Similar Datasets
Project description:A ubiquitous feature of eukaryotic transcriptional regulation is cooperative self-assembly between transcription factors (TFs) and DNA cis-regulatory motifs. It is thought that this strategy enables specific regulatory connections to be formed in gene networks between otherwise weakly interacting, low-specificity molecular components. Here, using synthetic gene circuits constructed in yeast, we find that high regulatory specificity can emerge from cooperative, multivalent interactions among artificial zinc-finger-based TFs. We show that circuits "wired" using the strategy of cooperative TF assembly are effectively insulated from aberrant misregulation of the host cell genome. As we demonstrate in experiments and mathematical models, this mechanism is sufficient to rescue circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-term continuous culture. Our naturally inspired approach offers a simple, generalizable means for building high-fidelity, evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.
| S-EPMC10528910 | biostudies-literature
Project description:In eukaryotes, links in gene regulatory networks are often maintained through cooperative self-assembly between transcriptional regulators (TR) and DNA cis-regulatory motifs, a strategy widely thought to enable highly specific regulatory connections to be formed between otherwise weakly-interacting, low-specificity molecular components. Here, we directly test whether this regulatory strategy can be used to engineer regulatory specificity in synthetic gene circuits constructed in yeast. We show that circuits composed of artificial zinc-finger TRs can be effectively insulated from aberrant misregulation of the host cell genome by using cooperative multivalent TR assemblies to program circuit connections. As we demonstrate in experiments and mathematical models, assembly-mediated regulatory connections enable mitigation of circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-term continuous culture. Our naturally-inspired approach offers a simple, generalizable means for building evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.
2022-05-20 | GSE203144 | GEO
Project description:In eukaryotes, links in gene regulatory networks are often maintained through cooperative self-assembly between transcriptional regulators (TR) and DNA cis-regulatory motifs, a strategy widely thought to enable highly specific regulatory connections to be formed between otherwise weakly-interacting, low-specificity molecular components. Here, we directly test whether this regulatory strategy can be used to engineer regulatory specificity in synthetic gene circuits constructed in yeast. We show that circuits composed of artificial zinc-finger TRs can be effectively insulated from aberrant misregulation of the host cell genome by using cooperative multivalent TR assemblies to program circuit connections. As we demonstrate in experiments and mathematical models, assembly-mediated regulatory connections enable mitigation of circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-term continuous culture. Our naturally-inspired approach offers a simple, generalizable means for building evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.
2022-05-20 | GSE203145 | GEO
Project description:Cooperative assembly confers regulatory specificity and long-term genetic circuit stability
| PRJNA838831 | ENA
Project description:Cooperative assembly confers regulatory specificity and long-term genetic circuit stability [ChIP-Seq]
| PRJNA838835 | ENA
Project description:Cooperative assembly confers regulatory specificity and long-term genetic circuit stability [RNA-seq]
| PRJNA838834 | ENA
Project description:Deep-sequencing of the engineered production genes in five E coli production chassis strains (BL21(DE3), MG1655, TOP10, W and W3110) producing two case metabolic products, 2,3-butanediol and mevalonic acid
2020-11-17 | E-MTAB-9800 | biostudies-arrayexpress
Project description:Insertional oncogene activation and aberrant splicing have proved to be major setbacks for retroviral stem cell gene therapy. Integrase-deficient human immunodeficiency virus-1-derived vectors provide a potentially safer approach, but their circular genomes are rapidly lost during cell division. Here we describe a novel lentiviral vector (LV) that incorporates human ß-interferon scaffold/matrix-associated region sequences to provide an origin of replication for long-term mitotic maintenance of the episomal LTR circles. The resulting 'anchoring' non-integrating lentiviral vector (aniLV) achieved initial transduction rates comparable with integrating vector followed by progressive establishment of long-term episomal expression in a subset of cells. Analysis of aniLV-transduced single cell-derived clones maintained without selective pressure for >100 rounds of cell division showed sustained transgene expression from episomes and provided molecular evidence for long-term episome maintenance. To evaluate aniLV performance in primary cells, we transduced lineage-depleted murine hematopoietic progenitor cells, observing GFP expression in clonogenic progenitor colonies and peripheral blood leukocyte chimerism following transplantation into conditioned hosts. In aggregate, our studies suggest that scaffold/matrix-associated region elements can serve as molecular anchors for non-integrating lentivector episomes, providing sustained gene expression through successive rounds of cell division and progenitor differentiation in vitro and in vivo.
| S-EPMC3985655 | biostudies-literature
Project description:Understanding the mechanisms that promote the assembly and maintenance of host-beneficial microbiomes is an open problem. Empirical evidence supports the idea that animal and plant hosts can combine 'private resources' with the ecological phenomenon known as 'community bistability' to favour some microbial strains over others. We briefly review evidence showing that hosts can: (i) protect the growth of beneficial strains in an isolated habitat, (ii) use antibiotics to suppress non-beneficial, competitor strains, and (iii) provide resources that only beneficial strains are able to translate into an increased rate of growth, reproduction, or antibiotic production. We then demonstrate in a spatially explicit, individual-based model that these three mechanisms act similarly by selectively promoting the initial proliferation of preferred strains, that is, by acting as a private resource. The faster early growth of preferred strains, combined with the phenomenon of 'community bistability,' allows those strains to continue to dominate the microbiome even after the private resource is withdrawn or made public. This is because after a beneficial colony reaches a sufficiently large size, it can resist invasion by parasites without further private support from the host. We further explicitly model localized microbial interactions and diffusion dynamics, and we show that an intermediate level of antibiotic diffusion is the most efficient mechanism in promoting preferred strains and that there is a wide range of parameters under which hosts can promote the assembly of a self-sustaining defensive microbiome. This in turn supports the idea that hosts readily evolve to promote host-beneficial defensive microbiomes.
| S-EPMC6576795 | biostudies-literature
Project description:Measures of genetic differentiation between populations are useful tools for understanding the long-term dynamics of parasite communities. We followed the allele frequencies of microsatellite markers in samples taken over a period of 16 yr from the Case Western Reserve University-Naval Medical Research Institute (CWRU-NMRI) laboratory strain of Schistosoma mansoni. DNA was isolated from pooled samples of adults, eggs, or cercariae collected at 46 time points and genotyped for 14 tri- or tetranucleotide microsatellite markers. For comparison, 2 S. mansoni reference strains (Biomedical Research Institute-NMRI, which has a common origin with the CWRU line, and PR-1) were analyzed over shorter periods of time. We observed that the long-term allele frequencies are generally stable in large laboratory populations of this parasite, and a high degree of similarity was observed between the allele frequencies of consecutive samples from different developmental stages. The CWRU strain, however, showed 2 periods of marked deviation from stability as demonstrated using genetic differentiation measures. The first period corresponds to an admixture event with the BRI strain in which a new equilibrium was established as the "migrants" became blended into the existing CWRU population, consistent with 23% admixture from BRI. The second corresponds to a period of genetic drift when the CWRU population size was greatly reduced with an accompanying loss in genetic diversity. Having demonstrated the utility of pooled samples for the genetic analysis of population dynamics in laboratory strains of schistosomes, this approach will be useful for analyzing field samples to determine the impact of schistosomiasis control programs on parasite population structure. Accounting only for the intensity or prevalence of parasite populations may fail to register significant changes in population structure that could have implications for resistance, morbidity, and the design of control measures.
| S-EPMC3881424 | biostudies-literature