Alternative Transcript Initiation and Splicing as a Response to DNA Damage

Carl N Sprung,Jason Li,Daniel Hovan,Michael J Mckay,Helen B Forrester,Eric J Bernhard

doi:10.1371/journal.pone.0025758

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.

Highlights

The transcriptional response to cellular stress is critical for cell survival
RNA processed from human lymphoblast and fibroblast cell lines exposed or sham-exposed to radiation was run on exon arrays to examine the transcriptional profile in response to radiation at the exon level
The exon arrays enabled the identification of genes, not previously reported to be statistically significantly modulated after Ionizing radiation (IR) in human lymphoblastoid cell lines (LCLs) (Table S4; e. g., from Table 1: EDA2R, FAM72A and C1orf183) or in fibroblasts (Table S5; e. g., from Table 2: ASAH3L (ACER1), EDA2R, PAG1, BCOR, CBL, FAM100B, FAM72A, SETD8 and TIGD1), some of these genes are IR-responsive in other experimental settings

Summary

Introduction

The transcriptional response to cellular stress is critical for cell survival. Ionizing radiation (IR) causes a broad spectrum of DNA damage for which the cells’ commitment to repair, programmed death, cell division arrest or senescence, is required for an organism’s survival. The rate of these normal tissue reactions, for which there is nearly a normal distribution across the population, is determined by a therapeutic ratio (tumour control/adverse normal tissue reactions) The outcome of this radiation response diversity is that the dosage all patients receive is limited by those few patients who are radiosensitive in their normal tissue, and thereby preclude optimal treatment for the majority of radiotherapy patients. Identification of those patients who are radiosensitive given current dose regimes, is paramount to enable individualization of RT. Identifying the IR transcriptional response profile benefits establishment of biological dosage predictors, understanding response to other radiological exposures and can contribute to the development of new radio-pharmaceuticals

Methods

Results

Conclusion