Promoters maintain their relative activity levels under different growth conditions
Abstract Most genes change expression levels across conditions, but it is unclear which of these changes represents specific regulation and what determines their quantitative degree. Here, we accurately measured activities of ∼900 S. cerevisiae and ∼1800 E. coli promoters using fluorescent reporters...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2013-10-01
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| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/msb.2013.59 |
| _version_ | 1826990455678566400 |
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| author | Leeat Keren Ora Zackay Maya Lotan‐Pompan Uri Barenholz Erez Dekel Vered Sasson Guy Aidelberg Anat Bren Danny Zeevi Adina Weinberger Uri Alon Ron Milo Eran Segal |
| author_facet | Leeat Keren Ora Zackay Maya Lotan‐Pompan Uri Barenholz Erez Dekel Vered Sasson Guy Aidelberg Anat Bren Danny Zeevi Adina Weinberger Uri Alon Ron Milo Eran Segal |
| author_sort | Leeat Keren |
| collection | DOAJ |
| description | Abstract Most genes change expression levels across conditions, but it is unclear which of these changes represents specific regulation and what determines their quantitative degree. Here, we accurately measured activities of ∼900 S. cerevisiae and ∼1800 E. coli promoters using fluorescent reporters. We show that in both organisms 60–90% of promoters change their expression between conditions by a constant global scaling factor that depends only on the conditions and not on the promoter's identity. Quantifying such global effects allows precise characterization of specific regulation—promoters deviating from the global scale line. These are organized into few functionally related groups that also adhere to scale lines and preserve their relative activities across conditions. Thus, only several scaling factors suffice to accurately describe genome‐wide expression profiles across conditions. We present a parameter‐free passive resource allocation model that quantitatively accounts for the global scaling factors. It suggests that many changes in expression across conditions result from global effects and not specific regulation, and provides means for quantitative interpretation of expression profiles. |
| first_indexed | 2024-03-07T16:41:31Z |
| format | Article |
| id | doaj.art-a01ccda68c6b4e9192fdfc7cfc7d92f6 |
| institution | Directory Open Access Journal |
| issn | 1744-4292 |
| language | English |
| last_indexed | 2025-02-18T08:20:50Z |
| publishDate | 2013-10-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj.art-a01ccda68c6b4e9192fdfc7cfc7d92f62024-11-03T12:55:37ZengSpringer NatureMolecular Systems Biology1744-42922013-10-019111710.1038/msb.2013.59Promoters maintain their relative activity levels under different growth conditionsLeeat Keren0Ora Zackay1Maya Lotan‐Pompan2Uri Barenholz3Erez Dekel4Vered Sasson5Guy Aidelberg6Anat Bren7Danny Zeevi8Adina Weinberger9Uri Alon10Ron Milo11Eran Segal12Department of Computer Science and Applied Mathematics, Weizmann Institute of ScienceDepartment of Computer Science and Applied Mathematics, Weizmann Institute of ScienceDepartment of Computer Science and Applied Mathematics, Weizmann Institute of ScienceDepartment of Plant Sciences, Weizmann Institute of ScienceDepartment of Molecular Cell Biology, Weizmann Institute of ScienceDepartment of Molecular Cell Biology, Weizmann Institute of ScienceDepartment of Molecular Cell Biology, Weizmann Institute of ScienceDepartment of Molecular Cell Biology, Weizmann Institute of ScienceDepartment of Computer Science and Applied Mathematics, Weizmann Institute of ScienceDepartment of Computer Science and Applied Mathematics, Weizmann Institute of ScienceDepartment of Molecular Cell Biology, Weizmann Institute of ScienceDepartment of Plant Sciences, Weizmann Institute of ScienceDepartment of Computer Science and Applied Mathematics, Weizmann Institute of ScienceAbstract Most genes change expression levels across conditions, but it is unclear which of these changes represents specific regulation and what determines their quantitative degree. Here, we accurately measured activities of ∼900 S. cerevisiae and ∼1800 E. coli promoters using fluorescent reporters. We show that in both organisms 60–90% of promoters change their expression between conditions by a constant global scaling factor that depends only on the conditions and not on the promoter's identity. Quantifying such global effects allows precise characterization of specific regulation—promoters deviating from the global scale line. These are organized into few functionally related groups that also adhere to scale lines and preserve their relative activities across conditions. Thus, only several scaling factors suffice to accurately describe genome‐wide expression profiles across conditions. We present a parameter‐free passive resource allocation model that quantitatively accounts for the global scaling factors. It suggests that many changes in expression across conditions result from global effects and not specific regulation, and provides means for quantitative interpretation of expression profiles.https://doi.org/10.1038/msb.2013.59gene expressiongrowth ratemodelingpromoter activitytranscription regulation |
| spellingShingle | Leeat Keren Ora Zackay Maya Lotan‐Pompan Uri Barenholz Erez Dekel Vered Sasson Guy Aidelberg Anat Bren Danny Zeevi Adina Weinberger Uri Alon Ron Milo Eran Segal Promoters maintain their relative activity levels under different growth conditions Molecular Systems Biology gene expression growth rate modeling promoter activity transcription regulation |
| title | Promoters maintain their relative activity levels under different growth conditions |
| title_full | Promoters maintain their relative activity levels under different growth conditions |
| title_fullStr | Promoters maintain their relative activity levels under different growth conditions |
| title_full_unstemmed | Promoters maintain their relative activity levels under different growth conditions |
| title_short | Promoters maintain their relative activity levels under different growth conditions |
| title_sort | promoters maintain their relative activity levels under different growth conditions |
| topic | gene expression growth rate modeling promoter activity transcription regulation |
| url | https://doi.org/10.1038/msb.2013.59 |
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