Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells

Gene expression is subject to stochastic noise, but to what extent and by which means such stochastic variations are coordinated among different genes are unclear. We hypothesize that neighboring genes on the same chromosome co-fluctuate in expression because of their common chromatin dynamics, and...

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Bibliographic Details
Published in:PLoS genetics Vol. 15; no. 9; p. e1008389
Main Authors: Sun, Mengyi, Zhang, Jianzhi
Format: Journal Article
Language:English
Published: United States Public Library of Science 16.09.2019
Public Library of Science (PLoS)
Subjects:
Analysis
Animals
Biology and Life Sciences
Cell cycle
Chromatin
Chromatin - genetics
Chromosome abnormalities
Chromosome Mapping - methods
Chromosomes
Chromosomes - genetics
Databases, Genetic
Evolution
Evolution, Molecular
Evolutionary biology
Gene expression
Gene Expression - genetics
Gene Expression Regulation - genetics
Genetic aspects
Genetic Linkage - genetics
Genome - genetics
Genomes
Genomics - methods
House mouse
Humans
Hypotheses
Mammalian cells
Mammals - genetics
Mice
Natural selection
Proteins
Ribonucleic acid
RNA
Selection, Genetic
Stochastic models
Stochastic Processes
Stochasticity
Yeast
United States
Ann Arbor Michigan
United States > US
ISSN:1553-7404, 1553-7390, 1553-7404
Online Access:Get full text
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Description
Summary:Gene expression is subject to stochastic noise, but to what extent and by which means such stochastic variations are coordinated among different genes are unclear. We hypothesize that neighboring genes on the same chromosome co-fluctuate in expression because of their common chromatin dynamics, and verify it at the genomic scale using allele-specific single-cell RNA-sequencing data of mouse cells. Unexpectedly, the co-fluctuation extends to genes that are over 60 million bases apart. We provide evidence that this long-range effect arises in part from chromatin co-accessibilities of linked loci attributable to three-dimensional proximity, which is much closer intra-chromosomally than inter-chromosomally. We further show that genes encoding components of the same protein complex tend to be chromosomally linked, likely resulting from natural selection for intracellular among-component dosage balance. These findings have implications for both the evolution of genome organization and optimal design of synthetic genomes in the face of gene expression noise.
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The authors have declared that no competing interests exist.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1008389