovery and characterization of reversible m6A methylation mediated by AtALKBH10B (encoded by At4g02940) in A. thaliana, and noticeable roles of this RNA demethylase in affecting plant development and floral transition. Our findings reveal potential broad functions of reversible mRNA methylation in plants. m6A peaks were identified from wild type Columbia-0 and atalkbh10b-1 mutant in two biological replicates
2016-03-24 | E-GEOD-79523 | biostudies-arrayexpress