Open Access Research article

DNA damage activates a complex transcriptional response in murine lymphocytes that includes both physiological and cancer-predisposition programs

Cynthia L Innes1, Jill E Hesse1, Stela S Palii1, Beth A Helmink2, Abigail J Holub2, Barry P Sleckman2 and Richard S Paules1*

Author Affiliations

1 Environmental Stress and Cancer Group, National Institute of Environmental Health Sciences, Research Triangle Park, , NC, 27709, USA

2 Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA

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BMC Genomics 2013, 14:163  doi:10.1186/1471-2164-14-163

Published: 12 March 2013

Additional files

Additional file 1:

Differentially regulated probes in response to DNA damage. This is a combined table of all probes that were significantly differentially regulated in response to 1 Gy IR (p ≤ 0.05, FC ≥ ±1.5) in WT pre-B cells lines and in response to RAG induced DSBs (p ≤ 0.05, FC ≥ ±1.5). Three independent WT lines were used to determine the response to genotoxic IR-induced DNA damage. These cells were exposed to STI-571 for 48 hours, treated with 0 or 1 Gy IR and mRNA expression was measured at 2 hours post IR. The intensity values were averaged from the 3 treated or untreated samples and used to determine fold change of 1 Gy/0 Gy. Significantly differentially regulated IR-induced probe fold change values are shown in column D. To determine differentially regulated probes in response to RAG-induced breaks, three independent Rag2-/- (no DSBs) lines and three independent Artemis-/- (unrepaired RAG-induced DSBs) lines were exposed to STI-571 for 48 hours and mRNA expression was measured. The intensity values were averaged for each genotype. Values are fold change of Artemis-/-/Rag2-/- and significantly differentially regulated fold change values are shown in column E. Differentially regulated probes common to IR- and RAG-induced break responses are indicated in column F with a # for a commonly expressed specific probe ID and ## for a commonly expressed gene. For the latter, multiple probes representing the same gene were differentially regulated in the same direction (up or down-regulated) following both IR- and RAG-induced breaks. Differentially regulated probes unique to IR-induced DNA damage response are indicated in column G with an *. This column includes all probes that were differentially regulated in the WT response to IR (p ≤ 0.05, FC ≥ ±1.5) but not in the physiological response to RAG-induced breaks. Annotation of all genes listed is based on build 32 from Affymetrix.

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Additional file 2:

qRT-PCR expression data for miR-155. Original CT values representing miR-155 and U6 expression levels from 3 WT Pre-B cell lines at 2 (A), 4 (B) and 8 (C) hr following IR are plotted. Data are from 5 technical replicates for each cell line, primer and time point.

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Additional file 3:

qRT-PCR expression data for Socs1. Original CT values representing Socs1 and 18S expression levels from 3 WT Pre-B cell lines at 2 (A), 4 (B) and 8 (C) hr following IR are plotted. Data are from 3 to 5 technical replicates for each cell line, primer and time point.

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Additional file 4:

qRT-PCR expression data for Txnrd1. Original CT values representing Txnrd1 and 18S expression levels from 3 WT Pre-B cell lines at 2 (A), 4 (B) and 8 (C) hr following IR are plotted. Data are from 3 to 5 technical replicates for each cell line, primer and time point.

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Additional file 5:

Protein expression of Nrf2 in WT Pre-B cell lines. Each Nrf2 and β-actin pair of panels comes from the same polyacrylamide gel and represents one of the 3 WT cell lines. The first 3 lanes are untreated cells and the last 3 lanes of each are the corresponding irradiated cells for each time point following IR, 2, 4 and 8 hr. The values in Figure 5 incorporate normalization to β-actin for each lane.

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