Transcriptional provirus silencing as a crosstalk of de novo DNA methylation and epigenomic features at the integration site

The autonomous transcription of integrated retroviruses strongly depends on genetic and epigenetic effects of the chromatin at the site of integration. These effects are mostly suppressive and proviral activity can be finally silenced by mechanisms, such as DNA methylation and histone modifications. To address the role of the integration site at the whole-genome-scale, we performed clonal analysis of provirus silencing with an avian leucosis/sarcoma virus-based reporter vector and correlated the transcriptional silencing with the epigenomic landscape of respective integrations. We demonstrate efficient provirus silencing in human HCT116 cell line, which is strongly but not absolutely dependent on the de novo DNA methyltransferase activity, particularly of Dnmt3b. Proviruses integrated close to the transcription start sites of active genes into the regions enriched in H3K4 trimethylation display long-term stability of expression and are resistant to the transcriptional silencing after over-expression of Dnmt3a or Dnmt3b. In contrast, proviruses in the intergenic regions tend to spontaneous transcriptional silencing even in Dnmt3a−/− Dnmt3b−/− cells. The silencing of proviruses within genes is accompanied with DNA methylation of long terminal repeats, whereas silencing in intergenic regions is DNA methylation-independent. These findings indicate that the epigenomic features of integration sites are crucial for their permissivity to the proviral expression

Ultrafast ellipsometric interferometry for direct detection of coherent phonon strain pulse profiles

We describe an ultrafast optical technique to quantitatively detect picosecond ultrasonic displacements of solid surfaces, thus giving access to the longitudinal strain pulse shape. Transient optical reflectance changes recorded at oblique optical incidence with a common-path interferometric configuration based on ultrafast ellipsometry monitor gigahertz coherent phonon pulses. We demonstrate for a tungsten film the quantitative extraction of the strain pulse shape free of distortions arising from the photoelastic effect, and analyze the results with the two-temperature model to obtain the value g approximate to 3 x 10(17) Wm(-3) K-1 for the electron-phonon coupling constant. Analysis of the data also reveals a thermo-optic contribution. (C) 2013 Optical Society of Americ