Compute the Significant Interactions of Hi-C data through HOMER
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE93834 | GEO | 2017/05/09
SECONDARY ACCESSION(S): PRJNA362564
REPOSITORIES: GEO
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Project description:Millions of cis-regulatory sequences have recently been found in the human genome, but the function of most cis-elements are not yet clear, in part due to the difficulty in determining their regulatory targets, which are often located millions of base pairs away and separated by one or more unrelated genes. To address this problem, the Hi-C method has been developed to identify long-range looping interactions in a genome-wide, unbiased fashion. However, current data analysis of Hi-C datasets cannot fully resolve regulatory interactions between enhancers and promoters due to the low resolution. Here, we generated a high-depth Hi-C dataset and applied a new analysis method that offers improved resolution permitting genome-wide identification of nearly one million chromatin interactions. We demonstrated the use of Hi-C to identify target promoters of enhancers regulated by NF-M-NM-:B signaling and signal-dependent dynamic chromatin interaction at these enhancers in human cells. Surprisingly, our results showed that most NF-M-NM-:B binding sites are looped to their regulatory targets prior to activation of the signaling pathway, and appear to undergo little change during signaling. This observation suggests that the chromatin organization landscape, once established in a cell type, is rather stable and may influence the selection and activation of target genes by a transcription factor. We performed Hi-C analysis using a human fibroblast cell line IMR90 before and after NF-M-NM-:B activation. In the meantime, we also performed ChIP-seq experiments to map the location of NF-M-NM-:B p65 subunit, RNA polymerase II, p300, and several histone modifications (including H3K4me1, H3K4me3, H3K27ac and H3K36me3) in IMR90 cells before and after transient TNF-M-NM-1 stimulation. Additionally, to monitor the dynamic transcription profiles, we also performed Global Run-On sequencing (GRO-seq).
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Project description:Compute the Significant Interactions of Hi-C data through HOMER
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Project description:Recent studies have characterized the genomic structures of many eukaryotic cells, often with a focus on their relation to gene expression. So far, these studies have largely only investigated cells grown in 2D culture, although the transcriptomes of 3D cultured cells are generally closer to their in vivo phenotype. To examine the effects of spatial constraints on chromosome conformation, we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C. Our results reveal significant differences in long-range genomic interactions, notably in compartment identity and strength as well as in TAD-TAD interactions, but only minor differences at the TAD level. RNA-seq analysis reveals an up-regulation in the 3D cultured cells of those genes involved in physiological hepatocyte functions. We find that these genes are associated with only a subset of the structural changes, suggesting that the differences in genomic structure are indeed critically important for transcriptional regulation but also that there are major structural differences owing to other functions than gene expression. Overall, our results indicate that growth in 3D significantly alters longer-range genomic interactions, which may be consequential for a subset of genes that are important for the physiological functioning of the cell.
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