Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array

<p>Abstract</p> <p>Background</p> <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 conte...

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Main Authors: Plass Christoph, Yan Pearlly, Wu Jiejun, Singer Gregory AC, Huang Tim HM, Davuluri Ramana V
Format: Article
Language:English
Published: BMC 2008-07-01
Series:BMC Genomics
Online Access:http://www.biomedcentral.com/1471-2164/9/349
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spelling doaj-6fce67f38acb40e69ca8dbd005f15cf62020-11-24T21:12:36ZengBMCBMC Genomics1471-21642008-07-019134910.1186/1471-2164-9-349Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling arrayPlass ChristophYan PearllyWu JiejunSinger Gregory ACHuang Tim HMDavuluri Ramana V<p>Abstract</p> <p>Background</p> <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.</p> <p>Results</p> <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.</p> <p>Conclusion</p> <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.</p> http://www.biomedcentral.com/1471-2164/9/349
collection DOAJ
language English
format Article
sources DOAJ
author Plass Christoph
Yan Pearlly
Wu Jiejun
Singer Gregory AC
Huang Tim HM
Davuluri Ramana V
spellingShingle Plass Christoph
Yan Pearlly
Wu Jiejun
Singer Gregory AC
Huang Tim HM
Davuluri Ramana V
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array
BMC Genomics
author_facet Plass Christoph
Yan Pearlly
Wu Jiejun
Singer Gregory AC
Huang Tim HM
Davuluri Ramana V
author_sort Plass Christoph
title 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_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_sort genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array
publisher BMC
series BMC Genomics
issn 1471-2164
publishDate 2008-07-01
description <p>Abstract</p> <p>Background</p> <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.</p> <p>Results</p> <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.</p> <p>Conclusion</p> <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.</p>
url http://www.biomedcentral.com/1471-2164/9/349
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