Diagenode

Chromosome contacts in activated T cells identify autoimmune disease candidate genes


Burren OS et al.

BACKGROUND:

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.

RESULTS:

Within 4 h, 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. By integrating promoter capture Hi-C data with genetic associations for five autoimmune diseases, we prioritised 245 candidate genes with a median distance from peak signal to prioritised gene of 153 kb. Just under half (108/245) prioritised genes 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.

CONCLUSIONS:

Our systematic experimental framework offers an alternative approach to candidate causal gene identification for variants with cell state-specific functional effects, with achievable sample sizes.

Tags
IP-Star
Antibody

Share this article

Published
September, 2017

Source

Products used in this publication

  • some alt
    B03000002
    IP-Star® Compact Automated System
  • Antibody ChIP-seq grade icon
    C15410196
    H3K27ac polyclonal antibody - Premium
  • Antibody ChIP-seq grade icon
    C15410195
    H3K27me3 polyclonal antibody - Premium
  • Antibody ChIP-seq grade icon
    C15410192
    H3K36me3 polyclonal antibody - Premium
  • Antibody ChIP-seq grade icon
    C15410194
    H3K4me1 polyclonal antibody - Premium
  • Antibody ChIP-seq grade icon
    C15410003-50
    H3K4me3 polyclonal antibody - Premium
  • Antibody ChIP-seq grade icon
    C15410193
    H3K9me3 polyclonal antibody - Premium
  • ChIP kit icon
    C05010020
    iDeal Library Preparation Kit x24 (incl. Index ...

Events

 See all events

Applications

 See all applications



The European Regional Development Fund and Wallonia are investing in your future.

Extension of industrial buildings and new laboratories.



  ABOUT SSL CERTIFICATES

         Site map   |   Contact us   |   Conditions of sales   |   Conditions of purchase   |   Privacy policy   |   Diagenode Diagnostics