In pursuit of design principles of regulatory sequences (Q38218965)

31 August 2017

In pursuit of design principles of regulatory sequences (English)

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31 August 2017

2

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31 August 2017

Michal Levo

1

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31 August 2017

10 June 2014

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31 August 2017

Nature Reviews Genetics

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31 August 2017

15

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31 August 2017

7

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31 August 2017

453-468

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https://scigraph.springernature.com/pub.10.1038/nrg3684

31 August 2017

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cites work

Genetic regulatory mechanisms in the synthesis of proteins

2 references

https://pubmed.ncbi.nlm.nih.gov/24913666

21 January 2018

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Transcriptional enhancers in animal development and evolution

1 reference

Enhancers: from developmental genetics to the genetics of common human disease.

21 January 2018

1 reference

Functional anatomy of distant-acting mammalian enhancers

21 January 2018

1 reference

Systematic localization of common disease-associated variation in regulatory DNA

21 January 2018

1 reference

Genomic views of distant-acting enhancers

21 January 2018

1 reference

Transcriptional enhancers in development and disease

21 January 2018

1 reference

Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

21 January 2018

1 reference

Lessons from functional analysis of genome-wide association studies

21 January 2018

1 reference

Yeast transcriptional regulatory mechanisms

21 January 2018

1 reference

Transcriptional activation by recruitment

21 January 2018

1 reference

Transcriptional regulatory code of a eukaryotic genome

21 January 2018

1 reference

A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces

21 January 2018

1 reference

Genome-wide mapping of in vivo protein-DNA interactions

21 January 2018

1 reference

Sequence and chromatin determinants of cell-type-specific transcription factor binding

21 January 2018

1 reference

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution

21 January 2018

1 reference

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

21 January 2018

1 reference

An expansive human regulatory lexicon encoded in transcription factor footprints

21 January 2018

1 reference

Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function

21 January 2018

1 reference

Measuring chromatin interaction dynamics on the second time scale at single-copy genes

21 January 2018

1 reference

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

21 January 2018

1 reference

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

21 January 2018

1 reference

Inferring binding energies from selected binding sites

21 January 2018

1 reference

DNA-binding specificities of human transcription factors

21 January 2018

1 reference

A systems approach to measuring the binding energy landscapes of transcription factors

21 January 2018

1 reference

De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis

21 January 2018

1 reference

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument

21 January 2018

1 reference

A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters

21 January 2018

1 reference

High-resolution DNA-binding specificity analysis of yeast transcription factors

21 January 2018

1 reference

A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors

21 January 2018

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Diversity and complexity in DNA recognition by transcription factors

21 January 2018

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A quantitative protein interaction network for the ErbB receptors using protein microarrays

21 January 2018

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Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex.

21 January 2018

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An integrated encyclopedia of DNA elements in the human genome

21 January 2018

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

21 January 2018

1 reference

Mapping the fine structure of a eukaryotic promoter input-output function

21 January 2018

1 reference

Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants

21 January 2018

1 reference

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

21 January 2018

1 reference

Predicting expression patterns from regulatory sequence in Drosophila segmentation.

21 January 2018

1 reference

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

21 January 2018

1 reference

Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.

21 January 2018

1 reference

Accurate prediction of inducible transcription factor binding intensities in vivo

21 January 2018

1 reference

Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4.

21 January 2018

1 reference

Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape

21 January 2018

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Master regulatory GATA transcription factors: mechanistic principles and emerging links to hematologic malignancies

21 January 2018

1 reference

Protein-DNA binding: complexities and multi-protein codes

21 January 2018

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Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins

21 January 2018

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Disentangling the many layers of eukaryotic transcriptional regulation

21 January 2018

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Animal transcription networks as highly connected, quantitative continua

21 January 2018

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Transcription factors: from enhancer binding to developmental control

21 January 2018

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Organization of developmental enhancers in the Drosophila embryo

21 January 2018

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Coordinate enhancers share common organizational features in the Drosophila genome

21 January 2018

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The words of the regulatory code are arranged in a variable manner in highly conserved enhancers.

21 January 2018

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Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers

21 January 2018

1 reference

Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation

21 January 2018

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Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

21 January 2018

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Combinatorial binding predicts spatio-temporal cis-regulatory activity

21 January 2018

1 reference

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

21 January 2018

1 reference

Extensive low-affinity transcriptional interactions in the yeast genome

21 January 2018

1 reference

Sparkling insights into enhancer structure, function, and evolution

21 January 2018

1 reference

The cis-regulatory logic of Hedgehog gradient responses: key roles for gli binding affinity, competition, and cooperativity

21 January 2018

1 reference

Morphogen gradients: from generation to interpretation

21 January 2018

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Pioneer transcription factors: establishing competence for gene expression

21 January 2018

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Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?

