Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development

• Published in: PLoS genetics Vol. 14; no. 6; p. e1007431
• Main Authors: Johanson, Timothy M, Coughlan, Hannah D, Lun, Aaron T L, Bediaga, Naiara G, Naselli, Gaetano, Garnham, Alexandra L, Harrison, Leonard C, Smyth, Gordon K, Allan, Rhys S
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 08.06.2018; Public Library of Science (PLoS)
• Subjects: Animals; Bioinformatics; Biology; Biology and Life Sciences; Cell cycle; Cell fate; Centromeres; Chromatin - chemistry; Chromatin - genetics; Chromatin - metabolism; Chromosomes; Chromosomes, Mammalian - chemistry; Chromosomes, Mammalian - genetics; Chromosomes, Mammalian - metabolism; Conformation; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - genetics; DNA - metabolism; Flow Cytometry; Funding; Gene expression; Gene Expression Regulation; Genetic aspects; Genetic regulation; Genetic research; Genome; Genome-wide association studies; Genomes; Humans; Immune system; Immunity, Cellular - genetics; Immunoglobulins; Lymphocytes; Male; Mammals; Mammals - physiology; Medical research; Medicine and Health Sciences; Mice; Mice, Inbred C57BL; Nucleic Acid Conformation; Software; Stereoisomerism; Supervision; Telomeres; Zoological research; Australia
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1007431

It has been proposed that interactions between mammalian chromosomes, or transchromosomal interactions (also known as kissing chromosomes), regulate gene expression and cell fate determination. Here we aimed to identify novel transchromosomal interactions in immune cells by high-resolution genome-wide chromosome conformation capture. Although we readily identified stable interactions in cis, and also between centromeres and telomeres on different chromosomes, surprisingly we identified no gene regulatory transchromosomal interactions in either mouse or human cells, including previously described interactions. We suggest that advances in the chromosome conformation capture technique and the unbiased nature of this approach allow more reliable capture of interactions between chromosomes than previous methods. Overall our findings suggest that stable transchromosomal interactions that regulate gene expression are not present in mammalian immune cells and that lineage identity is governed by cis, not trans chromosomal interactions.