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...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2019-09-01
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| Series: | PLoS Genetics |
| Online Access: | https://doi.org/10.1371/journal.pgen.1008389 |
| _version_ | 1818729559775772672 |
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| author | Mengyi Sun Jianzhi Zhang |
| author_facet | Mengyi Sun Jianzhi Zhang |
| author_sort | Mengyi Sun |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-17T22:47:49Z |
| format | Article |
| id | doaj.art-6388c69524ef43049d58f523aece7110 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-17T22:47:49Z |
| publishDate | 2019-09-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-6388c69524ef43049d58f523aece71102022-12-21T21:29:45ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042019-09-01159e100838910.1371/journal.pgen.1008389Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells.Mengyi SunJianzhi ZhangGene 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.https://doi.org/10.1371/journal.pgen.1008389 |
| spellingShingle | Mengyi Sun Jianzhi Zhang Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells. PLoS Genetics |
| title | Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells. |
| title_full | Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells. |
| title_fullStr | Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells. |
| title_full_unstemmed | Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells. |
| title_short | Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells. |
| title_sort | chromosome wide co fluctuation of stochastic gene expression in mammalian cells |
| url | https://doi.org/10.1371/journal.pgen.1008389 |
| work_keys_str_mv | AT mengyisun chromosomewidecofluctuationofstochasticgeneexpressioninmammaliancells AT jianzhizhang chromosomewidecofluctuationofstochasticgeneexpressioninmammaliancells |