Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry
Cells adapt to familiar changes in their environment by activating predefined regulatory programs that establish adaptive gene expression states. These hard-wired pathways, however, may be inadequate for adaptation to environments never encountered before. Here, we reveal evidence for an alternative...
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2018-04-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/31867 |
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| author | Lydia Freddolino Jamie Yang Amir Momen-Roknabadi Saeed Tavazoie |
| author_facet | Lydia Freddolino Jamie Yang Amir Momen-Roknabadi Saeed Tavazoie |
| author_sort | Lydia Freddolino |
| collection | DOAJ |
| description | Cells adapt to familiar changes in their environment by activating predefined regulatory programs that establish adaptive gene expression states. These hard-wired pathways, however, may be inadequate for adaptation to environments never encountered before. Here, we reveal evidence for an alternative mode of gene regulation that enables adaptation to adverse conditions without relying on external sensory information or genetically predetermined cis-regulation. Instead, individual genes achieve optimal expression levels through a stochastic search for improved fitness. By focusing on improving the overall health of the cell, the proposed stochastic tuning mechanism discovers global gene expression states that are fundamentally new and yet optimized for novel environments. We provide experimental evidence for stochastic tuning in the adaptation of Saccharomyces cerevisiae to laboratory-engineered environments that are foreign to its native gene-regulatory network. Stochastic tuning operates locally at individual gene promoters, and its efficacy is modulated by perturbations to chromatin modification machinery. |
| format | Article |
| id | doaj-art-1ab6927a0ac840be9988164ca8608d91 |
| institution | Kabale University |
| issn | 2050-084X |
| language | English |
| publishDate | 2018-04-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj-art-1ab6927a0ac840be9988164ca8608d912025-01-24T14:01:59ZengeLife Sciences Publications LtdeLife2050-084X2018-04-01710.7554/eLife.31867Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitryLydia Freddolino0https://orcid.org/0000-0002-5821-4226Jamie Yang1Amir Momen-Roknabadi2Saeed Tavazoie3https://orcid.org/0000-0003-2183-4162Department of Systems Biology, Columbia University, New York City, United States; Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, United StatesDepartment of Systems Biology, Columbia University, New York City, United States; Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, United StatesDepartment of Systems Biology, Columbia University, New York City, United States; Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, United StatesDepartment of Systems Biology, Columbia University, New York City, United States; Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, United StatesCells adapt to familiar changes in their environment by activating predefined regulatory programs that establish adaptive gene expression states. These hard-wired pathways, however, may be inadequate for adaptation to environments never encountered before. Here, we reveal evidence for an alternative mode of gene regulation that enables adaptation to adverse conditions without relying on external sensory information or genetically predetermined cis-regulation. Instead, individual genes achieve optimal expression levels through a stochastic search for improved fitness. By focusing on improving the overall health of the cell, the proposed stochastic tuning mechanism discovers global gene expression states that are fundamentally new and yet optimized for novel environments. We provide experimental evidence for stochastic tuning in the adaptation of Saccharomyces cerevisiae to laboratory-engineered environments that are foreign to its native gene-regulatory network. Stochastic tuning operates locally at individual gene promoters, and its efficacy is modulated by perturbations to chromatin modification machinery.https://elifesciences.org/articles/31867gene regulationadaptationgene expression noiseepigeneticsstress responsestochastic tuning |
| spellingShingle | Lydia Freddolino Jamie Yang Amir Momen-Roknabadi Saeed Tavazoie Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry eLife gene regulation adaptation gene expression noise epigenetics stress response stochastic tuning |
| title | Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry |
| title_full | Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry |
| title_fullStr | Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry |
| title_full_unstemmed | Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry |
| title_short | Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry |
| title_sort | stochastic tuning of gene expression enables cellular adaptation in the absence of pre existing regulatory circuitry |
| topic | gene regulation adaptation gene expression noise epigenetics stress response stochastic tuning |
| url | https://elifesciences.org/articles/31867 |
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