RT Journal Article
SR Electronic
T1 Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 130070
DO 10.1101/130070
A1 Sarah Rennie
A1 Maria Dalby
A1 Lucas van Duin
A1 Robin Andersson
YR 2017
UL http://biorxiv.org/content/early/2017/04/24/130070.abstract
AB 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.