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Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome.

ABSTRACT: Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome.

PROVIDER: PRJNA543094 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9060550_1.fastq.gz	Fastqsanger.gz
	SRR9060550_2.fastq.gz	Fastqsanger.gz
	SRR9060560.fastq.gz	Fastqsanger.gz
	SRR9060551_1.fastq.gz	Fastqsanger.gz
	SRR9060551_2.fastq.gz	Fastqsanger.gz

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Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome

Project description:mRNAs are regulated by nucleotide modifications that influence their cellular fate. Two of the most abundant modified nucleotides are N6-methyladenosine (m6A), found within mRNAs, and N6,2′-O-dimethyladenosine (m6Am), which is found at the first transcribed nucleotide. Distinguishing these modifications in mapping studies has been difficult. Here, we identify and biochemically characterize PCIF1, the methyltransferase that generates m6Am. We find that PCIF1 binds and is dependent on the m7G cap. By depleting PCIF1, we generated transcriptome-wide maps that distinguish m6Am and m6A. We find that m6A and m6Am misannotations arise from mRNA isoforms with alternative transcription start sites (TSSs). These isoforms contain m6Am that maps to “internal” sites, increasing the likelihood of misannotation. We find that depleting PCIF1 does not substantially affect mRNA translation but is associated with reduced stability of a subset of m6Am-annotated mRNAs. The discovery of PCIF1 and our accurate mapping technique will facilitate future studies to characterize m6Am’s function.

2019-07-03 | GSE122948 | GEO

Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome

Project description:Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome

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The mammalian cap-specific m6Am RNA methyltransferase PCIF1 regulates transcript levels in mouse tissues

Project description:The 5' end of eukaryotic mRNAs is protected by the m7G-cap structure. The transcription start site nucleotide is ribose methylated (Nm) in many eukaryotes, while an adenosine at this position is further methylated at the N6 position (m6A) by the mammalian Phosphorylated CTD-interacting Factor 1 (PCIF1) to generate m6Am. Here we show that while loss of cap-specific m6Am in mice does not affect viability or fertility, the Pcif1 mutants display reduced body-weight. Transcriptome analyses of mutant mouse tissues support a role for the cap-specific m6Am modification in stabilizing transcripts. In contrast, the Drosophila Pcif1 is catalytically-dead, but like its mammalian counterpart it retains the ability to associate with the Ser5-phosphorylated CTD of RNA pol II. Finally, we show that the Trypanosoma Pcif1 is an m6Am methylase that contributes to the N6,N6,2?-O-trimethyladenosine (m62Am) in the hypermethylated cap4 structure of Trypanosomatids. Thus, PCIF1 has evolved to function in catalytic and non-catalytic roles.

2020-08-28 | GSE151229 | GEO

HIV reprograms host m6Am RNA methylome by viral Vpr protein-mediated degradation of PCIF1

Project description:To identify m6Am genes that are responsible for HIV inhibition, m6Am-exo-seq was performed in control, PCIF1 KO T cells, and cells infected with HIV.

2021-08-09 | GSE171800 | GEO

m6Am RNA methylation enzyme PCIF1 restricts HIV infection and is degraded by viral Vpr protein

Project description:To identify m6Am genes that are responsible for HIV inhibition, MeRIP-seq was performed in control and PCIF1 KO T cells infected with HIV.

2021-08-09 | GSE154035 | GEO

The epitranscriptional factor PCIF1 orchestrates CD8+ T cell ferroptosis and activation to govern anti-tumor immunity

Project description:T cell-based cancer immunotherapies have revolutionized cancer treatment, yet durable responses remain elusive. Here, we report that PCIF1, an RNA N6, 2’-O-dimethyladenosine (m6Am) methyltransferase, negatively regulates CD8+ T cell anti-tumor responses. Whole-body or T cell-specific Pcif1 knockout (KO) significantly reduces tumor growth in mice. Single-cell RNA sequencing reveals heightened tumor-infiltrating cytotoxic CD8+ T cells in Pcif1-deficient mice. Mechanistically, proteomic and m6Am-sequencing analyses pinpoint that Pcif1 KO elevates crucial m6Am-modified targets, specifically ferroptosis suppressor genes (Fth1, Slc3a2), and T cell activation gene Cd69, imparting resistance to ferroptosis and enhancing CD8+ T cell activation. Of note, Pcif1-deficient mice with tumors exhibit enhanced responses to anti-PD-1 immunotherapy, and Pcif1 KO CAR T cells demonstrate improved tumor control. Clinically, cancer patients with low PCIF1 expression in T cells exhibit enhanced responses to immunotherapies. These findings suggest that PCIF1 suppresses CD8+ T cell activation and targeting PCIF1 as a promising strategy to boost anti-tumor immunity.

