scholarly journals Synthetic 5’ UTRs can either up- or down-regulate expression upon RBP binding

2017 ◽  
Author(s):  
Noa Katz ◽  
Roni Cohen ◽  
Oz Solomon ◽  
Beate Kaufmann ◽  
Orna Atar ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Cooperative Behavior ◽  
Transcriptional Level ◽  
Rna Molecules ◽  
Regulatory Modules ◽  
Regulatory Circuits ◽  
Rna Hairpins ◽  
Gene Regulatory ◽  
Gene Regulatory Circuits

SUMMARYThe construction of complex gene regulatory networks requires both inhibitory and up-regulatory modules. However, the vast majority of RNA-based regulatory “parts” are inhibitory. Using a synthetic biology approach combined with SHAPE-Seq, we explored the regulatory effect of RBP-RNA interactions in bacterial 5’-UTRs. By positioning a library of RNA hairpins upstream of a reporter gene and co-expressing them with the matching RBP, we observed a set of regulatory responses, including translational stimulation, translational repression, and cooperative behavior. Our combined approach revealed three distinct states in-vivo: in the absence of RBPs, the RNA molecules can be found either in a molten state that is amenable to translation, or a structured phase that inhibits translation. In the presence of RBPs, the RNA molecules are in a semi-structured phase with partial translational capacity. Our work provides new insight into RBP-based regulation and a blueprint for designing complete gene regulatory circuits at the post-transcriptional level.

scholarly journals Reconstruction of the global neural crest gene regulatory networkin vivo

2018 ◽  
Author(s):  
Ruth M Williams ◽  
Ivan Candido-Ferreira ◽  
Emmanouela Repapi ◽  
Daria Gavriouchkina ◽  
Upeka Senanayake ◽  
...  
Keyword(s):  
Neural Crest ◽  
Regulatory Networks ◽  
Transcriptome Profiling ◽  
Integrated Approach ◽  
Precise Control ◽  
Regulatory Circuits ◽  
A Genome ◽  
Gene Regulatory ◽  
Cell Transcriptome

AbstractPrecise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and transient dynamic molecular interactions. Here we present a genome-widein vivoreconstruction of the GRN underlying development of neural crest (NC), an emblematic embryonic multipotent cell population. By coupling NC-specific epigenomic and single-cell transcriptome profiling with genome/epigenome engineeringin vivo, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, noveltrans-factors andcis-signatures. Assembling the NC regulome has allowed the comprehensive reverse engineering of the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits that define canonical and neural NC fates. Our integrated approach, allowing dissection of cell-type-specific regulatory circuitsin vivo, has broad implications for GRN discovery and investigation.

scholarly journals A model for the spatio-temporal design of gene regulatory circuits

2019 ◽  
Author(s):  
Ruud Stoof ◽  
Alexander Wood ◽  
Ángel Goñi-Moreno
Keyword(s):  
Regulatory Networks ◽  
Bacterial Gene ◽  
Regulatory Circuits ◽  
Vital Functions ◽  
Gene Expression Dynamics ◽  
Gene Regulatory ◽  
Spatio Temporal ◽  
Gene Regulatory Circuits ◽  
Dna Components ◽  
Engineered Bacteria

AbstractThe design of increasingly complex gene regulatory networks relies upon mathematical modelling to link the gap that goes from conceptualisation to implementation. An overarching challenge is to update modelling abstractions and assumptions as new mechanistic information arises. Although models of bacterial gene regulation are often based on the assumption that the role played by intracellular physical distances between genetic elements is negligible, it has been shown that bacteria are highly ordered organisms, compartmentalizing their vital functions in both time and space. Here, we analysed the dynamical properties of regulatory interactions by explicitly modelling spatial constraints. Key to the model is the combined search by a regulator for its target promoter via 1D sliding along the chromosome and 3D diffusion through the cytoplasm. Moreover, this search was coupled to gene expression dynamics, with special attention to transcription factor-promoter interplay. As a result, promoter activity within the model depends on its physical separation from the regulator source. Simulations showed that by modulating the distance between DNA components in the chromosome, output levels changed accordingly. Finally, previous experimental results with engineered bacteria in which this distance was minimized or enlarged were successfully reproduced by the model. This suggests that the spatial specification of the circuit alone can be exploited as a design parameter to select programmable output levels.

scholarly journals Reprogramming, oscillations and transdifferentiation in epigenetic landscapes

2017 ◽  
Author(s):  
Bivash Kaity ◽  
Ratan Sarkar ◽  
Buddhapriya Chakrabarti ◽  
Mithun K. Mitra
Keyword(s):  
Cell Differentiation ◽  
Regulatory Networks ◽  
Delayed Feedback ◽  
Regulatory Circuits ◽  
Undifferentiated State ◽  
Gene Regulatory ◽  
Programming Process ◽  
Gene Regulatory Circuits ◽  
Differentiation Pathways ◽  
Time Delayed Feedback

