Mechanisms of Genotoxic Stress-regulated Gene Expression in Human Cells

Summary

Principal Investigator: Mats Ljungman
Abstract: DESCRIPTION (provided by applicant): Exposure of cells to ionizing radiation (IR) activates DNA damage responses leading to a comprehensive reprogramming of gene expression by regulation of both transcriptional and post- transcriptional events. The mechanisms regulating transcriptional and post-transcriptional events are not fully elucidated and a better knowledge about these mechanisms could help improve radiation therapy in the clinic. We will in this revised R21 grant proposal use the newly developed BrU-Seq technique to study these mechanisms in detail. In Specific Aim #1, the global effects of IR on the synthesis and stability of all RNAs in human fibroblasts will be explored. Preliminary experiments show that the stress kinase ATM is required for increased synthesis and stability of certain mRNAs such as BTG2 in human fibroblasts and the hypothesis to be tested is that there may be many more genes affected at the level of synthesis and/or stability in an ATM-dependent way following exposure to IR. In Specific Aim #2, the effects of IR on alternative splicing will be interrogated. Preliminry results show that intron retention is common among processed mRNAs in human fibroblasts and our hypothesis is that since a large number of splicing factors are substrates for activated ATM, IR may affect the splicing code signature in human cells in an ATM-dependent manner. In Specific Aim #3 the effects of IR on the activation of transcription start sites (TSS) and enhancer elements in the genome will be studied using a technique involving UV-irradiation prior to the BrU pulse-labeling to introduce random transcription-blocking lesions in the genome. Preliminary results show that with this technique, all transcription start sites and potentially enhancer elements can be mapped in the genome. The hypothesis to be tested is that IR may affect the selection of TSS and enhancer elements and that ATM may be involved in regulating these alterations. The major innovation of this R21 proposal is the use of the novel BrU-Seq technique for global exploration of how IR affects the "transcriptome", the "RNA stabilome", the splicing code and selection of TSS and enhancer elements. The analysis will not only include mRNAs but also non-coding RNAs such as microRNAs. These studies may have a great impact on not only our understanding of the mechanisms of altered gene and microRNA regulation following exposure to IR but also, this new technique will have general applications for studying mechanisms of gene expression in other settings.
Funding Period: 2012-05-01 - 2014-04-30
more information: NIH RePORT

Top Publications

  1. pmc Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response
    Michelle T Paulsen
    Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 110:2240-5. 2013
  2. pmc Genome-wide transcriptional effects of the anti-cancer agent camptothecin
    Artur Veloso
    Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, Michigan, United States of America Bioinformatics Program and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS ONE 8:e78190. 2013

Detail Information

Publications2

  1. pmc Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response
    Michelle T Paulsen
    Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 110:2240-5. 2013
    ....
  2. pmc Genome-wide transcriptional effects of the anti-cancer agent camptothecin
    Artur Veloso
    Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, Michigan, United States of America Bioinformatics Program and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS ONE 8:e78190. 2013
    ..These findings of the effects of camptothecin on transcription have important implications for its anti-cancer activities and may aid in the design of improved combinatorial treatments involving Top1 poisons. ..

Research Grants30

  1. Processing of Complex Lesions in the Mammalian Genome
    Randy J Legerski; Fiscal Year: 2013
    ..These approaches have excellent potential to yield useful technical and therapeutic advances in genetic manipulation. ..
  2. Transcriptional Signatures of Homologous Recombination Deficiency for Targeted Ch
    Robert W Sobol; Fiscal Year: 2013
    ..These studies will be a critical first step towards identifying signatures associated with specific DNA repair pathway defects in tumor samples that may be used as biomarkers to predict response to targeted chemotherapeutic agents. ..
  3. Development and Validation of BruChase-Seq and BrUV-Seq
    Mats Ljungman; Fiscal Year: 2013
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