The Environment-Dependent Regulatory Landscape of the E. coli Genome
Roeschinger, T.; Lee, H. J.; Pan, R. W.; Solini, G.; Faizi, K.; Quan, B.; Chou, T. F.; Mani, M.; Quake, S.; Phillips, R.
Show abstract
1All cells respond to changes in both their internal milieu and the environment around them through the regulation of their genes. Despite decades of effort, there remain huge gaps in our knowledge of both the function of many genes (the so-called y-ome) and how they adapt to changing environments via regulation. Here we describe a joint experimental and theoretical dissection of the regulation of a broad array of over 100 biologically interesting genes in E. coli across 39 diverse environments, permitting us to discover the binding sites and transcription factors that mediate regulatory control. Using a combination of mutagenesis, massively parallel reporter assays, mass spectrometry and tools from information theory and statistical physics, we go from complete ignorance of a promoters environment-dependent regulatory architecture to predictive models of its behavior. As a proof of principle of the biological insights to be gained from such a study, we chose a combination of genes from the y-ome, toxin-antitoxin pairs, and genes hypothesized to be part of regulatory modules; in all cases, we discovered a host of new insights into their underlying regulatory landscape and resulting biological function.
Matching journals
The top 4 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- ProteinWeaver: A Webtool to Visualize Ontology-Annotated Protein Networks 92%
- Analysis of computational codon usage models and their association with translationally slow codons 92%
- Saturated Transposon Analysis in Yeast as a One-step Method to Quantify the Fitness Effects of Gene Disruptions on a Genome-Wide Scale 92%
Similar papers in this journal
- Neural network modeling of differential binding between wild-type and mutant CTCF reveals putative binding preferences for zinc fingers 1-2 92%
- Epigenetic features improve TALE target prediction 92%
- Glucose-lactose mixture feeds in industry-like conditions: a gene regulatory network analysis on the hyperproducing Trichoderma reesei strain Rut-C30 91%
Similar papers in this journal
- Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention 94%
- Revisiting the Central Dogma: the distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana 94%
- Robustness and applicability of functional genomics tools on scRNA-seq data 93%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.