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Identification of cell cycle–regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors

We identify the cell cycle–regulated mRNA transcripts genome-wide in the osteosarcoma-derived U2OS cell line. This results in 2140 transcripts mapping to 1871 unique cell cycle–regulated genes that show periodic oscillations across multiple synchronous cell cycles. We identify genomic loci bound by...

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Autores principales: Grant, Gavin D., Brooks, Lionel, Zhang, Xiaoyang, Mahoney, J. Matthew, Martyanov, Viktor, Wood, Tammara A., Sherlock, Gavin, Cheng, Chao, Whitfield, Michael L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The American Society for Cell Biology 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842991/
https://www.ncbi.nlm.nih.gov/pubmed/24109597
http://dx.doi.org/10.1091/mbc.E13-05-0264
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author Grant, Gavin D.
Brooks, Lionel
Zhang, Xiaoyang
Mahoney, J. Matthew
Martyanov, Viktor
Wood, Tammara A.
Sherlock, Gavin
Cheng, Chao
Whitfield, Michael L.
author_facet Grant, Gavin D.
Brooks, Lionel
Zhang, Xiaoyang
Mahoney, J. Matthew
Martyanov, Viktor
Wood, Tammara A.
Sherlock, Gavin
Cheng, Chao
Whitfield, Michael L.
author_sort Grant, Gavin D.
collection PubMed
description We identify the cell cycle–regulated mRNA transcripts genome-wide in the osteosarcoma-derived U2OS cell line. This results in 2140 transcripts mapping to 1871 unique cell cycle–regulated genes that show periodic oscillations across multiple synchronous cell cycles. We identify genomic loci bound by the G2/M transcription factor FOXM1 by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and associate these with cell cycle–regulated genes. FOXM1 is bound to cell cycle–regulated genes with peak expression in both S phase and G2/M phases. We show that ChIP-seq genomic loci are responsive to FOXM1 using a real-time luciferase assay in live cells, showing that FOXM1 strongly activates promoters of G2/M phase genes and weakly activates those induced in S phase. Analysis of ChIP-seq data from a panel of cell cycle transcription factors (E2F1, E2F4, E2F6, and GABPA) from the Encyclopedia of DNA Elements and ChIP-seq data for the DREAM complex finds that a set of core cell cycle genes regulated in both U2OS and HeLa cells are bound by multiple cell cycle transcription factors. These data identify the cell cycle–regulated genes in a second cancer-derived cell line and provide a comprehensive picture of the transcriptional regulatory systems controlling periodic gene expression in the human cell division cycle.
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spelling pubmed-38429912014-02-16 Identification of cell cycle–regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors Grant, Gavin D. Brooks, Lionel Zhang, Xiaoyang Mahoney, J. Matthew Martyanov, Viktor Wood, Tammara A. Sherlock, Gavin Cheng, Chao Whitfield, Michael L. Mol Biol Cell Articles We identify the cell cycle–regulated mRNA transcripts genome-wide in the osteosarcoma-derived U2OS cell line. This results in 2140 transcripts mapping to 1871 unique cell cycle–regulated genes that show periodic oscillations across multiple synchronous cell cycles. We identify genomic loci bound by the G2/M transcription factor FOXM1 by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and associate these with cell cycle–regulated genes. FOXM1 is bound to cell cycle–regulated genes with peak expression in both S phase and G2/M phases. We show that ChIP-seq genomic loci are responsive to FOXM1 using a real-time luciferase assay in live cells, showing that FOXM1 strongly activates promoters of G2/M phase genes and weakly activates those induced in S phase. Analysis of ChIP-seq data from a panel of cell cycle transcription factors (E2F1, E2F4, E2F6, and GABPA) from the Encyclopedia of DNA Elements and ChIP-seq data for the DREAM complex finds that a set of core cell cycle genes regulated in both U2OS and HeLa cells are bound by multiple cell cycle transcription factors. These data identify the cell cycle–regulated genes in a second cancer-derived cell line and provide a comprehensive picture of the transcriptional regulatory systems controlling periodic gene expression in the human cell division cycle. The American Society for Cell Biology 2013-12-01 /pmc/articles/PMC3842991/ /pubmed/24109597 http://dx.doi.org/10.1091/mbc.E13-05-0264 Text en © 2013 Grant et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0). “ASCB®,” “The American Society for Cell Biology®,” and “Molecular Biology of the Cell®” are registered trademarks of The American Society of Cell Biology.
spellingShingle Articles
Grant, Gavin D.
Brooks, Lionel
Zhang, Xiaoyang
Mahoney, J. Matthew
Martyanov, Viktor
Wood, Tammara A.
Sherlock, Gavin
Cheng, Chao
Whitfield, Michael L.
Identification of cell cycle–regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors
title Identification of cell cycle–regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors
title_full Identification of cell cycle–regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors
title_fullStr Identification of cell cycle–regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors
title_full_unstemmed Identification of cell cycle–regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors
title_short Identification of cell cycle–regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors
title_sort identification of cell cycle–regulated genes periodically expressed in u2os cells and their regulation by foxm1 and e2f transcription factors
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842991/
https://www.ncbi.nlm.nih.gov/pubmed/24109597
http://dx.doi.org/10.1091/mbc.E13-05-0264
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