Chromosome conformation capture-based methods articles within Nature Communications

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• Article
  05 November 2022 | Open Access

  Learning the histone codes with large genomic windows and three-dimensional chromatin interactions using transformer

  Existing deep learning-based approaches for the prediction of gene expression by histone modifications (HMs) can only focus on narrow and linear genomic regions around promoters. Here, the authors address these problems by developing a transformer-based deep learning architecture named Chromoformer.

  • Dohoon Lee
  • , Jeewon Yang
  •  & Sun Kim

• Article
  03 July 2020 | Open Access

  Mapping effector genes at lupus GWAS loci using promoter Capture-C in follicular helper T cells

  T cells are a major cell type involved in systemic lupus erythematosus (SLE). Here, the authors use promoter capture-C and ATAC-seq in human follicular T helper cells to identify SLE genes distant from GWAS loci (via 3D interaction) and validate the function of key regulatory elements and genes in vitro.

  • Chun Su
  • , Matthew E. Johnson
  •  & Andrew D. Wells

• Article
  19 February 2015 | Open Access

  Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

  Multiple regulatory elements distant from their targets on the linear genome can influence gene expression through chromatin looping. Here, the authors report an improved chromosome conformation capture approach that can be used to identify long-range chromatin interactions in cancer risk loci.

  • Roland Jäger
  • , Gabriele Migliorini
  •  & Richard S. Houlston