Advances in promoter engineering: Novel applications and predefined transcriptional control

T cell circuits that sense antigen density with an ultrasensitive threshold

(2021) Rogelio A. Hernandez-Lopez et al.   SCIENCE

In-situ generation of large numbers of genetic combinations for metabolic reprogramming via CRISPR-guided base editing

(2021) Yu Wang et al.   Nature Communications

Comparison of machine learning and deep learning techniques in promoter prediction across diverse species

(2021) Nikita Bhandari et al.   PeerJ Computer Science

Reactivation of γ-globin expression through Cas9 or base editor to treat β-hemoglobinopathies

(2020) Liren Wang et al.   CELL RESEARCH

Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing

(2020) Kailong Li et al.   Nature Communications

Therapeutic base editing of human hematopoietic stem cells

(2020) Jing Zeng et al.   NATURE MEDICINE

Synthetic promoter design in Escherichia coli based on a deep generative network

(2020) Ye Wang et al.   NUCLEIC ACIDS RESEARCH

Model-driven generation of artificial yeast promoters

(2020) Benjamin J. Kotopka et al.   Nature Communications

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Automated design of thousands of nonrepetitive parts for engineering stable genetic systems

(2020) Ayaan Hossain et al.   NATURE BIOTECHNOLOGY

Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae

(2020) Hongting Tang et al.   Metabolites

Identification of the human DPR core promoter element using machine learning

(2020) Long Vo ngoc et al.   NATURE

Engineering a Synthesis-Friendly Constitutive Promoter for Mammalian Cell Expression

(2020) Chee Ka Candice Lam et al.   ACS Synthetic Biology

‘It will change everything’: DeepMind’s AI makes gigantic leap in solving protein structures

(2020) Ewen Callaway   NATURE

Precise T cell recognition programs designed by transcriptionally linking multiple receptors

(2020) Jasper Z. Williams et al.   SCIENCE

Metagenomic engineering of the mammalian gut microbiome in situ

(2019) Carlotta Ronda et al.   NATURE METHODS

Mapping DNA sequence to transcription factor binding energy in vivo

(2019) Stephanie L. Barnes et al.   PLoS Computational Biology

Recent advances in the applications of promoter engineering for the optimization of metabolite biosynthesis

(2019) Ning Xu et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence

(2019) Jacob D. Washburn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Transcription Factors: Regulation by Pick “N” Mix

(2019) Douglas F. Browning et al.   JOURNAL OF MOLECULAR BIOLOGY

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

DeePromoter: Robust Promoter Predictor Using Deep Learning

(2019) Mhaned Oubounyt et al.   Frontiers in Genetics

A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS)

(2019) Ming-Ru Wu et al.   Nature Communications

How to Choose the Right Inducible Gene Expression System for Mammalian Studies?

(2019) Kallunki et al.   Cells

Designing Eukaryotic Gene Expression Regulation Using Machine Learning

(2019) Ronald P.H. de Jongh et al.   TRENDS IN BIOTECHNOLOGY

Biosensors design in yeast and applications in metabolic engineering

(2019) Chenxi Qiu et al.   FEMS YEAST RESEARCH

Modulating transcription through development of semi-synthetic yeast core promoters

(2019) Thomas Decoene et al.   PLoS One

Transcriptional programming using engineered systems of transcription factors and genetic architectures

(2019) Ronald E. Rondon et al.   Nature Communications

Regulation of gene expression by altered promoter methylation using a CRISPR/Cas9-mediated epigenetic editing system

(2019) Jeong Gu Kang et al.   Scientific Reports

Fine-tuning the expression of target genes using a DDI2 promoter gene switch in budding yeast

(2019) Yong Wang et al.   Scientific Reports

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters

(2019) Carl G. de Boer et al.   NATURE BIOTECHNOLOGY

Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically-Encoded Multiplexed Reporter Assay in E. coli

(2018) Guillaume Urtecho et al.   BIOCHEMISTRY

RewiringYarrowia lipolyticatoward triacetic acid lactone for materials generation

(2018) Kelly A. Markham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Random sequences rapidly evolve into de novo promoters

(2018) Avihu H. Yona et al.   Nature Communications

Remote Control of Mammalian Cells with Heat-Triggered Gene Switches and Photothermal Pulse Trains

(2018) Ian C. Miller et al.   ACS Synthetic Biology

Toward Predictable 5′UTRs in Saccharomyces cerevisiae: Development of a yUTR Calculator

