Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE313848 | GEO | 2026/05/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

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

CUT&Tag analysis of R-loops in Ube2t knockdown P19 cells (optimized)

Project description:DNA sequencing of libraries from CUT&Tag with R-loops antibody (S9.6) in Ube2t knockdown and control P19 cells

2024-05-30 | GSE223410 | GEO

CUT&Tag of R-loops in Ube2t knockdown P19 cells

Project description:DNA sequencing of libraries from CUT&Tag with R-loops antibody (S9.6) in Ube2t knockdown and control P19 cells

2025-08-01 | GSE212081 | GEO

CUT&TAG analysis of R-loops in Mcm8 knockout MEFs and CUT&TAG analysis of R-loops and MCM8-binding sites in HEK293 cells

Project description:To reveal the role of MCM8 in suppressing R-loop accumulation, we performed the CUT&TAG assay using the S9.6 antibody to map genome-wide R-loops in Mcm8 wildtype MEFs and Mcm8 knockout MEFs. We also conducted the CUT&TAG assay to detect genome-wide R-loops in Ddx5 downregulated MEFs by adenovirus infection and in control MEFs. To investigate the underlying molecular mechanism of MCM8 suppressing R-loops, we conducted the DNA sequencing of libraries from CUT&TAG assay using the antibody against FLAG in HEK293 cells transfected with FLAG-MCM8 plasmid and using the S9.6 antibody in HEK293 cells. Besides, an IgG control and control of RNH1 overexpression were included.

2024-05-30 | GSE254352 | GEO

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

Genomic Profiling of Native R-Loops with a DNA-RNA Hybrid Recognition Sensor Protein

Project description:R-Loops are unique RNA-containing chromatin structures, which participate in various key biological processes and associate with multiple human diseases. Accurately and comprehensively profiling R-Loops in the genome is crucial to study their functions under the physiological and pathological conditions. However, the existing methodologies have produced broad discrepancies in R-Loop profiling and an independent strategy is urgently needed. Here, we constructed an artificial DNA-RNA hybrid recognition sensor protein GST-His6-2XHBD with the hybrid-binding domain of RNase H1, and found GST-His6-2XHBD could specifically interact with DNA-RNA hybrids and behaves similarly to the anti-DNA-RNA hybrid S9.6 antibody in DRIPc-seq. Furthermore, we established a convenient method, R-loop CUT&Tag, by combination of GST-His6-2XHBD with a Tn5-based cleavage under targets and tagmentation approach. R-Loop CUT&Tag generates highly specific signals for native R-Loops, and can sensitively detect the R-Loop signals at the promoter, genebody and enhancer. R-Loop CUT&Tag also provides possibilities to genome-widely map the native R-Loops with limited materials, and may benefit the resolving of the broad discrepancies between multiple R-Loop mapping methods.

2021-02-22 | GSE156400 | GEO

Profiling R loop using S9.6 antibody coupled cut&tag

Project description:Profiling R loop using S9.6 antibody coupled cut&tag

| PRJNA989270 | ENA

RNA-seq of young and quiescent (9 days) MRC-5 human fibroblasts

Project description:Comparison of gene expression profiles of quiescent MRC-5 fibroblasts and young MRC-5 fibroblasts. Jena Centre for Systems Biology of Ageing – JenAge (www.jenage.de)

2021-10-19 | GSE118693 | GEO

Mettl3-m6A-YTHDF1 axis promotion of mitochondrial dysfunction in metabolic dysfunction–associated steatotic liver disease (MASLD)

Project description:The N6-methyladenosine (m6A) mRNA modification and the mitochondrial respiratory chain (MRC) hold paramount importance in the advancement of MASLD. This study thoroughly investigates the relationship and impact of m6A mRNA modification and mitochondrial function in the progression of MASLD. Here we report that the mRNA and protein levels of mitochondrial respiratory chain (MRC) subunits showed inconsistent trends in vivo experiments. Abnormal m6A modification and mitochondrial dysfunction in MASLD were attributed to the upregulation of methyltransferase like 3 (Mettl3) and the downregulation of YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) induced by high-fat foods. Mettl3 promoted the MRC's function. However, knockout of the reader protein YTHDF1, which plays a crucial role in the m6A modification process, counteracted the effect of Mettl3 and suppressed MRC. In MASLD, damage to the MRC may be regulated by the Mettl3-m6A-YTHDF1 complex axis, especially by the role of YTHDF1. Our research has offered a novel perspective on the involvement of m6A mRNA methylation in the pathogenesis of MASLD.

2024-09-20 | PXD047819 | Pride

RNA-seq of young and quiescent MRC-5 human fibroblasts

Project description:Quiescent MRC-5 fibroblasts were compared to young fibroblasts Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

2014-11-06 | GSE60883 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data