{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Nie Chen"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15815"],"description":["Genomic integrity within transcriptionally active regions is crucial for averting oncogenic mutations, yet the precise mechanisms governing DNA double-strand break (DSB) repair in these areas remain elusive. This study reveals that the IRAK1-spliceosome axis orchestrates small nuclear RNA (snRNA) as a central molecular hub, potently activating the ATM at DSB sites within active chromatin to enable precise repair. Mechanistically, IRAK1 phosphorylates spliceosomal SR proteins to recruit snRNA to DSBs, inducing condensation of the MRN complex near transcriptionally active regions to create an ATM activation platform. Inhibition of the IRAK1-spliceosome-snRNA axis compromises ATM activation at damaged sites in active regions, leading to increased mutations exclusively within these regions and"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Cells were lysed with 1 mL pre-chilled Cell Lysis Buffer (10 mM HEPES, pH 7.5; 20 mM KCl; 1.5 mM MgCl2; 0.5 mM EDTA; 1 mM tris(2-carboxyethyl) phosphine [TCEP]; 0.5 mM PMSF; 0.1% NP-40). The lysate was incubated on ice for 10 minutes, followed by centrifugation. The nuclear pellet was treated with Nuclear Lysis Buffer (20 mM HEPES, pH 7.5; 50 mM KCl; 1.5 mM MnCl2; 1% NP-40; 0.4% sodium deoxycholate; 0.1% N-lauroylsarcosine; 1 mM TCEP; 0.5 mM PMSF). The cells were resuspended to a concentration of 5x106 cells/mL and incubated on ice for 10 minutes. The sample was then subjected to sonication for 6 minutes by Covaris M220 focused ultrasonicator. Following sonication, 100 µL of TURBO DNase (Invitrogen) was added to the sample, then incubated at 37 °C for 10 minutes. ","Sequencing - Libraries were pooled and sequenced on Illumina platforms with PE150 by Novogene.","Library Construction - ChIP-seq library preparation was proceeded as follows: the DNA fragments were end-repaired and A-tailed, then ligated with sequencing adaptors; the final DNA library was obtained after size selection and PCR amplification.","Sample Collection - DIvA cells were seeded in 15-cm dishes and treated with an IRAK1 inhibitor for 19 hours, followed by treatment with 300 nM 4OHT for 1 hour. Cells were washed once with PBS, then incubated at room temperature with gentle shaking in 7 mL of 2 mM Disuccinimidyl glutarate (DSG) solution in PBS for 45 minutes. After washing with PBS, cells were treated with 7 mL of 3% formaldehyde in PBS and incubated at room temperature for 10 minutes. The crosslinking reaction was quenched by adding glycine to a final concentration of 500 mM for 5 minutes at room temperature. Following fixation, cells were washed twice with cold PBS, collected, and counted. A total of 2x107 cells were prepared per group for subsequent steps."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The BAM files were converted to bigwig files using deepTools.","Sequence Alignment - Raw data was processed using Trim-Galore for quality control. The cleaned reads were then mapped to the hg38 genome using STAR, the parameters were set as follows: --outFilterMismatchNmax 10 --outFilterMatchNmin 10 --alignEndsType Local --seedSearchLmax 10 --outFilterScoreMinOverLread 0.1 --outFilterMatchNminOverLread 0.1. Duplicate reads were removed and the BAM files were sorted using Sambamba."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ChIP-seq"],"species":["Homo sapiens"],"pubmed_authors":["Nie Chen","Wang Jiadong"],"additional_accession":[]},"is_claimable":false,"name":"snRNA Orchestrates ATM Activation to Promote Accurate Repair within Transcriptionally Active Chromatin (RAP-seq)","description":"Genomic integrity within transcriptionally active regions is crucial for averting oncogenic mutations, yet the precise mechanisms governing DNA double-strand break (DSB) repair in these areas remain elusive. This study reveals that the IRAK1-spliceosome axis orchestrates small nuclear RNA (snRNA) as a central molecular hub, potently activating the ATM at DSB sites within active chromatin to enable precise repair. Mechanistically, IRAK1 phosphorylates spliceosomal SR proteins to recruit snRNA to DSBs, inducing condensation of the MRN complex near transcriptionally active regions to create an ATM activation platform. Inhibition of the IRAK1-spliceosome-snRNA axis compromises ATM activation at damaged sites in active regions, leading to increased mutations exclusively within these regions and","dates":{"release":"2026-08-31T00:00:00Z","modification":"2026-08-31T01:01:01.039Z","creation":"2025-10-22T12:16:39.304Z"},"accession":"E-MTAB-15815","cross_references":{"ENA":["ERP182701"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002692","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}