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In silico design of context-responsive mammalian promoters with user-defined functionality.

ABSTRACT: Comprehensive de novo-design of complex mammalian promoters is restricted by unpredictable combinatorial interactions between constituent transcription factor regulatory elements (TFREs). In this study, we show that modular binding sites that do not function cooperatively can be identified by analyzing host cell transcription factor expression profiles, and subsequently testing cognate TFRE activities in varying homotypic and heterotypic promoter architectures. TFREs that displayed position-insensitive, additive function within a specific expression context could be rationally combined together in silico to create promoters with highly predictable activities. As TFRE order and spacing did not affect the performance of these TFRE-combinations, compositions could be specifically arranged to preclude the formation of undesirable sequence features. This facilitated simple in silico-design of promoters with context-required, user-defined functionalities. To demonstrate this, we de novo-created promoters for biopharmaceutical production in CHO cells that exhibited precisely designed activity dynamics and long-term expression-stability, without causing observable retroactive effects on cellular performance. The design process described can be utilized for applications requiring context-responsive, customizable promoter function, particularly where co-expression of synthetic TFs is not suitable. Although the synthetic promoter structure utilized does not closely resemble native mammalian architectures, our findings also provide additional support for a flexible billboard model of promoter regulation.

SUBMITTER: Brown AJ

PROVIDER: S-EPMC5737543 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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In silico design of context-responsive mammalian promoters with user-defined functionality.

Brown Adam J AJ Gibson Suzanne J SJ Hatton Diane D James David C DC

Nucleic acids research 20171001 18

Comprehensive de novo-design of complex mammalian promoters is restricted by unpredictable combinatorial interactions between constituent transcription factor regulatory elements (TFREs). In this study, we show that modular binding sites that do not function cooperatively can be identified by analyzing host cell transcription factor expression profiles, and subsequently testing cognate TFRE activities in varying homotypic and heterotypic promoter architectures. TFREs that displayed position-inse ...[more]

PMID: 28977454

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Project description:BackgroundEcological momentary assessment (EMA) can be a useful tool for collecting real-time behavioral data in studies of health and health behavior. However, EMA administered through mobile technology can be burdensome, and it tends to suffer from suboptimal user engagement, particularly in low health-literacy populations.ObjectiveThis study aimed to report a case study involving the design and evaluation of a mobile EMA tool that supports context-sensitive EMA-reporting of location and social situations accompanying eating and sedentary behavior.MethodsAn iterative, user-centered design process with obese, middle-aged women seeking care in a safety-net health system was used to identify the preferred format of self-report measures and the look, feel, and interaction of the mobile EMA tool. A single-arm feasibility field trial with 21 participants receiving 12 prompts each day for momentary self-reports over a 4-week period (336 total prompts per participant) was used to determine user satisfaction with interface quality and user engagement, operationalized as response rate. A second trial among 38 different participants randomized to receive or not to receive a feature designed to improve engagement was conducted.ResultsThe feasibility trial results showed high interface satisfaction and engagement, with an average response rate of 50% over 4 weeks. Qualitative feedback pointed to the need for auditory alerts. We settled on 3 alerts at 10-min intervals to accompany each EMA-reporting prompt. The second trial testing this feature showed a statistically significant increase in the response rate between participants randomized to receive repeat auditory alerts versus those who were not (60% vs 40%).ConclusionsThis paper reviews the design research and a set of design constraints that may be considered in the creation of mobile EMA interfaces personalized to users' preferences. Novel aspects of the study include the involvement of low health-literacy adults in design research, the capture of data on time, place, and social context of eating and sedentary behavior, and reporting prompts tailored to an individual's location and schedule.Trial registrationClinicalTrials.gov NCT03083964; https://clinicaltrials.gov/ct2/show/NCT03083964.

Dataset Information

In silico design of context-responsive mammalian promoters with user-defined functionality.

Publications

In silico design of context-responsive mammalian promoters with user-defined functionality.

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