EXPERIMENT_TITLE: GSM8025457: HiC_H526_sgPOU2AF2-1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C experiments were performed following the Arima manufacture's protocol. Briefly, chromatin extracted from crosslinked cells was digested with restriction enzymes, followed by biotin labeling, proximity ligation and crosslink reversal. Chromatin was then sheared by sonication and sized selected. The biotin labeled DNA was then enriched and pulled down with streptavidin beads Hi-C libraries were performed following the protocol for KAPA HyperPrep kit.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Recent studies have identified a previously uncharacterized protein C11orf53 (now named POU2AF2/OCA-T1), functions as a new co-activator of POU2F3, the master transcription factor which is critical for both normal and neoplastic tuft cell identity and viability. Here, we demonstrated that POU2AF2 functions as an “Yin-Yang” factor which mediates both transcriptional activation and repression at distal enhance elements. Loss of POU2AF2 led to an inhibition of active enhancer nearby genes, such as tuft cell identity genes, and a derepression of Polycomb-dependent poised enhancer nearby genes, which are critical for cell viability and differentiation. Mechanistically, depletion of POU2AF2 leads to a global redistribution of the chromatin occupancy of SWI/SNF complex, resulting in a significant 3D genome structure change and a subsequent transcriptional reprogramming. Genome wide CRISPR screen further demonstrated that POU2AF2 depletion or SWI/SNF inhibition led to a PTEN-dependent cell growth defect, which revealed a potential role of POU2AF2-SWI/SNF axis in small cell lung cancer pathogenesis. Finally, pharmacological inhibition of SWI/SNF phenocopied POU2AF2 depletion in terms of gene expression alteration and cell viability decease in SCLC-P subtype cells. Therefore, impeding POU2AF2 mediated SWI/SNF function represents a potential therapeutic approach for human SCLC therapy. Overall design: To determine the transcriptional repression function of POU2AF2, we depleted POU2AF2 by two distinct sgRNAs in different SCLC cell lines and conducted RNA-seq experiments. To study the potential mechanisms, we determined the chromatin occupancy of BRG1 and PRC2 in POU2AF2 wild type and depleted cells by ChIP-seq. To understand how POU2AF2 impacts chromatin accessibility, we performed ATAC-seq in cells transduced with either non-targeting sgRNA or two distinct POU2AF2 sgRNAs. To study the high chromatin structure change, we employed Hi-C experiments.
SAMPLE_TITLE: HiC_H526_sgPOU2AF2-1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "NCI-H526"}, {"TAG": "cell line", "VALUE": "NCI-H526"}, {"TAG": "cell type", "VALUE": "small cell lung cancer"}, {"TAG": "genotype", "VALUE": "wild type"}, {"TAG": "treatment", "VALUE": "sgPOU2AF2 #1"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: HiC_H526_sgPOU2AF2-1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC_H526_sgPOU2AF2-1
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