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Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array
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| Zeitschriftentitel: | BMC Genomics |
|---|---|
| Personen und Körperschaften: | , , , , , |
| In: | BMC Genomics, 9, 2008, 1 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Springer Science and Business Media LLC
|
| Schlagwörter: |
| author_facet |
Singer, Gregory AC Wu, Jiejun Yan, Pearlly Plass, Christoph Huang, Tim HM Davuluri, Ramana V Singer, Gregory AC Wu, Jiejun Yan, Pearlly Plass, Christoph Huang, Tim HM Davuluri, Ramana V |
|---|---|
| author |
Singer, Gregory AC Wu, Jiejun Yan, Pearlly Plass, Christoph Huang, Tim HM Davuluri, Ramana V |
| spellingShingle |
Singer, Gregory AC Wu, Jiejun Yan, Pearlly Plass, Christoph Huang, Tim HM Davuluri, Ramana V BMC Genomics Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array Genetics Biotechnology |
| author_sort |
singer, gregory ac |
| spelling |
Singer, Gregory AC Wu, Jiejun Yan, Pearlly Plass, Christoph Huang, Tim HM Davuluri, Ramana V 1471-2164 Springer Science and Business Media LLC Genetics Biotechnology http://dx.doi.org/10.1186/1471-2164-9-349 <jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Independent lines of evidence suggested that a large fraction of human genes possess multiple promoters driving gene expression from distinct transcription start sites. Understanding which promoter is employed in which cellular context is required to unravel gene regulatory networks within the cell.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>We have developed a custom microarray platform that tiles roughly 35,000 alternative putative promoters from nearly 7,000 genes in the human genome. To demonstrate the utility of this array platform, we have analyzed the patterns of promoter usage in 17β-estradiol (E2)-treated and untreated MCF7 cells and show widespread usage of alternative promoters. Most intriguingly, we show that the downstream promoter in E2-sensitive multiple promoter genes tends to be very close to the 3'-terminus of the gene, suggesting exotic mechanisms of expression regulation in these genes.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>The usage of alternative promoters greatly multiplies the transcriptional complexity available within the human genome. The fact that many of these promoters are incapable of driving the synthesis of a meaningful protein-encoding transcript further complicates the story.</jats:p></jats:sec> Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array BMC Genomics |
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10.1186/1471-2164-9-349 |
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Springer Science and Business Media LLC, 2008 |
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BMC Genomics |
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| title |
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| title_unstemmed |
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| title_full |
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| title_fullStr |
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| title_full_unstemmed |
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| title_short |
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| title_sort |
genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| topic |
Genetics Biotechnology |
| url |
http://dx.doi.org/10.1186/1471-2164-9-349 |
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2008 |
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| description |
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Independent lines of evidence suggested that a large fraction of human genes possess multiple promoters driving gene expression from distinct transcription start sites. Understanding which promoter is employed in which cellular context is required to unravel gene regulatory networks within the cell.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>We have developed a custom microarray platform that tiles roughly 35,000 alternative putative promoters from nearly 7,000 genes in the human genome. To demonstrate the utility of this array platform, we have analyzed the patterns of promoter usage in 17β-estradiol (E2)-treated and untreated MCF7 cells and show widespread usage of alternative promoters. Most intriguingly, we show that the downstream promoter in E2-sensitive multiple promoter genes tends to be very close to the 3'-terminus of the gene, suggesting exotic mechanisms of expression regulation in these genes.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>The usage of alternative promoters greatly multiplies the transcriptional complexity available within the human genome. The fact that many of these promoters are incapable of driving the synthesis of a meaningful protein-encoding transcript further complicates the story.</jats:p></jats:sec> |
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| author | Singer, Gregory AC, Wu, Jiejun, Yan, Pearlly, Plass, Christoph, Huang, Tim HM, Davuluri, Ramana V |
| author_facet | Singer, Gregory AC, Wu, Jiejun, Yan, Pearlly, Plass, Christoph, Huang, Tim HM, Davuluri, Ramana V, Singer, Gregory AC, Wu, Jiejun, Yan, Pearlly, Plass, Christoph, Huang, Tim HM, Davuluri, Ramana V |
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| description | <jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Independent lines of evidence suggested that a large fraction of human genes possess multiple promoters driving gene expression from distinct transcription start sites. Understanding which promoter is employed in which cellular context is required to unravel gene regulatory networks within the cell.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>We have developed a custom microarray platform that tiles roughly 35,000 alternative putative promoters from nearly 7,000 genes in the human genome. To demonstrate the utility of this array platform, we have analyzed the patterns of promoter usage in 17β-estradiol (E2)-treated and untreated MCF7 cells and show widespread usage of alternative promoters. Most intriguingly, we show that the downstream promoter in E2-sensitive multiple promoter genes tends to be very close to the 3'-terminus of the gene, suggesting exotic mechanisms of expression regulation in these genes.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>The usage of alternative promoters greatly multiplies the transcriptional complexity available within the human genome. The fact that many of these promoters are incapable of driving the synthesis of a meaningful protein-encoding transcript further complicates the story.</jats:p></jats:sec> |
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| institution | DE-D275, DE-Bn3, DE-Brt1, DE-Zwi2, DE-D161, DE-Gla1, DE-Zi4, DE-15, DE-Pl11, DE-Rs1, DE-105, DE-14, DE-Ch1, DE-L229 |
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| spelling | Singer, Gregory AC Wu, Jiejun Yan, Pearlly Plass, Christoph Huang, Tim HM Davuluri, Ramana V 1471-2164 Springer Science and Business Media LLC Genetics Biotechnology http://dx.doi.org/10.1186/1471-2164-9-349 <jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Independent lines of evidence suggested that a large fraction of human genes possess multiple promoters driving gene expression from distinct transcription start sites. Understanding which promoter is employed in which cellular context is required to unravel gene regulatory networks within the cell.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>We have developed a custom microarray platform that tiles roughly 35,000 alternative putative promoters from nearly 7,000 genes in the human genome. To demonstrate the utility of this array platform, we have analyzed the patterns of promoter usage in 17β-estradiol (E2)-treated and untreated MCF7 cells and show widespread usage of alternative promoters. Most intriguingly, we show that the downstream promoter in E2-sensitive multiple promoter genes tends to be very close to the 3'-terminus of the gene, suggesting exotic mechanisms of expression regulation in these genes.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>The usage of alternative promoters greatly multiplies the transcriptional complexity available within the human genome. The fact that many of these promoters are incapable of driving the synthesis of a meaningful protein-encoding transcript further complicates the story.</jats:p></jats:sec> Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array BMC Genomics |
| spellingShingle | Singer, Gregory AC, Wu, Jiejun, Yan, Pearlly, Plass, Christoph, Huang, Tim HM, Davuluri, Ramana V, BMC Genomics, Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array, Genetics, Biotechnology |
| title | Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| title_full | Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| title_fullStr | Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| title_full_unstemmed | Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| title_short | Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| title_sort | genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| title_unstemmed | Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
| topic | Genetics, Biotechnology |
| url | http://dx.doi.org/10.1186/1471-2164-9-349 |