Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions

Summary

Resource data across the 76 cell types from FANTOM5 analysed in our paper titled "Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions".

Project abstract

Gene transcription is influenced by favourable chromosome positioning and chromatin architectures bringing regulatory elements in close proximity. However, it is unclear to what extent transcription is attributable to topological organisation or to gene-specific regulatory programs. Here, we develop a strategy to transcriptionally decompose expression data into two main components reflecting the positional relationship of neighbouring transcriptional units and effects independent from their positioning. 

We demonstrate that the positionally dependent component is highly informative of topological domain activity and organisation, revealing boundaries and chromatin compartments. Furthermore, features derived from transcriptional components can accurately predict individual chromatin interactions. We systematically investigate regulatory interactions and observe different transcriptional attributes governing long- and short-range interactions. Finally, we assess differences in regulatory organisations across 76 human cell types. In all, we demonstrate a close relationship between transcription and topological chromatin architecture and provide an unprecedented resource for investigations of regulatory organisations across cell types.

Included files

PD_component_76_cell_types.tar.gz - Contains the positionally dependent (PD) components for 76 human cell types.

PD_sd_component_76_cell_types.tar.gz - Contains the standard deviations of the positionally dependent (PD_sd) components for 76 human cell types.

PI_component_76_cell_types.tar.gz - Contains the positionally independent (PI) components for 76 human cell types.

PI_sd_component_76_cell_types.tar.gz - Contains the standard deviations  of the positionally independent (PI_sd) components for 76 human cell types.

predicted_EP_interactions_76_cell_types.tar.gz - Contains predicted enhancer-promoter interactions for 76 human cell types.

predicted_boundaries_76CT.txt - Matrix with 76 columns representing human cell types and 10kb genome-wide bins as rows, coded as 0 or 1 according to whether a XAD boundary was predicted in the bin for a given cell type.