CHANGES IN THE GENOME-WIDE LOCALIZATION PATTERN OF SIR3 IN SACCHAROMYCES CEREVISIAE DURING DIFFERENT GROWTH STAGES
In budding yeast, the Sir2, Sir3 and Sir4 proteins form SIR complexes, required for the assembly of silent heterochromatin domains, and which mediate transcription silencing at the telomeres as well as at silent mating type loci. In this study, under fluorescence microscopy, we found most Sir3-GFP e...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2013-04-01
|
| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037014600246 |
| _version_ | 1818550331105083392 |
|---|---|
| author | Shu-Yun Tung Kuan-Wei Lee Jia-Yang Hong Sue-Ping Lee Hsiao-Hsuian Shen Gunn-Guang Liou |
| author_facet | Shu-Yun Tung Kuan-Wei Lee Jia-Yang Hong Sue-Ping Lee Hsiao-Hsuian Shen Gunn-Guang Liou |
| author_sort | Shu-Yun Tung |
| collection | DOAJ |
| description | In budding yeast, the Sir2, Sir3 and Sir4 proteins form SIR complexes, required for the assembly of silent heterochromatin domains, and which mediate transcription silencing at the telomeres as well as at silent mating type loci. In this study, under fluorescence microscopy, we found most Sir3-GFP expressions in the logarithmic phase cells appeared as multiple punctations as expected. However, some differences in the distribution of fluorescent signals were detected in the diauxic∼early stationary phase cells. To clarify these, we then used ChIP on chip assays to investigate the genome-wide localization of Sir3. In general, Sir3 binds to all 32 telomere proximal regions, the silent mating type loci and also binds to the rDNA region. However, the genome-wide localization patterns of Sir3 are different between these two distinct growth phases. We also confirmed that Sir3 binds to a recently identified secondary binding site, PAU genes, and further identified 349 Sir3-associated cluster regions. These results provide additional support in roles for Sir3 in the modulation of gene expression during physical conditions such as diauxic∼early stationary phase growing. Moreover, they imply that Sir3 may be not only involved in the formation of conventional silent heterochromatin, but also able to associate with some other chromatin regions involved in epigenetic regulation. |
| first_indexed | 2024-12-12T08:45:01Z |
| format | Article |
| id | doaj.art-4b0108c620fd48b1a9202eab823acaf9 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-12T08:45:01Z |
| publishDate | 2013-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-4b0108c620fd48b1a9202eab823acaf92022-12-22T00:30:34ZengElsevierComputational and Structural Biotechnology Journal2001-03702013-04-017810.5936/csbj.201304001CHANGES IN THE GENOME-WIDE LOCALIZATION PATTERN OF SIR3 IN SACCHAROMYCES CEREVISIAE DURING DIFFERENT GROWTH STAGESShu-Yun Tung0Kuan-Wei Lee1Jia-Yang Hong2Sue-Ping Lee3Hsiao-Hsuian Shen4Gunn-Guang Liou5Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, ROCInstitute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 35053, Taiwan, ROCInstitute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 35053, Taiwan, ROCInstitute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, ROCInstitute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 35053, Taiwan, ROCInstitute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 35053, Taiwan, ROCIn budding yeast, the Sir2, Sir3 and Sir4 proteins form SIR complexes, required for the assembly of silent heterochromatin domains, and which mediate transcription silencing at the telomeres as well as at silent mating type loci. In this study, under fluorescence microscopy, we found most Sir3-GFP expressions in the logarithmic phase cells appeared as multiple punctations as expected. However, some differences in the distribution of fluorescent signals were detected in the diauxic∼early stationary phase cells. To clarify these, we then used ChIP on chip assays to investigate the genome-wide localization of Sir3. In general, Sir3 binds to all 32 telomere proximal regions, the silent mating type loci and also binds to the rDNA region. However, the genome-wide localization patterns of Sir3 are different between these two distinct growth phases. We also confirmed that Sir3 binds to a recently identified secondary binding site, PAU genes, and further identified 349 Sir3-associated cluster regions. These results provide additional support in roles for Sir3 in the modulation of gene expression during physical conditions such as diauxic∼early stationary phase growing. Moreover, they imply that Sir3 may be not only involved in the formation of conventional silent heterochromatin, but also able to associate with some other chromatin regions involved in epigenetic regulation.http://www.sciencedirect.com/science/article/pii/S2001037014600246ChIP on chipheterochromatingenome-wideSir3 |
| spellingShingle | Shu-Yun Tung Kuan-Wei Lee Jia-Yang Hong Sue-Ping Lee Hsiao-Hsuian Shen Gunn-Guang Liou CHANGES IN THE GENOME-WIDE LOCALIZATION PATTERN OF SIR3 IN SACCHAROMYCES CEREVISIAE DURING DIFFERENT GROWTH STAGES Computational and Structural Biotechnology Journal ChIP on chip heterochromatin genome-wide Sir3 |
| title | CHANGES IN THE GENOME-WIDE LOCALIZATION PATTERN OF SIR3 IN SACCHAROMYCES CEREVISIAE DURING DIFFERENT GROWTH STAGES |
| title_full | CHANGES IN THE GENOME-WIDE LOCALIZATION PATTERN OF SIR3 IN SACCHAROMYCES CEREVISIAE DURING DIFFERENT GROWTH STAGES |
| title_fullStr | CHANGES IN THE GENOME-WIDE LOCALIZATION PATTERN OF SIR3 IN SACCHAROMYCES CEREVISIAE DURING DIFFERENT GROWTH STAGES |
| title_full_unstemmed | CHANGES IN THE GENOME-WIDE LOCALIZATION PATTERN OF SIR3 IN SACCHAROMYCES CEREVISIAE DURING DIFFERENT GROWTH STAGES |
| title_short | CHANGES IN THE GENOME-WIDE LOCALIZATION PATTERN OF SIR3 IN SACCHAROMYCES CEREVISIAE DURING DIFFERENT GROWTH STAGES |
| title_sort | changes in the genome wide localization pattern of sir3 in saccharomyces cerevisiae during different growth stages |
| topic | ChIP on chip heterochromatin genome-wide Sir3 |
| url | http://www.sciencedirect.com/science/article/pii/S2001037014600246 |
| work_keys_str_mv | AT shuyuntung changesinthegenomewidelocalizationpatternofsir3insaccharomycescerevisiaeduringdifferentgrowthstages AT kuanweilee changesinthegenomewidelocalizationpatternofsir3insaccharomycescerevisiaeduringdifferentgrowthstages AT jiayanghong changesinthegenomewidelocalizationpatternofsir3insaccharomycescerevisiaeduringdifferentgrowthstages AT suepinglee changesinthegenomewidelocalizationpatternofsir3insaccharomycescerevisiaeduringdifferentgrowthstages AT hsiaohsuianshen changesinthegenomewidelocalizationpatternofsir3insaccharomycescerevisiaeduringdifferentgrowthstages AT gunnguangliou changesinthegenomewidelocalizationpatternofsir3insaccharomycescerevisiaeduringdifferentgrowthstages |