Complex molecular responses preserve gene expression accuracy and genome integrity in the face of environmental perturbations. Here we report that, in response to UV irradiation, RNA polymerase II (RNAPII) molecules are dynamically and synchronously released from promoter-proximal regions into elongation to promote uniform and accelerated surveillance of the whole transcribed genome. The maximised influx of de novo released RNAPII correlates with increased damage-sensing, as confirmed by RNAPII progressive accumulation at dipyrimidine sites and by the average slow-down of elongation rates in gene bodies. In turn, this transcription elongation ‘safe’ mode guarantees efficient DNA repair regardless of damage location, gene size and transcription level. Accordingly, we detect low and homogenous rates of mutational signatures associated with UV exposure or cigarette smoke across all active genes. Our study reveals a novel advantage for transcription regulation at the promoter-proximal level and provides unanticipated insights into how active transcription shapes the mutagenic landscape of cancer genomes.

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Background:The transcription factor NF-B is a critical regulator of immune response pathways. Results: 11% of total NF-B binding events in humans occur at the Alu-B element present in Alu repeats. Conclusion: NF-B has a primate-specific function and a role in human evolution. Significance: Repetitive elements expand the repertoire of binding sites to engage new genes into regulatory networks.

Poly(N-isopropylacrylamide) (PNIPAm) co-polymers responsive to temperature and pH were prepared with side chain chemistries in order to exhibit phase transitions under physiologically relevant conditions. Fluorescence spectroscopy, gel retardation assays, dynamic light scattering and atomic force microscopy were used to characterize the binding of plasmid DNA to these materials and to control polymers poly(ethyleneimine) (PEI) and poly(ethyleneimine)-octanamide. Complexes of plasmid DNA with thermoresponsive cationic polymers containing PNIPAm displayed variations in gel retardation behaviour above and below polymer phase transition temperatures, with a high molecular weight linear cationic PNIPAm co-polymer forming complexes with reduced affinity above LCST whereas a branched PEI-PNIPAm co-polymer bound with higher affinity above the PNIPAm phase transition. The thermoresponsive polymers also exhibited changes in particle morphology across the same temperature ranges with polymer DNA complexes prepared at N/P ratios of 2:1 generating spherical particles varying in radius between 30-70 nm at 25 degrees C and 60-100 nm at 40-45 degrees C. The transport of DNA within these complexes to cell nuclei was demonstrated to occur within 24 h in tissue culture via confocal microscopy, and low level transfection of mouse muscle cells by a reporter gene encoding green fluorescent protein was achieved with the branched thermoresponsive PEI-PNIPAm conjugate.

Neuroblastoma is a pediatric tumor that originates from precursor cells of the sympathetic nervous system with less than 40% long-term survival in children diagnosed with high-risk disease. These clinical observations underscore the need for novel insights in the mechanisms of malignant transformation and progression. Accordingly, it was recently reported that Prox1, a homeobox transcription regulator, is expressed in higher levels in human neuroblastoma with favorable prognosis. Consistently, we have recently shown that Prox1 exerts a strong antiproliferative effect on neural precursor cells during embryonic development. Thus, Prox1 is a candidate gene with a critical role in suppressing malignant neuroblastoma transformation. Here, we provide evidence that Prox1 strongly suppresses the proliferation of mouse and human neuroblastoma cell lines and blocks the growth of neuroblastoma tumors in SCID mice. Conversely, short hairpin RNA (shRNA) -mediated knockdown of basal Prox1 expression significantly induces proliferation, genomic instability and the ability of neuroblastoma cells to form tumors. Mechanistically, analysis of an inducible Prox1-overexpressing Neuro2A cell line indicates that Prox1 is sufficient to suppress CyclinD1, CyclinA and CyclinB1, consistent with a role in cell cycle arrest. Surprisingly, Prox1 strongly induces CyclinE1 expression in the same system despite its action on blocking cell cycle progression, which could account for the context dependent oncogenic function of Prox1. Most importantly, Prox1 was sufficient to decrease Cdc25A and induce p27-Kip1, but not p21-Cip1 or p53. By alleviating the Prox1 action in Cdc25A and p27-Kip1 expression, we were able to rescue its effect on cell cycle arrest. Together these data suggest that Prox1 negatively regulates neuroblastoma carcinogenesis through suppression of Cdc25A and induction of p27-Kip1 to counteract CyclinE1 overexpression and block cell cycle progression. Furthermore, these observations render Prox1 a candidate target for the treatment of neuroblastoma tumors.