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

Grant GD, Brooks L, Zhang X, Mahoney JM, Martyanov V, Wood TA, Sherlock G, Cheng C, Whitfield ML - Mol. Biol. Cell (2013)

Bottom Line: This results in 2140 transcripts mapping to 1871 unique cell cycle-regulated genes that show periodic oscillations across multiple synchronous cell cycles.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305.

ABSTRACT
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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Periodically expressed genes in the U2OS cell cycle. (A) The 2830 probes that show periodic expression in U2OS cells, ordered by the point of their peak expression as calculated from their sine and cosine values in the Fourier transform. Phase assignments were performed using the correlation coefficients with the ideal vectors defined in Figure 1. The color bar on the right indicates the phase of peak expression (G1/S, green; S, blue; G2, red; G2/M, yellow; and M/G1, black); blended colors indicate interspersed phase assignments. (B) The 2830 periodically expressed probes from U2OS cells were ordered by average linkage hierarchical clustering. The enriched biological processes of select clusters is indicated.
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Figure 2: Periodically expressed genes in the U2OS cell cycle. (A) The 2830 probes that show periodic expression in U2OS cells, ordered by the point of their peak expression as calculated from their sine and cosine values in the Fourier transform. Phase assignments were performed using the correlation coefficients with the ideal vectors defined in Figure 1. The color bar on the right indicates the phase of peak expression (G1/S, green; S, blue; G2, red; G2/M, yellow; and M/G1, black); blended colors indicate interspersed phase assignments. (B) The 2830 periodically expressed probes from U2OS cells were ordered by average linkage hierarchical clustering. The enriched biological processes of select clusters is indicated.

Mentions: To display the selected genes in the order of their timing of peak expression within the cell division cycle, we organized genes by their phase of peak expression determined by Fourier analysis (Figure 2A). The alternating pattern of high and low gene expression levels shows persistent waves of gene expression across multiple synchronous cell cycles. The phase of peak expression of each gene was assigned based on peak correlation to the idealized phase expression profiles shown in Figure 1. This method assigns the probes to G1/S (1018 probes; 702 unique genes), S phase (546 probes; 355 unique genes), G2 phase (390 probes; 278 unique genes), G2/M (598 probes; 392 unique genes), and M/G1 (278 probes; 144 unique genes; Figure 2A).


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

Grant GD, Brooks L, Zhang X, Mahoney JM, Martyanov V, Wood TA, Sherlock G, Cheng C, Whitfield ML - Mol. Biol. Cell (2013)

Periodically expressed genes in the U2OS cell cycle. (A) The 2830 probes that show periodic expression in U2OS cells, ordered by the point of their peak expression as calculated from their sine and cosine values in the Fourier transform. Phase assignments were performed using the correlation coefficients with the ideal vectors defined in Figure 1. The color bar on the right indicates the phase of peak expression (G1/S, green; S, blue; G2, red; G2/M, yellow; and M/G1, black); blended colors indicate interspersed phase assignments. (B) The 2830 periodically expressed probes from U2OS cells were ordered by average linkage hierarchical clustering. The enriched biological processes of select clusters is indicated.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3842991&req=5

Figure 2: Periodically expressed genes in the U2OS cell cycle. (A) The 2830 probes that show periodic expression in U2OS cells, ordered by the point of their peak expression as calculated from their sine and cosine values in the Fourier transform. Phase assignments were performed using the correlation coefficients with the ideal vectors defined in Figure 1. The color bar on the right indicates the phase of peak expression (G1/S, green; S, blue; G2, red; G2/M, yellow; and M/G1, black); blended colors indicate interspersed phase assignments. (B) The 2830 periodically expressed probes from U2OS cells were ordered by average linkage hierarchical clustering. The enriched biological processes of select clusters is indicated.
Mentions: To display the selected genes in the order of their timing of peak expression within the cell division cycle, we organized genes by their phase of peak expression determined by Fourier analysis (Figure 2A). The alternating pattern of high and low gene expression levels shows persistent waves of gene expression across multiple synchronous cell cycles. The phase of peak expression of each gene was assigned based on peak correlation to the idealized phase expression profiles shown in Figure 1. This method assigns the probes to G1/S (1018 probes; 702 unique genes), S phase (546 probes; 355 unique genes), G2 phase (390 probes; 278 unique genes), G2/M (598 probes; 392 unique genes), and M/G1 (278 probes; 144 unique genes; Figure 2A).

Bottom Line: This results in 2140 transcripts mapping to 1871 unique cell cycle-regulated genes that show periodic oscillations across multiple synchronous cell cycles.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305.

ABSTRACT
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.

Show MeSH