@article {Burren100958, author = {Oliver S Burren and Arcadio Rubio Garc{\'\i}a and Biola-Maria Javierre and Daniel B Rainbow and Jonathan Cairns and Nicholas J Cooper and John J Lambourne and Ellen Schofield and Xaquin Castro Dopico and Ricardo C Ferreira and Richard Coulson and Frances Burden and Sophia P Rowlston and Kate Downes and Steven W Wingett and Mattia Frontini and Willem H Ouwehand and Peter Fraser and Mikhail Spivakov and John A Todd and Linda S Wicker and Antony J Cutler and Chris Wallace}, title = {Chromosome contacts in activated T cells identify autoimmune disease-candidate genes}, elocation-id = {100958}, year = {2017}, doi = {10.1101/100958}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Autoimmune disease-associated variants are preferentially found in regulatory regions in immune cells, particularly CD4+ T cells. Linking such regulatory regions to gene promoters in disease-relevant cell contexts facilitates identification of candidate disease genes. Here we show that, within four hours, activation of CD4+ T cells invokes changes in histone modifications and enhancer RNA transcription that correspond to altered expression of the interacting genes identified by promoter capture Hi-C (PCHi-C). By integrating PCHi-C data with genetic associations for five autoimmune diseases we prioritised 252 candidate genes, of which 116 were related to activation-sensitive interactions. This included IL2RA, where allele-specific expression analyses were consistent with its interaction-mediated regulation, illustrating the utility of the approach.}, URL = {https://www.biorxiv.org/content/early/2017/01/17/100958}, eprint = {https://www.biorxiv.org/content/early/2017/01/17/100958.full.pdf}, journal = {bioRxiv} }