In pursuit of design principles of regulatory sequences

M Levo, E Segal - Nature Reviews Genetics, 2014 - nature.com
Instructions for when, where and to what level each gene should be expressed are encoded
within regulatory sequences. The importance of motifs recognized by DNA-binding …

In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

P Maia, M Rocha, I Rocha - Microbiology and Molecular Biology …, 2016 - Am Soc Microbiol
Shifting from chemical to biotechnological processes is one of the cornerstones of 21st
century industry. The production of a great range of chemicals via biotechnological means is …

Digital logic circuits in yeast with CRISPR-dCas9 NOR gates

MW Gander, JD Vrana, WE Voje, JM Carothers… - Nature …, 2017 - nature.com
Natural genetic circuits enable cells to make sophisticated digital decisions. Building equally
complex synthetic circuits in eukaryotes remains difficult, however, because commonly used …

Integrative comparison of the role of the PHOSPHATE RESPONSE1 subfamily in phosphate signaling and homeostasis in rice

M Guo, W Ruan, C Li, F Huang, M Zeng, Y Liu… - Plant …, 2015 - academic.oup.com
Phosphorus (P), an essential macronutrient for all living cells, is indispensable for
agricultural production. Although Arabidopsis (Arabidopsis thaliana) PHOSPHATE …

Unraveling determinants of transcription factor binding outside the core binding site

M Levo, E Zalckvar, E Sharon, ACD Machado… - Genome …, 2015 - genome.cshlp.org
Binding of transcription factors (TFs) to regulatory sequences is a pivotal step in the control
of gene expression. Despite many advances in the characterization of sequence motifs …

The robustness and evolvability of transcription factor binding sites

JL Payne, A Wagner - Science, 2014 - science.org
Robustness, the maintenance of a character in the presence of genetic change, can help
preserve adaptive traits but also may hinder evolvability, the ability to bring forth novel …

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

B Knight, S Kubik, B Ghosh, MJ Bruzzone… - Genes & …, 2014 - genesdev.cshlp.org
In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138
ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and …

Core promoter sequence in yeast is a major determinant of expression level

S Lubliner, I Regev, M Lotan-Pompan… - Genome …, 2015 - genome.cshlp.org
The core promoter is the regulatory sequence to which RNA polymerase is recruited and
where it acts to initiate transcription. Here, we present the first comprehensive study of yeast …

[PDF][PDF] Recent applications of synthetic biology tools for yeast metabolic engineering

MK Jensen, JD Keasling - FEMS Yeast Res, 2015 - haseloff.plantsci.cam.ac.uk
The last 20 years of metabolic engineering has enabled bio-based production of fuels and
chemicals from renewable carbon sources using cost-effective bioprocesses. Much of this …

Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif

VR Yella, D Bhimsaria, D Ghoshdastidar… - Nucleic acids …, 2018 - academic.oup.com
Spatial and temporal expression of genes is essential for maintaining phenotype integrity.
Transcription factors (TFs) modulate expression patterns by binding to specific DNA …