EXPERIMENT_TITLE: GSM5278115: OmniC_HeLa_6hours_A485_Replicate2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Samples were then processed using the Omni-C™ kit (Dovetail Genomics®) to perofrm crosslinking, in situ Nuclease digestion, proximity ligation followed by library preparation (end repair, adapter ligation, and DNA purification), and finally ligation capture and index PCR, all according to the manufactures instructions. Pooled Omni-C™ libraries were sequenced on the NovaSeq 6000 (Ilumina) in a PE150/150 run. An average of 200-250 million paired reads was generated per sample.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: To test the long-standing paradigm directly linking histone acetylation with chromatin decompaction and transcriptional output, we used integrated epigenomic and transcriptomic analyses following acute inhibition of major cellular lysine acetyltransferases P300 and CBP. We discovered that P300/CBP inhibition dynamically perturbs acetylation kinetics and dramatically suppresses core-transcriptional networks in the absence of changes to chromatin accessibility. CRISPR/Cas9 screening identified NCOR1 and HDAC3 transcriptional co-repressors as the principle antagonists of P300/CBP by counteracting acetylation turnover kinetics. Finally, deacetylation of H3K27 provides nucleation sites for reciprocal methylation switching, a feature that can be exploited therapeutically by concomitant KDM6A and P300 inhibition. Overall, this study indicates that the steady-state histone acetylation-methylation equilibrium functions as a molecular rheostat governing cellular transcription that is amenable to therapeutic exploitation as an anti-cancer regimen. Overall design: Examination of changes in chromosome conformation by Hi-C following catalytic inhibition of P300/CBP
SAMPLE_TITLE: OmniC_HeLa_6hours_A485_Replicate2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Cervical adenocarcinoma"}, {"TAG": "cell line", "VALUE": "HeLa"}, {"TAG": "timepoint", "VALUE": "6 hours"}]
Pool_Member_@attributes_sample_title: OmniC_HeLa_6hours_A485_Replicate2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: OmniC_HeLa_6hours_A485_Replicate2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR14408530.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/SRR014/14408/SRR14408530/SRR14408530.lite.1", "size": "19618169259", "date": "2022-08-11 05:34:03", "md5": "59bb142b91f721e76d7794d20f55523e", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR14408530", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14408530/SRR14408530", "size": "27125352619", "date": "2021-05-04 22:55:21", "md5": "a2fd02c911b3214e80fd4c077ec58dbd", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A485-3_HT5HHDRXX_ACCGGAGT-AAGGAAGG_L001_R2.fastq.gz", "size": "18995989687", "date": "2021-05-04 22:46:12", "md5": "885282a26f49b7f6548190ffc8b5683a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A485-3_HT5HHDRXX_ACCGGAGT-AAGGAAGG_L001_R1.fastq.gz", "size": "18374348387", "date": "2021-05-04 22:41:56", "md5": "425718512e18d6c6a5e12d7cf08a7afb", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]