Genomic Analysis of Glucocorticoid-regulated Promoters in Murine T-lymphoma Cells

Lu Chen, Celeste Finnerty, William C. Gustafson, Craig R. Bush, Ping Chi, Huiping Guo, Bruce Luxon, Alan P Fields, E Aubrey Thompson

Research output: Contribution to journalArticle

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Abstract

We have undertaken a high-throughput analysis to identify targets of glucocorticoid regulation in P1798 murine T-lymphoma cells. G1/S-arrested cultures were treated for 8 hours with 0.1 μM dexamethasone (dex) in the presence and absence of 1 μg/ml cycloheximide. Untreated cultures and cultures exposed to cycloheximide alone were prepared as controls. RNA was isolated and gene expression analyzed using Affymetrix MG-U74A oligonucleotide arrays (Gene Chips®). Three independent experiments were performed. The data were analyzed using a variety of statistical and analytical approaches in order to identify primary transcriptional targets of the glucocorticoid receptor. We identified 44 genes that increase by > 2-fold in both dex-treated and dex + cycloheximide-treated cultures (relative to control and cycloheximide-treated cultures) in three replicate experiments. Statistical analysis of control data indicate that the probability that a given probeset would, as a result of random error, increase > 2-fold both in the presence and absence of cycloheximide in two independent experiments is approximately 7 × 10-9. We have retrieved from the Celera mouse genomic sequence 8 kb of promoter sequence, spanning 4 kb either side of the 5′-end of the cDNA from eight of the induced genes. These sequences were analyzed for potential glucocorticoid receptor binding sites. Five of these genes contain the sequence ACAnnnTGTnCT within 4 kb of the presumptive transcriptional start site. Eight control genes were selected at random and analyzed for the sequence ACAnnnTGTnCT. Two control genes had such sequences within 4 kb of the transcriptional start site.

Original languageEnglish (US)
Pages (from-to)155-174
Number of pages20
JournalRecent Progress in Hormone Research
Volume58
DOIs
StatePublished - 2003
Externally publishedYes

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T-Cell Lymphoma
Cycloheximide
Glucocorticoids
Dexamethasone
Genes
Glucocorticoid Receptors
Oligonucleotide Array Sequence Analysis
Statistical Data Interpretation
Complementary DNA
Binding Sites
RNA
Gene Expression

ASJC Scopus subject areas

  • Endocrinology

Cite this

Genomic Analysis of Glucocorticoid-regulated Promoters in Murine T-lymphoma Cells. / Chen, Lu; Finnerty, Celeste; Gustafson, William C.; Bush, Craig R.; Chi, Ping; Guo, Huiping; Luxon, Bruce; Fields, Alan P; Thompson, E Aubrey.

In: Recent Progress in Hormone Research, Vol. 58, 2003, p. 155-174.

Research output: Contribution to journalArticle

Chen, Lu ; Finnerty, Celeste ; Gustafson, William C. ; Bush, Craig R. ; Chi, Ping ; Guo, Huiping ; Luxon, Bruce ; Fields, Alan P ; Thompson, E Aubrey. / Genomic Analysis of Glucocorticoid-regulated Promoters in Murine T-lymphoma Cells. In: Recent Progress in Hormone Research. 2003 ; Vol. 58. pp. 155-174.
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