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Alternative transcript initiation and splicing as a response to DNA damage.

Sprung CN, Li J, Hovan D, McKay MJ, Forrester HB - PLoS ONE (2011)

Bottom Line: Dose-response and time course kinetics have also been characterized.Interestingly, most genes showing alternative transcript induction maintained these isoforms over the dose range and times tested.This study provides novel insights into alternative transcripts as a mechanism for response to DNA damage and cell stress responses in general.

View Article: PubMed Central - PubMed

Affiliation: Centre for Innate Immunity and Infectious Disease, Monash Institute for Medical Research, Monash University, Clayton, Victoria, Australia. carl.sprung@monash.edu

ABSTRACT
Humans are exposed to the DNA damaging agent, ionizing radiation (IR), from background radiation, medical treatments, occupational and accidental exposures. IR causes changes in transcription, but little is known about alternative transcription in response to IR on a genome-wide basis. These investigations examine the response to IR at the exon level in human cells, using exon arrays to comprehensively characterize radiation-induced transcriptional expression products. Previously uncharacterized alternative transcripts that preferentially occur following IR exposure have been discovered. A large number of genes showed alternative transcription initiation as a response to IR. Dose-response and time course kinetics have also been characterized. Interestingly, most genes showing alternative transcript induction maintained these isoforms over the dose range and times tested. Finally, clusters of co-ordinately up- and down-regulated radiation response genes were identified at specific chromosomal loci. These data provide the first genome-wide view of the transcriptional response to ionizing radiation at the exon level. This study provides novel insights into alternative transcripts as a mechanism for response to DNA damage and cell stress responses in general.

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Time course and dose response of gene transcripts induced in LCLs by IR as determined from exon level microarrays.Transcripts for CDKN1A and VWCE were isolated 4 hrs after exposure to 1, 2, 5, 10 or 20 Gy (A, B) of ionizing radiation or exposed to 10 Gy IR and transcripts isolated 1, 2, 4, 8, 24 or 48 hours post-IR (C, D). Relative expression (y-axis) is plotted for each PSR (points along x-axis). PSRs are oriented 5′ to 3′ across the gene from left to right. Relative expression levels are plotted on a log2 scale. 12 cancer patient samples were used for each point (n = 12). Error bars = SEM.
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pone-0025758-g007: Time course and dose response of gene transcripts induced in LCLs by IR as determined from exon level microarrays.Transcripts for CDKN1A and VWCE were isolated 4 hrs after exposure to 1, 2, 5, 10 or 20 Gy (A, B) of ionizing radiation or exposed to 10 Gy IR and transcripts isolated 1, 2, 4, 8, 24 or 48 hours post-IR (C, D). Relative expression (y-axis) is plotted for each PSR (points along x-axis). PSRs are oriented 5′ to 3′ across the gene from left to right. Relative expression levels are plotted on a log2 scale. 12 cancer patient samples were used for each point (n = 12). Error bars = SEM.

Mentions: Investigation of dose response was completed using a range from 1 Gy to 20 Gy of IR. RNA was collected at 4 hours post-IR, processed and run on exon arrays for four cell lines for each cell type. Examples of genes that showed modulation with dose are plotted (Figure 7A and 7C). In general, the responses increased with dose, however, it was common for a gene to show substantial modulation at the low dose (1 Gy) with less relative modulation at increasing doses. For example, in LCLs, CDKN1A showed a strong induction at 4 hours after 1 Gy and then gradually increased with increase in radiation dose (Figure 7A). Also, the alternatively spliced form was clearly present at all doses. For example, compare CDKN1A-PSR177 to the other PSR expression level changes (Figure 7A). The VWCE transcript showed induction in response to radiation at every dose, but the induction was more gradual compared to CDKN1A (Figure 7C). VWCE-PSR229, a region that did not change much in response to IR, was modulated similarly at all doses. Whole gene expression with varying dose was also determined. Selected genes are plotted that show a variety of kinetics for gene dose responses (Figure 8A and 8B; Tables S12 and S13).


