M6A sequencing of HIV viral genomic RNA and infected host cell samples
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE85724 | GEO | 2016/08/18
SECONDARY ACCESSION(S): PRJNA339176
REPOSITORIES: GEO
Similar Datasets
Project description:N6-methyladenosine (m6A) is the most abundant internal messenger (mRNA) modification in mammalian mRNA. This modification is reversible and non-stoichiometric, which potentially adds an additional layer of variety and dynamic control of mRNA metabolism. The m6A-modified mRNA can be selectively recognized by the YTH family “reader” proteins. The preferential binding of m6A-containing mRNA by YTHDF2 is known to reduce the stability of the target transcripts; however, the exact effects of m6A on translation has yet to be elucidated. Here we show that another m6A reader protein, YTHDF1, promotes ribosome loading of its target transcripts. YTHDF1 forms a complex with translation initiation factors to elevate the translation efficiency of its bound mRNA. In a unified mechanism of translation control through m6A, the YTHDF2-mediated decay controls the lifetime of target transcripts; whereas, the YTHDF1-based translation promotion increases the translation efficiency to ensure effective protein production from relatively short-lived transcripts that are marked by m6A. PAR-CLIP and RIP was used to identify YTHDF1 binding sites followed by ribosome profling and RNA seq to assess the consequences of YTHDF1 siRNA knock-down
2015-06-09 | E-GEOD-63591 | biostudies-arrayexpress
Project description:N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA). Recent conceptual and technological advances have sparked extensive research interests in the functions of m6A, which led to the discovery of its writers, erasers and readers; as well as its regulatory roles in a number of biological processes. However, the physiological roles of mRNA m6A in B cells remained unknown. Here, we report that loss of Mettl14, the core component of the m6A writer complex, severely blocked B cell development in mice. In the bone marrow, deletion of Mettl14 in B lineage cells impaired key processes of B lymphopoiesis, including the recombination of immunoglobulin heavy chain (IgH), the IL-7-induced pro-B cell proliferation, and the transition from the large cycling pre-B stage to the small pre-B stage. Associated with these broad biological effects, Mettl14 deficiency in developing B cells dramatically decreased m6A levels in over 40% transcripts of the whole transcriptome. Global gene expression analysis in Mettl14 KO B cells showed extensive abnormalities in gene expression programs important for B cell development. To further characterize the underlying molecular mechanisms, we investigated the role of two m6A reader proteins YTHDF2 and YTHDF1. Loss of Ythdf2 impaired the IgH recombination and IL-7-induced proliferation of pro-B cells but did not affect the large pre-B-to-small pre-B cell transition. In contrast, Ythdf1 deficiency did not cause any significant defects in B cell development. These data highlighted the complexity of reader proteins that may have distinct, overlapping, or synergistic roles. Altogether, our data demonstrate that mRNA m6A modification represents a novel regulatory mechanism in early B cell development.
2020-06-22 | GSE112022 | GEO
Project description:N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA). Recent conceptual and technological advances have sparked extensive research interests in the functions of m6A, which led to the discovery of its writers, erasers and readers; as well as its regulatory roles in a number of biological processes. However, the physiological roles of mRNA m6A in B cells remained unknown. Here, we report that loss of Mettl14, the core component of the m6A writer complex, severely blocked B cell development in mice. In the bone marrow, deletion of Mettl14 in B lineage cells impaired key processes of B lymphopoiesis, including the recombination of immunoglobulin heavy chain (IgH), the IL-7-induced pro-B cell proliferation, and the transition from the large cycling pre-B stage to the small pre-B stage. Associated with these broad biological effects, Mettl14 deficiency in developing B cells dramatically decreased m6A levels in over 40% transcripts of the whole transcriptome. Global gene expression analysis in Mettl14 KO B cells showed extensive abnormalities in gene expression programs important for B cell development. To further characterize the underlying molecular mechanisms, we investigated the role of two m6A reader proteins YTHDF2 and YTHDF1. Loss of Ythdf2 impaired the IgH recombination and IL-7-induced proliferation of pro-B cells but did not affect the large pre-B-to-small pre-B cell transition. In contrast, Ythdf1 deficiency did not cause any significant defects in B cell development. These data highlighted the complexity of reader proteins that may have distinct, overlapping, or synergistic roles. Altogether, our data demonstrate that mRNA m6A modification represents a novel regulatory mechanism in early B cell development.
