Study of in vitro transcriptional binding effects and noise using constitutive promoters combined with UP element sequences in Escherichia coli

Background UP elements (upstream element) are DNA sequences upstream of a promoter that interact with the α-subunit of RNA polymerase (RNAP) and can affect transcription by altering the binding RNAP to DNA. However, details of UP element and binding affinity effects on transcriptional strength are unclear. Results Here, we investigated the effects of UP element sequences on gene transcription, binding affinity, and gene expression noise. Addition of UP elements resulted in increased gene expression (maximum 95.7-fold increase) and reduced gene expression noise (8.51-fold reduction). Half UP element sequences at the proximal subsite has little effect on transcriptional strength despite increasing binding affinity by 2.28-fold. In vitro binding assays were used to determine dissociation constants (Kd) and in the in vitro system, the full range of gene expression occurs in a small range of dissociation constants (25 nM \u3c Kd \u3c 45 nM) indicating that transcriptional strength is highly sensitive to small changes in binding affinity. Conclusions These results demonstrate the utility of UP elements and provide mechanistic insight into the functional relationship between binding affinity and transcription. Given the centrality of gene expression via transcription to biology, additional insight into transcriptional mechanisms can foster both fundamental and applied research. In particular, knowledge of the DNA sequence-specific effects on expression strength can aid in promoter engineering for different organisms and for metabolic engineering to balance pathway fluxes

Higgs Pair Production: Improved Description by Matrix Element Matching

Higgs pair production is crucial for measuring the Higgs boson self-coupling. The dominant channel at hadron colliders is gluon fusion via heavy-quark loops. We present the results of a fully exclusive simulation of gluon fusion Higgs pair production based on the matrix elements for hh + 0, 1 partons including full heavy-quark loop dependence, matched to a parton shower. We examine and validate this new description by comparing it with (a) Higgs Effective Theory predictions, (b) exact hh + 0-parton sample showered by pythia, and (c) exact hh+1-parton distributions, by looking at the most relevant kinematic distributions, such as PTh, PThh, Mhh spectra, and jet rate as well. We find that matched samples provide an state-of-the-art accurate exclusive description of the final state. The relevant LHE files for Higgs pair productions at the LHC can be accessed via http://hepfarm02.phy.pku.edu.cn/foswiki/CMS/HH, which can be used for relevant experimental analysis.Comment: accepted version in Phys. Rev. D. arXiv admin note: substantial text overlap with arXiv:1110.172