(2018) Thomas Decoene et al.   ACS Synthetic Biology

Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria

(2018) Jennifer A. N. Brophy et al.   Nature Microbiology

CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming

(2018) Yanxia Liu et al.   Cell Stem Cell

Base editing: precision chemistry on the genome and transcriptome of living cells

(2018) Holly A. Rees et al.   NATURE REVIEWS GENETICS

Engineering the 5′ UTR-Mediated Regulation of Protein Abundance in Yeast Using Nucleotide Sequence Activity Relationships

(2018) Wentao Ding et al.   ACS Synthetic Biology

The punctilious RNA polymerase II core promoter

(2017) Long Vo ngoc et al.   GENES & DEVELOPMENT

Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences

(2017) Josh T. Cuperus et al.   GENOME RESEARCH

New inducible promoter for gene expression and synthetic biology in Yarrowia lipolytica

(2017) Marion Trassaert et al.   Microbial Cell Factories

SAGA Is a General Cofactor for RNA Polymerase II Transcription

(2017) Tiago Baptista et al.   MOLECULAR CELL

Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes

(2017) Gaelen T. Hess et al.   MOLECULAR CELL

Discovery of stimulation-responsive immune enhancers with CRISPR activation

(2017) Dimitre R. Simeonov et al.   NATURE

Transcription regulation by the Mediator complex

(2017) Julie Soutourina   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2017) Adam J. Brown et al.   NUCLEIC ACIDS RESEARCH

YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae

(2017) Miguel C Teixeira et al.   NUCLEIC ACIDS RESEARCH

Engineering canker-resistant plants through CRISPR/Cas9-targeted editing of the susceptibility gene CsLOB1 promoter in citrus

(2017) Aihong Peng et al.   PLANT BIOTECHNOLOGY JOURNAL

Construction and Characterization of Broad-Spectrum Promoters for Synthetic Biology

(2017) Sen Yang et al.   ACS Synthetic Biology

Engineered and Natural Promoters and Chromatin-Modifying Elements for Recombinant Protein Expression in CHO Cells

(2017) Nadiya Romanova et al.   Biotechnology Journal

Mammalian Transcription Factor Networks: Recent Advances in Interrogating Biological Complexity

(2017) Adam C. Wilkinson et al.   Cell Systems

Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors

(2016) Leonardo Morsut et al.   CELL

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex

(2016) Philip J. Robinson et al.   CELL

Tet-On Systems For Doxycycline-inducible Gene Expression

(2016) Atze T. Das et al.   CURRENT GENE THERAPY

Recombinant protein production from stable mammalian cell lines and pools

(2016) David L Hacker et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

Zooming in on Transcription Preinitiation

(2016) Kapil Gupta et al.   JOURNAL OF MOLECULAR BIOLOGY

Local and global regulation of transcription initiation in bacteria

(2016) Douglas F. Browning et al.   NATURE REVIEWS MICROBIOLOGY

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

(2016) Ivan Yevshin et al.   NUCLEIC ACIDS RESEARCH

Engineering of synthetic, stress-responsive yeast promoters

(2016) Arun S. Rajkumar et al.   NUCLEIC ACIDS RESEARCH

Engineered Promoters for Potent Transient Overexpression

(2016) Dan Y. Even et al.   PLoS One

Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection

(2016) Irina O. Vvedenskaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories

(2016) Yongjin J. Zhou et al.   Nature Communications

CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter

(2016) Samrat Roy Choudhury et al.   Oncotarget

Quantitative Analyses of Core Promoters Enable Precise Engineering of Regulated Gene Expression in Mammalian Cells

(2016) Christopher Ede et al.   ACS Synthetic Biology

Synthetic Core Promoters as Universal Parts for Fine-Tuning Expression in Different Yeast Species

(2016) Rui M. C. Portela et al.   ACS Synthetic Biology

A Tet-On Inducible System for Controlling CD19-Chimeric Antigen Receptor Expression upon Drug Administration

(2016) R. Sakemura et al.   Cancer Immunology Research

Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae

(2016) Anssi Rantasalo et al.   PLoS One

The core promoter: At the heart of gene expression

(2015) Yehuda M. Danino et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Development and physiological characterization of cellobiose-consumingYarrowia lipolytica

