@article{adkins_swygert_kaur_niu_grigoryev_sung_wang_peterson_2017, title={Nucleosome-like, Single-stranded DNA (ssDNA)-Histone Octamer Complexes and the Implication for DNA Double Strand Break Repair}, volume={292}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.m117.776369}, abstractNote={Repair of DNA double strand breaks (DSBs) is key for maintenance of genome integrity. When DSBs are repaired by homologous recombination, DNA ends can undergo extensive processing, producing long stretches of single-stranded DNA (ssDNA). In vivo, DSB processing occurs in the context of chromatin, and studies indicate that histones may remain associated with processed DSBs. Here we demonstrate that histones are not evicted from ssDNA after in vitro chromatin resection. In addition, we reconstitute histone-ssDNA complexes (termed ssNucs) with ssDNA and recombinant histones and analyze these particles by a combination of native gel electrophoresis, sedimentation velocity, electron microscopy, and a recently developed electrostatic force microscopy technique, DREEM (dual-resonance frequency-enhanced electrostatic force microscopy). The reconstituted ssNucs are homogenous and relatively stable, and DREEM reveals ssDNA wrapping around histones. We also find that histone octamers are easily transferred in trans from ssNucs to either double-stranded DNA or ssDNA. Furthermore, the Fun30 remodeling enzyme, which has been implicated in DNA repair, binds ssNucs preferentially over nucleosomes, and ssNucs are effective at activating Fun30 ATPase activity. Our results indicate that ssNucs may be a hallmark of processes that generate ssDNA, and that posttranslational modification of ssNucs may generate novel signaling platforms involved in genome stability.}, number={13}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Adkins, Nicholas L. and Swygert, Sarah G. and Kaur, Parminder and Niu, Hengyao and Grigoryev, Sergei A. and Sung, Patrick and Wang, Hong and Peterson, Craig L.}, year={2017}, month={Mar}, pages={5271–5281} }
 @article{wambaugh_wang_dionisio_frame_egeghy_judson_setzer_2014, title={High Throughput Heuristics for Prioritizing Human Exposure to Environmental Chemicals}, volume={48}, ISSN={["1520-5851"]}, DOI={10.1021/es503583j}, abstractNote={The risk posed to human health by any of the thousands of untested anthropogenic chemicals in our environment is a function of both the hazard presented by the chemical and the extent of exposure. However, many chemicals lack estimates of exposure intake, limiting the understanding of health risks. We aim to develop a rapid heuristic method to determine potential human exposure to chemicals for application to the thousands of chemicals with little or no exposure data. We used Bayesian methodology to infer ranges of exposure consistent with biomarkers identified in urine samples from the U.S. population by the National Health and Nutrition Examination Survey (NHANES). We performed linear regression on inferred exposure for demographic subsets of NHANES demarked by age, gender, and weight using chemical descriptors and use information from multiple databases and structure-based calculators. Five descriptors are capable of explaining roughly 50% of the variability in geometric means across 106 NHANES chemicals for all the demographic groups, including children aged 6-11. We use these descriptors to estimate human exposure to 7968 chemicals, the majority of which have no other quantitative exposure prediction. For thousands of chemicals with no other information, this approach allows forecasting of average exposure intake of environmental chemicals.}, number={21}, journal={ENVIRONMENTAL SCIENCE & TECHNOLOGY}, author={Wambaugh, John F. and Wang, Anran and Dionisio, Kathie L. and Frame, Alicia and Egeghy, Peter and Judson, Richard and Setzer, R. Woodrow}, year={2014}, month={Nov}, pages={12760–12767} }