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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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Genes that show modulated transcription expression products, including use of alternative transcripts, after IR in LCLs.Up- (A, C, E–H) and down-regulated (B, D) gene probe selection regions (PSRs) 4 hours following 10 Gy IR in LCLs, which identifies transcript expression at the exon level. Exon expression examples are shown for the following genes: EDAR2 (A), DEPDC1 (B), CDKN1A (C), CENPA (D), ASTN2 (E), C1orf183 (F), VWCE (G) and PLK2 (H). Relative PSR flourescence (y-axis) is plotted for each PSR (points along x-axis). Samples were either sham irradiated (red) or irradiated with 10 Gy (blue). PSRs are oriented 5′ to 3′ across the gene from left to right on the x-axis. Relative expression levels are plotted on a log2 scale. Arrow represents a PSR or PSR region that was used for subsequent PCR validation. At least 6 cancer patient samples were used for each point (n≥6). Error bars = SEM.
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pone-0025758-g001: Genes that show modulated transcription expression products, including use of alternative transcripts, after IR in LCLs.Up- (A, C, E–H) and down-regulated (B, D) gene probe selection regions (PSRs) 4 hours following 10 Gy IR in LCLs, which identifies transcript expression at the exon level. Exon expression examples are shown for the following genes: EDAR2 (A), DEPDC1 (B), CDKN1A (C), CENPA (D), ASTN2 (E), C1orf183 (F), VWCE (G) and PLK2 (H). Relative PSR flourescence (y-axis) is plotted for each PSR (points along x-axis). Samples were either sham irradiated (red) or irradiated with 10 Gy (blue). PSRs are oriented 5′ to 3′ across the gene from left to right on the x-axis. Relative expression levels are plotted on a log2 scale. Arrow represents a PSR or PSR region that was used for subsequent PCR validation. At least 6 cancer patient samples were used for each point (n≥6). Error bars = SEM.

Mentions: The relative expression of each core PSR for a selection of individual genes with a variety of profiles in LCLs (Figure 1) and fibroblasts (Figure 2) 4 h after 10 Gy IR are shown. In LCLs, EDA2R showed a relatively consistent increase at each exon region across the entire gene (Figure 1A), and DEPDC1 shows a dramatic decrease in transcription across most exon regions (Figure 1B). CDKN1A shows an obvious differential increase between exon regions: PSR two is induced less than the rest of the gene and is consistent with a known AS product in CDKN1A (Figure 1C). The expression levels of the PSRs in CENPA are decreased in response to IR except for the first two PSRs, which show the same expression before and after irradiation (Figure 1D). We observed that the 5′ region of the ASTN2 gene showed much less induction than the 3′ regions after IR which is consistent with the two main known isoforms for this gene (Figure 1E). C1orf183 (Figure 1F), VWCE (Figure 1G) and PLK2 (Figure 1H) also have internal PSRs with a differential increase in expression indicating that different isoforms are expressed after IR. These three genes also show the first PSR is not as up-regulated compared to most other PSRs of the transcript (Figure 1F–G).


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

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

Genes that show modulated transcription expression products, including use of alternative transcripts, after IR in LCLs.Up- (A, C, E–H) and down-regulated (B, D) gene probe selection regions (PSRs) 4 hours following 10 Gy IR in LCLs, which identifies transcript expression at the exon level. Exon expression examples are shown for the following genes: EDAR2 (A), DEPDC1 (B), CDKN1A (C), CENPA (D), ASTN2 (E), C1orf183 (F), VWCE (G) and PLK2 (H). Relative PSR flourescence (y-axis) is plotted for each PSR (points along x-axis). Samples were either sham irradiated (red) or irradiated with 10 Gy (blue). PSRs are oriented 5′ to 3′ across the gene from left to right on the x-axis. Relative expression levels are plotted on a log2 scale. Arrow represents a PSR or PSR region that was used for subsequent PCR validation. At least 6 cancer patient samples were used for each point (n≥6). Error bars = SEM.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3198437&req=5

pone-0025758-g001: Genes that show modulated transcription expression products, including use of alternative transcripts, after IR in LCLs.Up- (A, C, E–H) and down-regulated (B, D) gene probe selection regions (PSRs) 4 hours following 10 Gy IR in LCLs, which identifies transcript expression at the exon level. Exon expression examples are shown for the following genes: EDAR2 (A), DEPDC1 (B), CDKN1A (C), CENPA (D), ASTN2 (E), C1orf183 (F), VWCE (G) and PLK2 (H). Relative PSR flourescence (y-axis) is plotted for each PSR (points along x-axis). Samples were either sham irradiated (red) or irradiated with 10 Gy (blue). PSRs are oriented 5′ to 3′ across the gene from left to right on the x-axis. Relative expression levels are plotted on a log2 scale. Arrow represents a PSR or PSR region that was used for subsequent PCR validation. At least 6 cancer patient samples were used for each point (n≥6). Error bars = SEM.
Mentions: The relative expression of each core PSR for a selection of individual genes with a variety of profiles in LCLs (Figure 1) and fibroblasts (Figure 2) 4 h after 10 Gy IR are shown. In LCLs, EDA2R showed a relatively consistent increase at each exon region across the entire gene (Figure 1A), and DEPDC1 shows a dramatic decrease in transcription across most exon regions (Figure 1B). CDKN1A shows an obvious differential increase between exon regions: PSR two is induced less than the rest of the gene and is consistent with a known AS product in CDKN1A (Figure 1C). The expression levels of the PSRs in CENPA are decreased in response to IR except for the first two PSRs, which show the same expression before and after irradiation (Figure 1D). We observed that the 5′ region of the ASTN2 gene showed much less induction than the 3′ regions after IR which is consistent with the two main known isoforms for this gene (Figure 1E). C1orf183 (Figure 1F), VWCE (Figure 1G) and PLK2 (Figure 1H) also have internal PSRs with a differential increase in expression indicating that different isoforms are expressed after IR. These three genes also show the first PSR is not as up-regulated compared to most other PSRs of the transcript (Figure 1F–G).

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