(2015) Stephan Lane et al.   BIOTECHNOLOGY AND BIOENGINEERING

Dynamic metabolic engineering: New strategies for developing responsive cell factories

(2015) Irene M. Brockman et al.   Biotechnology Journal

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

The development and characterization of synthetic minimal yeast promoters

(2015) Heidi Redden et al.   Nature Communications

A tetO Toolkit To Alter Expression of Genes in Saccharomyces cerevisiae

(2015) Josh T. Cuperus et al.   ACS Synthetic Biology

Engineering Promoter Architecture in Oleaginous Yeast Yarrowia lipolytica

(2015) Murtaza Shabbir Hussain et al.   ACS Synthetic Biology

Development of a Synthetic Malonyl-CoA Sensor in Saccharomyces cerevisiae for Intracellular Metabolite Monitoring and Genetic Screening

(2015) Sijin Li et al.   ACS Synthetic Biology

Dynamic metabolic engineering: New strategies for developing responsive cell factories

(2015) Irene M. Brockman et al.   Biotechnology Journal

Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective

(2014) Andrey Feklístov et al.   Annual Review of Microbiology

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch

(2014) Yuki Soma et al.   METABOLIC ENGINEERING

Carbon source dependent promoters in yeasts

(2014) Katrin Weinhandl et al.   Microbial Cell Factories

In pursuit of design principles of regulatory sequences

(2014) Michal Levo et al.   NATURE REVIEWS GENETICS

Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae

(2014) R. Scott McIsaac et al.   NUCLEIC ACIDS RESEARCH

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Design of synthetic yeast promoters via tuning of nucleosome architecture

(2014) Kathleen A. Curran et al.   Nature Communications

Isolation of fully synthetic promoters for high-level gene expression inCorynebacterium glutamicum

(2013) Sung Sun Yim et al.   BIOTECHNOLOGY AND BIOENGINEERING

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Molecular Mechanisms of Transcription Elongation in Archaea

(2013) Finn Werner   CHEMICAL REVIEWS

Genetic engineering of Yarrowia lipolytica for enhanced production of trans-10, cis-12 conjugated linoleic acid

(2013) Baixi Zhang et al.   Microbial Cell Factories

Engineering dynamic pathway regulation using stress-response promoters

(2013) Robert H Dahl et al.   NATURE BIOTECHNOLOGY

Determinants of nucleosome positioning

(2013) Kevin Struhl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

Sequence features of yeast and human core promoters that are predictive of maximal promoter activity

(2013) Shai Lubliner et al.   NUCLEIC ACIDS RESEARCH

Transient and Stable Expression of the Neurotensin Receptor NTS1: A Comparison of the Baculovirus-Insect Cell and the T-REx-293 Expression Systems

(2013) Su Xiao et al.   PLoS One

Architecture of an RNA Polymerase II Transcription Pre-Initiation Complex

(2013) K. Murakami et al.   SCIENCE

Human mitochondrial RNA polymerase: Structure–function, mechanism and inhibition

(2012) Jamie J. Arnold et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Controlling promoter strength and regulation inSaccharomyces cerevisiaeusing synthetic hybrid promoters

(2012) John Blazeck et al.   BIOTECHNOLOGY AND BIOENGINEERING

Promoter engineering: Recent advances in controlling transcription at the most fundamental level

(2012) John Blazeck et al.   Biotechnology Journal

Dynamic control of gene expression in Saccharomyces cerevisiae engineered for the production of plant sesquitepene α-santalene in a fed-batch mode

(2012) Gionata Scalcinati et al.   METABOLIC ENGINEERING

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

From gene switches to mammalian designer cells: present and future prospects

(2012) Simon Ausländer et al.   TRENDS IN BIOTECHNOLOGY

Tuning Gene Expression in Yarrowia lipolytica by a Hybrid Promoter Approach

(2011) John Blazeck et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq

(2011) J. Schodel et al.   BLOOD

Transcriptional Regulation inSaccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators

(2011) Steven Hahn et al.   GENETICS

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

(2011) C. G. de Boer et al.   NUCLEIC ACIDS RESEARCH

High-quality annotation of promoter regions for 913 bacterial genomes

(2010) Vetriselvi Rangannan et al.   BIOINFORMATICS

Heat shock factors: integrators of cell stress, development and lifespan

(2010) Malin Åkerfelt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Synthetic design of strong promoters

(2010) M. R. Schlabach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE