The DNA damage response: nucleic acid regulation in sequence

Abstract

Novel technologies and their applications fuel new insights and discoveries in any field of molecular life sciences, medicine, molecular epidemiology and biotechnology. One of those revolutions represents technologies that monitor a (nearly) complete class of biomolecules in a process of interest. These data-dense technologies have been designated omics technologies, in which the suffix -omics refers to the respective technologies monitoring (I) DNA in the context of complete genomes (genomics), (II) genome-wide RNA transcript expression levels representing the transcriptome (transcriptomics), (III) global protein and/or posttranslational modifications (PTMs), designated the proteome (proteomics), or (IV) nearly all cellular metabolites, named the metabolome (metabolomics). The principle of both proteomics and metabolomics relies on mass differences measured with great accuracy by mass spectrometry due to protein/metabolite levels or the presence of PTMs. Sophisticated and stringent isolation methods of PTMs and stable isotope labelling of amino acids allowing quantitative analysis of protein samples have further propelled proteomics technology. The genome and transcriptome have been extensively investigated by microarray technology over the past decade. Microarrays are based on comparative hybridization of fluorescently labeled DNA or cDNA (in case of RNA expression) under stringent conditions to capture probes (complementary oligonucleotides) printed on a solid surface. This allows the analysis of (tens of) thousands of molecules simultaneously, revolutionizing the scale and depth in which DNA and RNA could be investigated. The recent emergence of next generation sequencing (NGS) has further changed the landscape of genome and transcriptome analysis. NGS, also named massive parallel sequencing, can sequence hundreds of millions DNA molecules simultaneously. A single NGS run can sequence the human genome ∼37 times in 27h, thereby tremendously facilitating whole genome (re)sequencing projects and genome analyses such as single nucleotide polymorphisms (SNP), mutation, insertion/deletion and DNA methylation detection. In addition, NGS can map protein–DNA and DNA–DNA interactions at nucleotide resolution. Transcriptomics of large and small RNAs can be performed by simultaneously sequencing millions of cDNA molecules. Since NGS does not rely on capture probe design and their presence on arrays, novel non-coding RNAs, splice variants, post-transcriptional modifications and nascent RNA synthesis can be quantitatively analysed. In this review, we will discuss the contribution of omics technologies to understanding the DNA damage response (DDR), with the emphasis on genomics and transcriptomics in particular by NGS technologies, and the future prospective of omics research in the DDR research field.