Poster Presentation 39th Annual Lorne Genome Conference 2018

Investigating computational analysis pipelines and genomic proximity interactions in T lymphocytes (#181)

Ning Liu 1 2 , Tim Sadlon 1 3 , Stephen Pederson 2 , Simon Barry 1 3 , James Breen 1 2
  1. Robinson Reseach Institute, University of Adelaide, Adelaide, SA, Australia
  2. Bioinformatics Hub, University of Adelaide, Adelaide, SA, Australia
  3. Division of Paediatric Medicine, Women's and Children's Hospital, Adelaide, SA, Australia

Chromosome Conformation Capture (3C) technology is a method used for investigating three-dimensional (3D) genome structure, whereby segments of a genome that are in close-proximity can be identified and used to infer their spatial relationship. A 3C-derived method, High-resolution Chromosome Conformation Capture sequencing (HiC-seq) have been used to identify genes that can be affected by distal interactions such as long-range promoter-enhancer contacts that interact with immune system regulators. Although HiC-seq has been widely used to identify 3D interactions genome-wide in many species, many of the analysis tools have yet to be critically assessed. Here, we used publically available HiC-seq data to investigate and compare three major steps of HiC-seq data analysis workflow, including raw HiC-seq data processing, topologically-associated domains (TADs) identification algorithms and visualisation tools. We then applied our validated toolset to a DNaseI-treated, HiC-seq dataset sampled from human conventional T cells (Tconv cells) to investigate the ability of the tools at analysing relative low-coverage datasets. Whilst HiC-seq data analysis requires a significant sequencing coverage, applying HiC-Pro, an insulation score algorithm for TAD identification and HiCPlotter for visualisation, we identified a total of 4,818,855 long-range interactions, leading to the prediction of 3275 TADs genome-wide. Using this HiC-seq data along with other conformation assays (i.e. 4C-seq), we show that an upstream super-enhancer and promoter of the master T cell regulator SATB1 are located within the same TAD region, supporting the hypothesis that long-range interactions regulate the function of SATB1, and that sequence variants in enhancer elements may effect the pathogenicity of autoimmune diseases.