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About the Authors:
Danielle G. Lemay
* E-mail: [email protected] (DGL); [email protected] (MR)
Affiliation: Genome Center, University of California Davis, Davis, California, United States of America
Katherine S. Pollard
Affiliation: Gladstone Institutes, Institute for Human Genetics, and Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
William F. Martin
Affiliation: Department of Food Science and Technology, University of California Davis, Davis, California, United States of America
Courtneay Freeman Zadrowski
Affiliation: USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
Joseph Hernandez
Affiliation: USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
Ian Korf
Affiliation: Genome Center, University of California Davis, Davis, California, United States of America
J. Bruce German
Affiliation: Department of Food Science and Technology, University of California Davis, Davis, California, United States of America
Monique Rijnkels
* E-mail: [email protected] (DGL); [email protected] (MR)
Affiliation: USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
Introduction
Bacterial operons exemplify how a gene's expression is affected by proximity to neighboring genes. When a gene translocates from one genomic position to another, the expression of that gene often changes. Likewise in mammalian genomes, the alteration of a gene's neighborhood over evolutionary time can alter gene expression [1], [2]. Essential genes – those required for an organism's survival – are more resistant to altered gene expression that results from genomic rearrangement [1]. Neighborhoods of mammalian co-expressed genes often form through tandem duplications and are preferentially maintained when they are composed of functionally linked, non-essential genes [3]. However, the mechanisms by which neighboring genes are co-expressed in eukaryotic genomes are incompletely understood.
The chromatin configuration surrounding a gene – its epigenetic state – also influences the capacity of that gene to be expressed. Nuclear DNA is packaged into chromatin; this organizes the genome into regions that are more or less accessible to the transcription machinery. The cumulative epigenetic state of all genes in a cell determines the cell's expression capacity and is associated with its differentiation state and cell identity [4], [5]. We hypothesized that the epigenetic state contributes to the co-regulation of gene neighborhoods.
We...