Waddington’s epigenetic landscape provides a phenomenological understanding of the cell differentiation pathways from the pluripotent to mature lineage-committed cell lines. In light of recent successes in the reverse programming process there has been significant interest in quantifying the underlying landscape picture through the mathematics of gene regulatory networks. We investigate the role of time delays arising from multistep chemical reactions and epigenetic rearrangement on the cell differentiation landscape for a realistic two-gene regulatory network, consisting of selfpromoting and mutually inhibiting genes. Our work provides the first theoretical basis of the transdifferentiation process in the presence of delays, where one differentiated cell type can transition to another directly without passing through the undifferentiated state. Additionally, the interplay of time-delayed feedback and a time dependent chemical drive leads to long-lived oscillatory states in appropriate parameter regimes. This work emphasizes the important role played by time-delayed feedback loops in gene regulatory circuits and provides a framework for the characterization of epigenetic landscapes.

scholarly journals In vitro gene regulatory networks predict in vivo function of liver

2010 ◽  
Vol 4 (1) ◽  
Author(s):  
Youping Deng ◽  
David R Johnson ◽  
Xin Guan ◽  
Choo Y Ang ◽  
Junmei Ai ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Gene Regulatory

scholarly journals Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets

2016 ◽  
Vol 113 (13) ◽  
pp. E1835-E1843 ◽  
Author(s):  
Mina Fazlollahi ◽  
Ivor Muroff ◽  
Eunjee Lee ◽  
Helen C. Causton ◽  
Harmen J. Bussemaker
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Nonsynonymous Mutation ◽  
Gene Regulatory ◽  
Genetic Modulators

Regulation of gene expression by transcription factors (TFs) is highly dependent on genetic background and interactions with cofactors. Identifying specific context factors is a major challenge that requires new approaches. Here we show that exploiting natural variation is a potent strategy for probing functional interactions within gene regulatory networks. We developed an algorithm to identify genetic polymorphisms that modulate the regulatory connectivity between specific transcription factors and their target genes in vivo. As a proof of principle, we mapped connectivity quantitative trait loci (cQTLs) using parallel genotype and gene expression data for segregants from a cross between two strains of the yeast Saccharomyces cerevisiae. We identified a nonsynonymous mutation in the DIG2 gene as a cQTL for the transcription factor Ste12p and confirmed this prediction empirically. We also identified three polymorphisms in TAF13 as putative modulators of regulation by Gcn4p. Our method has potential for revealing how genetic differences among individuals influence gene regulatory networks in any organism for which gene expression and genotype data are available along with information on binding preferences for transcription factors.

Towards In Vivo Nanomachines

2008 ◽  
Vol 58 ◽  
pp. 120-126
Author(s):  
Eike Friedrichs ◽  
Ralf Jungmann ◽  
Angeliki Tsokou ◽  
Stephan Renner ◽  
Friedrich C. Simmel
Keyword(s):  
Nucleic Acid ◽  
Molecular Devices ◽  
Rna Transcription ◽  
Rna Molecules ◽  
Regulatory Motifs ◽  
One Step ◽  
Gene Regulatory

DNA has been recently used to construct a variety of nanoscale machines and switches, among them devices which can translocate, compute, or bind and release molecules. For future applications it is interesting to investigate whether these "artificial" functions can also be implemented in vivo. As one step towards in vivo applications, we currently utilize RNA molecules for construction or control of molecular devices. RNA molecules can be transcribed from "artificial genes" and either fold into functional nanoassemblies themselves or drive other nucleic acid-based devices as a "fuel". Furthermore, coupling of nanomachines to RNA transcription enables control of their behavior using gene regulatory motifs.

scholarly journals Predicting effective microRNA target sites in mammalian mRNAs

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Vikram Agarwal ◽  
George W Bell ◽  
Jin-Wu Nam ◽  
David P Bartel
Keyword(s):  
Regulatory Networks ◽  
Quantitative Model ◽  
Seed Region ◽  
Microrna Target ◽  
Functional Sites ◽  
Uv Crosslinking ◽  
Gene Regulatory ◽  
Mirna Seed ◽  
Better Than

MicroRNA targets are often recognized through pairing between the miRNA seed region and complementary sites within target mRNAs, but not all of these canonical sites are equally effective, and both computational and in vivo UV-crosslinking approaches suggest that many mRNAs are targeted through non-canonical interactions. Here, we show that recently reported non-canonical sites do not mediate repression despite binding the miRNA, which indicates that the vast majority of functional sites are canonical. Accordingly, we developed an improved quantitative model of canonical targeting, using a compendium of experimental datasets that we pre-processed to minimize confounding biases. This model, which considers site type and another 14 features to predict the most effectively targeted mRNAs, performed significantly better than existing models and was as informative as the best high-throughput in vivo crosslinking approaches. It drives the latest version of TargetScan (v7.0; targetscan.org), thereby providing a valuable resource for placing miRNAs into gene-regulatory networks.

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