Quantitative analysis of the transcription control mechanism
Abstract Gene transcription requires a sequence of promoter state transitions, including chromatin remodeling, assembly of the transcription machinery, and clearance of the promoter by RNA polymerase. The rate‐limiting steps in this sequence are regulated by transcriptional activators that bind at s...
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| Format: | Article |
| Language: | English |
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Springer Nature
2010-11-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.1038/msb.2010.83 |
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| _version_ | 1849225804505939968 |
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| author | Changhui Mao Christopher R Brown Elena Falkovskaia Shawfeng Dong Eva Hrabeta‐Robinson Lauren Wenger Hinrich Boeger |
| author_facet | Changhui Mao Christopher R Brown Elena Falkovskaia Shawfeng Dong Eva Hrabeta‐Robinson Lauren Wenger Hinrich Boeger |
| author_sort | Changhui Mao |
| collection | DOAJ |
| description | Abstract Gene transcription requires a sequence of promoter state transitions, including chromatin remodeling, assembly of the transcription machinery, and clearance of the promoter by RNA polymerase. The rate‐limiting steps in this sequence are regulated by transcriptional activators that bind at specific promoter elements. As the transition kinetics of individual promoters cannot be observed, the identity of the activator‐controlled steps has remained a matter of speculation. In this study, we investigated promoter chromatin structure, and the intrinsic noise of expression over a wide range of expression values for the PHO5 gene of yeast. Interpretation of our results with regard to a stochastic model of promoter chromatin remodeling and gene expression suggests that the regulatory architecture of the gene expression process is measurably reflected in its intrinsic noise profile. Our chromatin structure and noise analyses indicate that the activator of PHO5 transcription stimulates the rates of promoter nucleosome disassembly, and assembly of the transcription machinery after nucleosome removal, but no other rates of the expression process. |
| format | Article |
| id | doaj-art-e7aa0b57e9b846b38242b8285094fb03 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2010-11-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-e7aa0b57e9b846b38242b8285094fb032025-08-24T12:00:21ZengSpringer NatureMolecular Systems Biology1744-42922010-11-016111210.1038/msb.2010.83Quantitative analysis of the transcription control mechanismChanghui Mao0Christopher R Brown1Elena Falkovskaia2Shawfeng Dong3Eva Hrabeta‐Robinson4Lauren Wenger5Hinrich Boeger6Department of Molecular, Cell, and Developmental Biology, University of California Santa CruzDepartment of Molecular, Cell, and Developmental Biology, University of California Santa CruzDepartment of Molecular, Cell, and Developmental Biology, University of California Santa CruzDepartment of Astronomy and Astrophysics, University of California Santa CruzDepartment of Molecular, Cell, and Developmental Biology, University of California Santa CruzDepartment of Molecular, Cell, and Developmental Biology, University of California Santa CruzDepartment of Molecular, Cell, and Developmental Biology, University of California Santa CruzAbstract Gene transcription requires a sequence of promoter state transitions, including chromatin remodeling, assembly of the transcription machinery, and clearance of the promoter by RNA polymerase. The rate‐limiting steps in this sequence are regulated by transcriptional activators that bind at specific promoter elements. As the transition kinetics of individual promoters cannot be observed, the identity of the activator‐controlled steps has remained a matter of speculation. In this study, we investigated promoter chromatin structure, and the intrinsic noise of expression over a wide range of expression values for the PHO5 gene of yeast. Interpretation of our results with regard to a stochastic model of promoter chromatin remodeling and gene expression suggests that the regulatory architecture of the gene expression process is measurably reflected in its intrinsic noise profile. Our chromatin structure and noise analyses indicate that the activator of PHO5 transcription stimulates the rates of promoter nucleosome disassembly, and assembly of the transcription machinery after nucleosome removal, but no other rates of the expression process.https://doi.org/10.1038/msb.2010.83chromatin dynamicsexpression noisegene regulationstochastic model |
| spellingShingle | Changhui Mao Christopher R Brown Elena Falkovskaia Shawfeng Dong Eva Hrabeta‐Robinson Lauren Wenger Hinrich Boeger Quantitative analysis of the transcription control mechanism Molecular Systems Biology chromatin dynamics expression noise gene regulation stochastic model |
| title | Quantitative analysis of the transcription control mechanism |
| title_full | Quantitative analysis of the transcription control mechanism |
| title_fullStr | Quantitative analysis of the transcription control mechanism |
| title_full_unstemmed | Quantitative analysis of the transcription control mechanism |
| title_short | Quantitative analysis of the transcription control mechanism |
| title_sort | quantitative analysis of the transcription control mechanism |
| topic | chromatin dynamics expression noise gene regulation stochastic model |
| url | https://doi.org/10.1038/msb.2010.83 |
| work_keys_str_mv | AT changhuimao quantitativeanalysisofthetranscriptioncontrolmechanism AT christopherrbrown quantitativeanalysisofthetranscriptioncontrolmechanism AT elenafalkovskaia quantitativeanalysisofthetranscriptioncontrolmechanism AT shawfengdong quantitativeanalysisofthetranscriptioncontrolmechanism AT evahrabetarobinson quantitativeanalysisofthetranscriptioncontrolmechanism AT laurenwenger quantitativeanalysisofthetranscriptioncontrolmechanism AT hinrichboeger quantitativeanalysisofthetranscriptioncontrolmechanism |