2020-06-23 | GSE136419 | GEO
Project description:N6-methyladenosine (m6A) occurs extensively on multiple RNA species and is the most abundant internal modification of eukaryotic messenger RNA (mRNA). RNA m6A methylation is a dynamic and reversible process subjected to regulation by three categories of m6A modifier proteins, including m6A methyltransferases/writers (e.g., METTL3/14 methyltransferase complex and METTL16), m6A demethylases/erasers (e.g., FTO and ALKBH5) and m6A binding proteins/readers (e.g., YTH family proteins and IGF2BPs). The dynamic and adjustable nature makes m6A a key regulator in RNA metabolism, and the fate of m6A-modified RNA is modulated by m6A readers. Previous studies have demonstrated that fever can benefit survival of cancer patients, and currently hyperthermia (elevating body temperature beyond normal) is either administered alone or in combination with radiotherapy or chemotherapy to treat various neoplasms with unclear mechanisms. Accruing evidence has revealed favorable effects of fever/hyperthermia in cancer treatment through affecting the properties of oncogenic proteins (e.g., stability, posttranslational modification, ability to interact with other molecules). Accordingly, we sought to investigate whether and how heat stress affects cancer development by m6A modification.
2022-02-25 | GSE197247 | GEO
Project description:The recently described role of RNA methylation in regulating immune cell infiltration into tumors has attracted interest, given its potential impact on immunotherapy response. YTHDF1 is a versatile and powerful m6A reader, but the understanding of its impact on immune evasion is limited. Here, we performed proteomics to reveal the altered proteins between wildtype and YTHDF1 knockout group.
2022-12-06 | PXD036931 | Pride
Project description:N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNAs (mRNAs), and plays important roles in cell differentiation and organism development. It regulates multiple steps throughout the RNA life cycle including RNA processing, translation, and metabolism, via the recognition by selective binding proteins. In cytoplasm, m6A binding protein YTHDF1 facilitates translation of m6A-modified mRNAs, and YTHDF2 accelerates the decay of m6A-modified transcripts. The biological function of YTHDF3, another cytoplasmic m6A binder of the YTH domain family, remains unknown. Here, we report that YTHDF3 promotes protein synthesis in synergy with YTHDF1, and affects methylated mRNA decay mediated by YTHDF2. Cells deficient in all of YTHDF proteins experience the most dramatic accumulation of the m6A-methylated transcripts. These results indicate that in cytoplasm, YTHDF proteins act in an integrated and cooperative network to accelerate metabolism of m6A-modified mRNAs. The combinative and dynamic nature of YTHDF proteins may collectively impact fundamental biological processes and diseases related to m6A RNA methylation.
2016-09-15 | GSE86214 | GEO
Project description:As the most common post-transcriptional RNA modification, m6A methylation extensively regulates the structure and function of RNA. The dynamic and reversible modification of m6A is coordinated by m6A writers and erasers. m6A reader proteins recognize m6A modification on RNA, mediating different downstream biological functions. mRNA m6A modification and its corresponding regulators play an important role in cancers, but its characteristics in the precancerous stage are still unclear. In this study, we used oral precancerous DOK cells as a model to explore the characteristics of transcriptome-wide m6A modification and major m6A regulator expression in the precancerous stage compared with normal oral epithelial cell HOEC and oral cancer cell SCC-9 through MeRIP-seq and RT-PCR. Compared with HOEC cells, we found 1180 hyper-methylated and 1606 hypo-methylated m6A peaks and 354 differentially expressed mRNAs with differential m6A peaks in DOK cells. Although the change of m6A modification in DOK cells was less than that in SCC-9 cells, mRNAs with differential m6A in both cell lines were enriched into many identical GO terms and KEGG pathways. Among the 20 known m6A regulatory genes, FTO, ALKBH5, METTL3 and VIRMA were slightly upregulated or downregulated in DOK cells, but the expression of 10 genes such as METTL14/16, FTO and IGF2BP2/3 changed significantly in SCC-9 cells. Our data suggest that precancerous cells showed, to some extent, changes of m6A modification. Identifying some key m6A targets and corresponding regulators in precancerous stage may provide potential intervention targets for the prevention of cancer development through epigenetic modification in the future.