Alternative transcript initiation and splicing as a response to DNA damage.

Sprung CN, Li J, Hovan D, McKay MJ, Forrester HB - PLoS ONE (2011)

Time course and dose response of gene transcripts induced in LCLs by IR as determined from exon level microarrays.Transcripts for CDKN1A and VWCE were isolated 4 hrs after exposure to 1, 2, 5, 10 or 20 Gy (A, B) of ionizing radiation or exposed to 10 Gy IR and transcripts isolated 1, 2, 4, 8, 24 or 48 hours post-IR (C, D). Relative expression (y-axis) is plotted for each PSR (points along x-axis). PSRs are oriented 5′ to 3′ across the gene from left to right. Relative expression levels are plotted on a log2 scale. 12 cancer patient samples were used for each point (n = 12). Error bars = SEM.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3198437&req=5

pone-0025758-g007: Time course and dose response of gene transcripts induced in LCLs by IR as determined from exon level microarrays.Transcripts for CDKN1A and VWCE were isolated 4 hrs after exposure to 1, 2, 5, 10 or 20 Gy (A, B) of ionizing radiation or exposed to 10 Gy IR and transcripts isolated 1, 2, 4, 8, 24 or 48 hours post-IR (C, D). Relative expression (y-axis) is plotted for each PSR (points along x-axis). PSRs are oriented 5′ to 3′ across the gene from left to right. Relative expression levels are plotted on a log2 scale. 12 cancer patient samples were used for each point (n = 12). Error bars = SEM.
Mentions: Investigation of dose response was completed using a range from 1 Gy to 20 Gy of IR. RNA was collected at 4 hours post-IR, processed and run on exon arrays for four cell lines for each cell type. Examples of genes that showed modulation with dose are plotted (Figure 7A and 7C). In general, the responses increased with dose, however, it was common for a gene to show substantial modulation at the low dose (1 Gy) with less relative modulation at increasing doses. For example, in LCLs, CDKN1A showed a strong induction at 4 hours after 1 Gy and then gradually increased with increase in radiation dose (Figure 7A). Also, the alternatively spliced form was clearly present at all doses. For example, compare CDKN1A-PSR177 to the other PSR expression level changes (Figure 7A). The VWCE transcript showed induction in response to radiation at every dose, but the induction was more gradual compared to CDKN1A (Figure 7C). VWCE-PSR229, a region that did not change much in response to IR, was modulated similarly at all doses. Whole gene expression with varying dose was also determined. Selected genes are plotted that show a variety of kinetics for gene dose responses (Figure 8A and 8B; Tables S12 and S13).

Bottom Line: Dose-response and time course kinetics have also been characterized.Interestingly, most genes showing alternative transcript induction maintained these isoforms over the dose range and times tested.This study provides novel insights into alternative transcripts as a mechanism for response to DNA damage and cell stress responses in general.

View Article: PubMed Central - PubMed

Affiliation: Centre for Innate Immunity and Infectious Disease, Monash Institute for Medical Research, Monash University, Clayton, Victoria, Australia. carl.sprung@monash.edu

ABSTRACT
Humans are exposed to the DNA damaging agent, ionizing radiation (IR), from background radiation, medical treatments, occupational and accidental exposures. IR causes changes in transcription, but little is known about alternative transcription in response to IR on a genome-wide basis. These investigations examine the response to IR at the exon level in human cells, using exon arrays to comprehensively characterize radiation-induced transcriptional expression products. Previously uncharacterized alternative transcripts that preferentially occur following IR exposure have been discovered. A large number of genes showed alternative transcription initiation as a response to IR. Dose-response and time course kinetics have also been characterized. Interestingly, most genes showing alternative transcript induction maintained these isoforms over the dose range and times tested. Finally, clusters of co-ordinately up- and down-regulated radiation response genes were identified at specific chromosomal loci. These data provide the first genome-wide view of the transcriptional response to ionizing radiation at the exon level. This study provides novel insights into alternative transcripts as a mechanism for response to DNA damage and cell stress responses in general.

Show MeSH
Related in: MedlinePlus