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Transcriptome coexpression map of human embryonic stem cells
BACKGROUND: Human embryonic stem (ES) cells hold great promise for medicine and science. The transcriptome of human ES cells has been studied in detail in recent years. However, no systematic analysis has yet addressed whether gene expression in human ES cells may be regulated in chromosomal domains...
Autores principales: | , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2006
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1523211/ https://www.ncbi.nlm.nih.gov/pubmed/16670017 http://dx.doi.org/10.1186/1471-2164-7-103 |
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author | Li, Huai Liu, Ying Shin, Soojung Sun, Yu Loring, Jeanne F Mattson, Mark P Rao, Mahendra S Zhan1, Ming |
author_facet | Li, Huai Liu, Ying Shin, Soojung Sun, Yu Loring, Jeanne F Mattson, Mark P Rao, Mahendra S Zhan1, Ming |
author_sort | Li, Huai |
collection | PubMed |
description | BACKGROUND: Human embryonic stem (ES) cells hold great promise for medicine and science. The transcriptome of human ES cells has been studied in detail in recent years. However, no systematic analysis has yet addressed whether gene expression in human ES cells may be regulated in chromosomal domains, and no chromosomal domains of coexpression have been identified. RESULTS: We report the first transcriptome coexpression map of the human ES cell and the earliest stage of ES differentiation, the embryoid body (EB), for the analysis of how transcriptional regulation interacts with genomic structure during ES self-renewal and differentiation. We determined the gene expression profiles from multiple ES and EB samples and identified chromosomal domains showing coexpression of adjacent genes on the genome. The coexpression domains were not random, with significant enrichment in chromosomes 8, 11, 16, 17, 19, and Y in the ES state, and 6, 11, 17, 19 and 20 in the EB state. The domains were significantly associated with Giemsa-negative bands in EB, yet showed little correlation with known cytogenetic structures in ES cells. Different patterns of coexpression were revealed by comparative transcriptome mapping between ES and EB. CONCLUSION: The findings and methods reported in this investigation advance our understanding of how genome organization affects gene expression in human ES cells and help to identify new mechanisms and pathways controlling ES self-renewal or differentiation. |
format | Text |
id | pubmed-1523211 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-15232112006-07-28 Transcriptome coexpression map of human embryonic stem cells Li, Huai Liu, Ying Shin, Soojung Sun, Yu Loring, Jeanne F Mattson, Mark P Rao, Mahendra S Zhan1, Ming BMC Genomics Research Article BACKGROUND: Human embryonic stem (ES) cells hold great promise for medicine and science. The transcriptome of human ES cells has been studied in detail in recent years. However, no systematic analysis has yet addressed whether gene expression in human ES cells may be regulated in chromosomal domains, and no chromosomal domains of coexpression have been identified. RESULTS: We report the first transcriptome coexpression map of the human ES cell and the earliest stage of ES differentiation, the embryoid body (EB), for the analysis of how transcriptional regulation interacts with genomic structure during ES self-renewal and differentiation. We determined the gene expression profiles from multiple ES and EB samples and identified chromosomal domains showing coexpression of adjacent genes on the genome. The coexpression domains were not random, with significant enrichment in chromosomes 8, 11, 16, 17, 19, and Y in the ES state, and 6, 11, 17, 19 and 20 in the EB state. The domains were significantly associated with Giemsa-negative bands in EB, yet showed little correlation with known cytogenetic structures in ES cells. Different patterns of coexpression were revealed by comparative transcriptome mapping between ES and EB. CONCLUSION: The findings and methods reported in this investigation advance our understanding of how genome organization affects gene expression in human ES cells and help to identify new mechanisms and pathways controlling ES self-renewal or differentiation. BioMed Central 2006-05-02 /pmc/articles/PMC1523211/ /pubmed/16670017 http://dx.doi.org/10.1186/1471-2164-7-103 Text en Copyright © 2006 Li 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 Li, Huai Liu, Ying Shin, Soojung Sun, Yu Loring, Jeanne F Mattson, Mark P Rao, Mahendra S Zhan1, Ming Transcriptome coexpression map of human embryonic stem cells |
title | Transcriptome coexpression map of human embryonic stem cells |
title_full | Transcriptome coexpression map of human embryonic stem cells |
title_fullStr | Transcriptome coexpression map of human embryonic stem cells |
title_full_unstemmed | Transcriptome coexpression map of human embryonic stem cells |
title_short | Transcriptome coexpression map of human embryonic stem cells |
title_sort | transcriptome coexpression map of human embryonic stem cells |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1523211/ https://www.ncbi.nlm.nih.gov/pubmed/16670017 http://dx.doi.org/10.1186/1471-2164-7-103 |
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