Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA386511 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5547800_1.fastq.gz | Fastqsanger.gz | |||
| SRR5547800_2.fastq.gz | Fastqsanger.gz | |||
| SRR5547810_1.fastq.gz | Fastqsanger.gz | |||
| SRR5547810_2.fastq.gz | Fastqsanger.gz | |||
| SRR5547801_1.fastq.gz | Fastqsanger.gz |
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Project description:Aims and methods: To analyze how IFNγ induces coding and non-coding nascent transcriptional changes, SNU-seq is used to measure genome-wide changes in nascent transcription in untreated, 0.5hr, 2hr and 24hr IFNγ treated Hep3B cells. SNU-seq identifies the last transcribed nucleotide at near single-nucleotide resolution. 3'-end RNA-seq is used to examine RNA levels. ChIPmentation and ATAC-seq are used to assess the differential chromatin landscape upon IFNγ treatments, measuring H3K27ac, H3K4me3 and CTCF genome-wide changes as well as DNA accessibility in untreated, 0.5hr, 2hr and 24hr IFNγ treated Hep3B cells. Higher-order chromatin structure is investigated upon IFNγ treatments using Capture-C to measure promoter interactions of three gene promoters; IRF1, STAT1, and CD274. Results: 3'-end RNA-seq reveals IFNγ stimulated genes. SNU-seq identifies dynamic transcription at genes and non-coding intergenic regions and is used to demonstrate differential APA upon IFNγ treatments. By measuring transcription at nucleosome depleted regions, differential enhancer activity was demonstrated. IFNγ induces hundreds of methylation changes and thousands of acetylation changes over 24hrs. Unlike H3K4me3 which is deposited at late timepoints, H3K27ac is dynamically deposited. This acetylation is sometimes sustained throughout 24hrs but is often transiently deposited. CTCF shows very few binding changes throughout the timecourse. IFNγ induces significant changes in promoter:enhancer interactions at IRF1 and STAT1. The CD274 promoter loops to the nearest gene promoter; PLGRKT.
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Project description:To gain insight into the relationship between chromatin structure and gene expression, we conducted a Tethered Chromatin Capture (TCC) analysis using MCF7 breast cancer and PANC1 pancreatic cancer cells. We applied a novel Hi-C analysis algorithm and identified hundreds of thousands of Interacting Loci Pairs (ILPs) in each of the two cell types. We classified ILPs according to location with respect to gene structure, gene expression, different histone modifications, DNase hypersensitivity, and RNA polymerase II and CTCF binding, identifying distinct classes of ILPs. Interestingly, we found that only 5% of the ILPs involved promoter regions, with even fewer promoter-enhancer loops. We find that genes associated with promoter-enhancer loops have cell type-specific functional annotations. We then tested the impact of pharmacological inhibition of histone acetylation on genes having promoter-enhancer ILPs in PANC1 cells. We found that genes with promoter-enhancer ILPs show reduced expression in response to drug treatment, suggesting that the chromatin loops we identified are functional.
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