Synthetic rewiring and boosting type I interferon responses for visualization and counteracting viral infections

Abstract

Mammalian first line of defense against viruses is accomplished by the interferon (IFN) system. Viruses have evolved numerous mechanisms to reduce the IFN action allowing them to invade the host and/or to establish latency. We generated an IFN responsive intracellular hub by integrating the synthetic transactivator tTA into the chromosomal Mx2 locus for IFN-based activation of tTA dependent expression modules. The additional implementation of a synthetic amplifier module with positive feedback even allowed for monitoring and reacting to infections of viruses that can antagonize the IFN system. Low and transient IFN amounts are sufficient to trigger these amplifier cells. This gives rise to higher and sustained—but optionally de-activatable—expression even when the initial stimulus has faded out. Amplification of the IFN response induced by IFN suppressing viruses is sufficient to protect cells from infection. Together, this interfaced sensor/actuator system provides a toolbox for robust sensing and counteracting viral infections.

The Blueprint of Logical Decisions in a NF-κB Signaling System

“…We demonstrate the possibility of creating a biomolecular computer using our theoretical calculations for the NF-κB system. The unique regulatory feature of the NF-κB system shares the possibility of forming active assemblies under various stimuli conditions. , We explored the building blocks of such biomolecular computers by exploiting the programmed DNA loop and variability of stimuli-dependent TF activation. We show that various active self-assemblies formed under two input conditions, a feature mimicking modern computer chips.…”

“…The enhancer− promoter looping is controllable dose-dependent as found in stimuli-dependent osteopontin expression for various immune cells. 43,62 ■ RESULTS…”

“…The binding of the p300 promotes DNA looping through an interaction with the bound enhancer proteins. The enhancer–promoter looping is controllable dose-dependent as found in stimuli-dependent osteopontin expression for various immune cells. , …”

Streamlining differential exon and 3′ UTR usage with diffUTR

“…1000 transcripts from different genes were randomly chosen. The last exon of all these transcripts was lengthened to the next, second next or third next downstream APA site annotated in the polyAsite database [ 15 ]. Duplicates of these transcripts were generated, which had less or no lengthening of their last exon, generating pairs of transcripts with different UTR lengths.…”

“…A number of methods for 3′ end sequencing have been developed with the goal to map APA sites [ 4 , 9 – 14 ], leading to the development of atlases such as PolyASite [ 15 ] or PolyA_DB [ 16 ]. As such methods are only marginally used, however, it would be beneficial to leverage the widespread availability of traditional RNA-seq for the purpose of identifying changes in 3′ UTR usage.…”