2022-09-21 | GSE213714 | GEO
Project description:The role of N6-methyladenosine (m6A) modification of host mRNA during bacterial infection is unclear. Here, we show that Helicobacter pylori infection upregulated major m6A “writers” and increased m6A level in gastric epithelial cells. Attenuating m6A increase by hemizygotic deletion of Mettl3 in mice or small interfering RNAs targeting m6A “writers” exacerbated H. pylori colonization. LOX-1 mRNA was identified as a key m6A-regulated target during H. pylori infection. m6A modification destabilized LOX-1 mRNA and reduced LOX-1 protein level. LOX-1 acted as a membrane receptor for H. pylori catalase to mediate the bacterial adhesion. BI-0115, a small-molecule inhibitor of LOX-1, suppressed H. pylori adhesion and colonization. Genetic ablation of Lox-1 also reduced H. pylori colonization in mice. In sum, this study reveals that m6A modification is an auto-protective mechanism against H. pylori infection by downregulating LOX-1 to prevent H. pylori adhesion. LOX-1 could be a druggable target for controlling H. pylori infection.
2022-12-17 | GSE220721 | GEO
Project description:The role of N6-methyladenosine (m6A) modification of host mRNA during bacterial infection is unclear. Here, we show that Helicobacter pylori infection upregulated major m6A “writers” and increased m6A level in gastric epithelial cells. Attenuating m6A increase by hemizygotic deletion of Mettl3 in mice or small interfering RNAs targeting m6A “writers” exacerbated H. pylori colonization. LOX-1 mRNA was identified as a key m6A-regulated target during H. pylori infection. m6A modification destabilized LOX-1 mRNA and reduced LOX-1 protein level. LOX-1 acted as a membrane receptor for H. pylori catalase to mediate the bacterial adhesion. BI-0115, a small-molecule inhibitor of LOX-1, suppressed H. pylori adhesion and colonization. Genetic ablation of Lox-1 also reduced H. pylori colonization in mice. In sum, this study reveals that m6A modification is an auto-protective mechanism against H. pylori infection by downregulating LOX-1 to prevent H. pylori adhesion. LOX-1 could be a druggable target for controlling H. pylori infection.
2022-12-11 | GSE220541 | GEO
Project description:N6-methyladenosine (m6A) RNA modification is the most common and conserved epigenetic modification in mRNA and has been shown to play important roles in cancer biology. As the m6A reader YTHDF1 has been reported to promote progression of hepatocellular carcinoma (HCC), it represents a potential therapeutic target. In this study, we evaluated the clinical significance of YTHDF1 using human HCC samples and found that YTHDF1 was significantly upregulated in HCCs with high stemness scores and was positively associated with recurrence and poor prognosis. Analysis of hepatoma spheroids revealed that YTHDF1 was highly expressed in liver cancer stem cells (CSCs). Stem cell-specific conditional Ythdf1 knock-in (CKI) mice treated with diethylnitrosamine showed elevated tumor burden compared with wild type mice. YTHDF1 promoted CSC renewal and resistance to the multiple tyrosine kinase inhibitors lenvatinib and sorafenib in patient-derived organoids and HCC cell lines, which could be abolished by catalytically inactive mutant YTHDF1. RNA immunoprecipitation sequencing, m6A methylated RNA immunoprecipitation sequencing, ribosome profiling, and RNA sequencing identified NOTCH1 as a direct downstream of YTHDF1. YTHDF1 bound to m6A modified NOTCH1 mRNA to enhance its stability and translation, which led to increased NOTCH1 target genes expression. NOTCH1 overexpression rescued HCC stemness in YTHDF1 deficient cells in vitro and in vivo. Lipid nanoparticles targeting YTHDF1 significantly enhanced the efficacy of lenvatinib and sorafenib in HCC in vivo. Taken together, YTHDF1 drives HCC stemness and drug resistance through a YTHDF1-m6A-NOTCH1 epitranscriptomic axis, and YTHDF1 is a potential therapeutic target for treating HCC.
2024-01-11 | GSE252752 | GEO