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RNA exonuclease REXO4 resolves m6A-marked R-loops and suppresses anti-tumor immunity

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE289626 | GEO | 2026/05/28

REPOSITORIES: GEO

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RNA exonuclease REXO4 resolves m6A-marked R-loops and suppresses anti-tumor immunity [END_seq]

Project description:To investigate the features of DNA structures that are protected by REXO4, we performed END-seq, a method that maps DSBs at nucleotide resolution in REXO4-depleted cells.

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RNA exonuclease REXO4 resolves m6A-marked R-loops and suppresses anti-tumor immunity [RNAseq]

Project description:Transcription blockage frequently occurs in tumor cells, and aberrant R-loop forming during this process drives genome instability. However, the regulation of R-loop homeostasis and its dysregulation in tumorigenesis are still under investigation. Here, we report that the RNA exonuclease REXO4 preserves genome stability by reducing excessive R-loops. Mechanistically, REXO4 resolves R-loops by 3’-5’ exonucleolytic cleavage of the RNA strand on RNA-DNA hybrids, where an accessible end is created by RNA endonuclease and N6-methyladenosine (m6A) modification on RNA moieties promotes REXO4 localization and R-loop removal. REXO4 ablation-induced DNA damage stimulates interferon response and tumor immune infiltration to suppress squamous cell carcinoma (SCC) growth and metastasis. Importantly, targeting the exonuclease activity of REXO4 via the inhibitor we developed synergizes with PD-1 blockade to inhibit SCC progression by recruiting and activating CD8+ T cells. Thus, our study provides mechanistic insight into how m6A couples with exonuclease in R-loop clearance and genome maintenance, and uncovers a druggable epi-transcriptional machinery that blocks innate immune response and enables SCC immune evasion.

2026-05-28 | GSE289625 | GEO

RNA exonuclease REXO4 resolves m6A-marked R-loops and suppresses anti-tumor immunity [ChIP-Rx]

Project description:To determine whether R-loop accumulation upon REXO4 loss results from RNA Polymerase stalling, we performed Pol II chromatin-immunoprecipitation followed by sequencing with reference exogenous genome (ChIP-Rx).

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RNA exonuclease REXO4 resolves m6A-marked R-loops and suppresses anti-tumor immunity [MRC-seq]

Project description:To achieve a more specific mapping of m6A-marked R-loops, we developed an m6A-marked R-loop CUT&Tag sequencing (MRC-seq) approach to map m6A-marked R-loops, which involves the specific isolation of R-loops using an S9.6 antibody-based CUT&Tag approach followed by m6A immunoprecipitation.

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RNA exonuclease REXO4 resolves m6A-marked R-loops and suppresses anti-tumor immunity [CUT&Tag-seq]

Project description:To map the genome-wide distribution of R-loops and REXO4, we performed CUT&Tag-seq with antibodies against S9.6 (for R-loops) and REXO4.

2026-05-28 | GSE313850 | GEO

RNA exonuclease REXO4 resolves m6A-marked R-loops and suppresses anti-tumor immunity [RNAseq in REXO4-dTAG HeLa cells]

Project description:To determine if REXO4 depletion directly induces R-loop accumulation independent of transcription, we generated a HeLa cell line expressing endogenous REXO4 tagged with an N-terminal HA-FKBP12/F36V degron (REXO4-dTAG) via microhomology-mediated end joining (MMEJ)-based CRISPR/Cas9. Acute REXO4 degradation, achieved by a 4-hr treatment with dTAG-13 (dTAG), was then analyzed by RNA-seq to assess transcriptomic changes

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PRMT1 suppresses anti-tumor immunity

Project description:PRMT1 suppresses anti-tumor immunity

| PRJNA840921 | ENA

PRMT1 suppresses anti-tumor immunity

Project description:PRMT1 is known as a regulator of immune function by directly interacting with interferon receptors, methylating STAT1, and promoting B cell and macrophage differentiation by methylating CDK4 or B cell antigen receptor However, the function of PRMT1 as a therapeutic target of cancer remains largely elusive, particularly for its role in cancer immunosurveillance. Here, we performed bulk RNA-seq for CT26, a mouse tumor cell line, after either knocking down of endogeneous Prmt1 or blocking PRMT1 by two specific inhibitors, namely MS023 and GSK3368715.

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