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

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-wi...

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Published inPLoS 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
LanguageEnglish
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
Online AccessGet full text

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Abstract 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.
AbstractList 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.
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. It is a widely held belief that, in the darkness of the nucleus, strands of DNA that make up different chromosomes frequently meet to ‘kiss’. These kisses, or transchromosomal interactions, are thought to be important for the expression of genes and thus cell development. Here, we aimed to identify novel transchromosomal interactions in mouse and human immune cells by high-resolution genome-wide chromosome conformation capture methods. Although we readily identified stable interactions within chromosomes and also between centromeres and telomeres on different chromosomes, surprisingly we identified no gene regulatory transchromosomal interactions in either mouse or human cells, including those previously described. Overall our findings suggest that stable transchromosomal interactions that regulate gene expression are not present in mammalian immune cells and that chromosomes are doing far less kissing than was previously believed.
Audience Academic
Author Smyth, Gordon K
Bediaga, Naiara G
Naselli, Gaetano
Harrison, Leonard C
Lun, Aaron T L
Garnham, Alexandra L
Coughlan, Hannah D
Johanson, Timothy M
Allan, Rhys S
AuthorAffiliation 3 School of Mathematics and Statistics, The University of Melbourne, Parkville, Australia
1 The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
2 Department of Medical Biology, The University of Melbourne, Parkville, Australia
Stanford University School of Medicine, UNITED STATES
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Snippet It has been proposed that interactions between mammalian chromosomes, or transchromosomal interactions (also known as kissing chromosomes), regulate gene...
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StartPage e1007431
SubjectTerms 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
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Title Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development
URI https://www.ncbi.nlm.nih.gov/pubmed/29883495
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https://search.proquest.com/docview/2052809293
https://pubmed.ncbi.nlm.nih.gov/PMC6010296
https://doaj.org/article/45da5c743d81473eb4350b4219b44f50
http://dx.doi.org/10.1371/journal.pgen.1007431
Volume 14
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