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Driven by improvements in speed and resolution of mass spectrometers (MS), the field of proteomics, which involves the large-scale detection and analysis of proteins in cells, tissues and organisms, continues to expand in scale and complexity. There is a resulting growth in datasets of both raw MS files and processed peptide and protein identifications. MS-based proteomics technology is also used increasingly to measure additional protein properties affecting cellular function and disease mechanisms, including post-translational modifications, protein-protein interactions, subcellular and tissue distributions. Consequently, biologists and clinicians need innovative tools to conveniently analyse, visualize and explore such large, complex proteomics data and to integrate it with genomics and other related large-scale datasets. We have created the Encyclopedia of Proteome Dynamics (EPD) to meet this need (https://peptracker.com/epd/). The EPD combines a polyglot persistent database and web-application that provides open access to integrated proteomics data for >30 000 proteins from published studies on human cells and model organisms. It is designed to provide a user-friendly interface, featuring graphical navigation with interactive visualizations that facilitate powerful data exploration in an intuitive manner. The EPD offers a flexible and scalable ecosystem to integrate proteomics data with genomics information, RNA expression and other related, large-scale datasets., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

A conditional expression system has allowed us to vary the expression level of the xeroderma pigmentosum group A (XPA) photoproduct-specific DNA-binding protein in human cells and so control the response of cells to damage by UV light. Using a form of XPA that contains a single missense mutation (R207G) enabled us to study a lower range of function than that obtained with the wild-type sequence. This form of XPA has been previously shown to stimulate pyrimidine dimer excision preferentially in actively transcribed genes. We found that UV resistance increased as a linear function of XPA expression levels. Excision of (6-4) pyrimidine-pyrimidone photoproducts in the whole genome increased to a maximum at about the haploid level of XPA expression, but there was little pyrimidine dimer excision from the whole genome. SCE frequency induced by UV light was high in cells with no SPA expression and fell rapidly with increasing levels of SPA expression within 0-50% of the haploid level of expression. No further reduction in SCE frequency was produced at the highest levels of XPA expression, when repair replication extended to the overall genome. We speculate that a low level of repair, especially that occurring in actively transcribed genes, may selectively eliminate photoproducts that are particularly important in causing cell killing and SCEs.

Three processes associated with DNA damage and genomic instability have been defined experimentally as operating during or soon after DNA replication: mismatch repair, post-replication repair and sister chromatid exchange. All these processes appear to operate on damage and/or errors in newly replicated DNA. Both mismatch repair and post-replication repair involve resynthesis of up to 1 kb of newly synthesized DNA: mismatch repair operates on single-base or slippage errors; post-replication repair operates on persistent gaps in newly synthesized DNA caused by damage on parental strands. Using colon cancer cells with different mismatch repair capacity, together with normal cells and excision-repair-defective and post-replication-repair-defective xeroderma pigmentosum (XP) cells, we analysed possible interactions between these processes. No evidence for overlap of mismatch repair with excision or post-replication repair was found. However, post-replication-repair-defective XP variant cells that were SV40 transformed showed higher UV-induced sister chromatid exchange frequencies than did untransformed cells. This suggests that sister chromatid exchanges in the XP variant are closely involved with UV-induced replication errors that are enhanced by transformation.

When human lymphocytes are treated with [3H]thymidine ([ 3H]dThd), the observed number of chromosomal aberrations induced by [3H]dThd and subsequent doses of X-rays is less than the number induced by X-rays alone. Experiments in which cells were examined at various times after exposure to the X-rays showed that this phenomenon, termed an adaptive response to the endogenous radiation from tritium, is not an artefact caused by radiation-induced mitotic delays, which could result in the sampling of metaphase cells that were irradiated in different parts of the G2 phase of the cell cycle, where sensitivity to X-rays changes dramatically. Reconstruction experiments in which labelled female cells were co-cultured with unlabelled male cells now show that labelled and unlabelled cells progress to metaphase equally, and therefore that the adaptive response is not the result of selection against a radiosensitive population of cells that have incorporated [3H]dThd. Measurements of chromosomal aberrations induced in the labelled female cells and unlabelled male cells that had been co-cultured show that the adaptive response is restricted to those cells exposed to radiation from the incorporation of [3H]dThd and that diffusible factors are not involved. The results are consistent with the proposal that this adaptive response is the result of the induction of a hitherto unknown chromosomal repair mechanism. It has now been found that this repair mechanism is induced at levels of radiation from [3H]dThd that in themselves are too low to induce any discernible chromosomal aberrations and that its activity is dependent on the enzyme poly(ADP-ribose) polymerase, because 3-aminobenzamide, an inhibitor of poly(ADP-ribosyl)ation, prevents the adaptive response.