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Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array
BACKGROUND: 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 with...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527337/ https://www.ncbi.nlm.nih.gov/pubmed/18655706 http://dx.doi.org/10.1186/1471-2164-9-349 |
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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 |
author_sort | Singer, Gregory AC |
collection | PubMed |
description | BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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. |
format | Text |
id | pubmed-2527337 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-25273372008-08-30 Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array Singer, Gregory AC Wu, Jiejun Yan, Pearlly Plass, Christoph Huang, Tim HM Davuluri, Ramana V BMC Genomics Research Article BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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. BioMed Central 2008-07-25 /pmc/articles/PMC2527337/ /pubmed/18655706 http://dx.doi.org/10.1186/1471-2164-9-349 Text en Copyright © 2008 Singer et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Singer, Gregory AC Wu, Jiejun Yan, Pearlly Plass, Christoph Huang, Tim HM Davuluri, Ramana V Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array |
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 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527337/ https://www.ncbi.nlm.nih.gov/pubmed/18655706 http://dx.doi.org/10.1186/1471-2164-9-349 |
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