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Effect of PCIF1 knockdown on gene exppression in HeLa S3 cells

Project description:We previously identified PCIF1 (Phosphorylated CTD Interacting Factor 1) as a novel phosphorylated C-terminal domain (CTD) of RNA polymerase II. We also recently identified PCIF1 as a new cap-specific adenine N6 methyltransferase (CAPAM) responsible for creating N6, 2’-O-dimethyladenosine (m6Am) at the 5’-end of mRNAs. However, it remains unclear how PCIF1 regulates gene expression. To identify genes whose expression levels are affected by PCIF1 knockdown in human cultured cells, we performed gene expression profiling by microarray analysis.

2023-09-30 | GSE156768 | GEO

The mammalian cap-specific m6Am RNA methyltransferase PCIF1 regulates transcript levels in mouse tissues

Project description:The mammalian cap-specific m6Am RNA methyltransferase PCIF1 regulates transcript levels in mouse tissues

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Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome.

Project description:During stress, while global mRNA translation is reduced, specific stress-responsive transcripts are translated. How stress-responsive mRNAs are selectively translated is unknown. Ribosome modifications may facilitate selective translation of specific transcripts in different cell types under differing conditions. Here we identify METL-5 as a C. elegans N6-adenosine methyltransferase that methylates adenosine 1717 on 18S rRNA. METL-5 specifically enhances ribosomal binding and selective translation of a cytochrome P450 mRNA, cyp-29A3, whose protein product oxidizes the omega-3 polyunsaturated fatty acid (PUFA) eicosapentaenoic acid to eicosanoids, important signaling molecules in stress responses. In fact although mutant metl-5 C. elegans grow normally under homeostatic conditions, they are resistant to a variety of stresses, including heat shock, cold, oxidants and UV irradiation. metl-5 mutant worms have reduced overall lipid levels and of bioactive lipid eicosanoids. Moreover, dietary supplementation of eicosanoid products of CYP-29A3 restores stress sensitivity of metl-5 mutant worms. Thus methylation of a specific residue of 18S rRNA by METL-5 selectively enhances translation of cyp-29A3, to increase production of eicosanoids that increase stress-related death.

2019-12-31 | GSE131269 | GEO

SERBP1–PCIF1 complex–controlled m6Am modification in S1HLGlu neurons is required for neuropathic pain in mice

Project description:Nerve injury-induced changes in pain-associated genes contribute to genesis of neuropathic pain and comorbid anxiety. Phosphorylated CTD interacting factor-1 (PCIF1)-triggered N6, 2′-O-dimethyladenosine (m6Am) mRNA modification represents an additional layer of gene regulation. However, the role of PCIF1 in these disorders is elusive. Here, we report PCIF1 is increased in glutamatergic neurons of primary somatosensory cortex hindlimb (S1HLGlu) in neuropathic pain mouse with anxiety, but not inflammatory pain or anxiety alone. Serpine-1 mRNA-binding protein-1 (SERBP1) is identified as a PCIF1 cofactor, their complex contributes to m6Am deposition onto mRNA. Blocking increase in SERBP1-PCIF1 in S1HLGlu abolishes m6Am gain in maf1 homolog, negative regulator of RNA polymerase III (Maf1), elevates MAF1 level, and mitigates neuropathic pain and anxiety. Conversely, mimicking this increase adds m6Am onto Maf1, reduces MAF1, leads to comorbidity symptoms. These findings highlight m6Am significance in neuropathic pain-anxiety comorbidity and identify S1HLGlu SERBP1–PCIF1 as a potential therapeutic target.

2025-06-30 | PXD065634 |

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