Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks

Madrid-Mencía, Miguel; Raineri, Emanuele; Cao, Tran Bich Ngoc; Pancaldi, Vera

doi:http://dx.doi.org/10.1093/nar/gkaa159

Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks

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Madrid-Mencía M, Raineri E, Cao TBN, Pancaldi V. Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks. Nucleic Acids Res. 2020 May 7; 48(8): 4066-4080. DOI: 10.1093/nar/gkaa159

Abstract

We introduce an R package and a web-based visualization tool for the representation, analysis and integration of epigenomic data in the context of 3D chromatin interaction networks. GARDEN-NET allows for the projection of user-submitted genomic features on pre-loaded chromatin interaction networks, exploiting the functionalities of the ChAseR package to explore the features in combination with chromatin network topology properties. We demonstrate the approach using published epigenomic and chromatin structure datasets in haematopoietic cells, including a collection of gene expression, DNA methylation and histone modifications data in primary healthy myeloid cells from hundreds of individuals. These datasets allow us to test the robustness of chromatin assortativity, which highlights which epigenomic features, alone or in combination, are more strongly associated with 3D genome architecture. We find evidence for genomic regions with specific histone modifications, DNA methylation, and gene expression levels to be forming preferential contacts in 3D nuclear space, to a different extent depending on the cell type and lineage. Finally, we examine replication timing data and find it to be the genomic feature most strongly associated with overall 3D chromatin organization at multiple scales, consistent with previous results from the literature.