21 January 2018

1 reference

Role of architecture in the function and specificity of two Notch-regulated transcriptional enhancer modules

21 January 2018

1 reference

Immunity regulatory DNAs share common organizational features in Drosophila

21 January 2018

1 reference

Evolution acts on enhancer organization to fine-tune gradient threshold readouts

21 January 2018

1 reference

Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer

21 January 2018

1 reference

An Atomic Model of the Interferon-β Enhanceosome

21 January 2018

1 reference

Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome

21 January 2018

1 reference

A transcription factor collective defines cardiac cell fate and reflects lineage history

21 January 2018

1 reference

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

21 January 2018

1 reference

Massively parallel functional dissection of mammalian enhancers in vivo

21 January 2018

1 reference

Complex effects of nucleotide variants in a mammalian cis-regulatory element.

21 January 2018

1 reference

Mechanisms of transcriptional precision in animal development.

21 January 2018

1 reference

High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints

21 January 2018

1 reference

Two strategies for gene regulation by promoter nucleosomes

21 January 2018

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Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

21 January 2018

1 reference

Genome-wide structure and organization of eukaryotic pre-initiation complexes

21 January 2018

1 reference

Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun.

21 January 2018

1 reference

Flanking sequence composition differentially affects the binding and functional characteristics of glucocorticoid receptor homo- and heterodimers

21 January 2018

1 reference

Selected base sequence outside the target binding site of zinc finger protein Sp1.

21 January 2018

1 reference

Differential binding of the related transcription factors Pho4 and Cbf1 can tune the sensitivity of promoters to different levels of an induction signal.

21 January 2018

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Origins of specificity in protein-DNA recognition.

21 January 2018

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Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome

21 January 2018

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Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

21 January 2018

1 reference

Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development

21 January 2018

1 reference

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns.

21 January 2018

1 reference

Determinants of nucleosome positioning

21 January 2018

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The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome

21 January 2018

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G+C content dominates intrinsic nucleosome occupancy

21 January 2018

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A nucleosome-guided map of transcription factor binding sites in yeast

21 January 2018

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Incorporating nucleosomes into thermodynamic models of transcription regulation

21 January 2018

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An ensemble model of competitive multi-factor binding of the genome

21 January 2018

1 reference

A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites.

21 January 2018

1 reference

Poly(dA:dT) tracts: major determinants of nucleosome organization

21 January 2018

1 reference

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

21 January 2018

1 reference

High nucleosome occupancy is encoded at human regulatory sequences

21 January 2018

1 reference

Nucleosome-driven transcription factor binding and gene regulation

21 January 2018

1 reference

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks.

21 January 2018

1 reference

DNase I sensitivity QTLs are a major determinant of human expression variation

21 January 2018

1 reference

Linking disease associations with regulatory information in the human genome

21 January 2018

1 reference

Dissecting the regulatory architecture of gene expression QTLs

21 January 2018

1 reference

Learning a prior on regulatory potential from eQTL data

21 January 2018

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Robust prediction of expression differences among human individuals using only genotype information

21 January 2018

1 reference

Transcriptional regulation by the numbers: models.

21 January 2018

1 reference

From DNA sequence to transcriptional behaviour: a quantitative approach

21 January 2018

1 reference

Perspectives on the RNA polymerase II core promoter

21 January 2018

1 reference

TATA is a modular component of synthetic promoters

21 January 2018

1 reference

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

21 January 2018

1 reference

Erratum: Regulation of cytoplasmic mRNA decay

21 January 2018

1 reference

Alternative splicing: a pivotal step between eukaryotic transcription and translation

21 January 2018

1 reference

Ribosome profiling: new views of translation, from single codons to genome scale

21 January 2018

1 reference

Noncoding transcription at enhancers: general principles and functional models

21 January 2018

1 reference

Enhancer RNAs and regulated transcriptional programs

21 January 2018

1 reference

An atlas of active enhancers across human cell types and tissues

21 January 2018

1 reference

A tunable zinc finger-based framework for Boolean logic computation in mammalian cells

21 January 2018

1 reference

Development and characterization of AND-gate dynamic controllers with a modular synthetic GAL1 core promoter in Saccharomyces cerevisiae

21 January 2018

1 reference

Synergistic and tunable human gene activation by combinations of synthetic transcription factors

21 January 2018

1 reference

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

21 January 2018

1 reference

High-resolution mapping of transcription factor binding sites on native chromatin

21 January 2018

1 reference

Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH.

21 January 2018

1 reference

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

21 January 2018

1 reference

Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo

21 January 2018

1 reference

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

21 January 2018

1 reference

Histone modifications at human enhancers reflect global cell-type-specific gene expression

21 January 2018

1 reference

Mapping and analysis of chromatin state dynamics in nine human cell types

21 January 2018

1 reference

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.

21 January 2018

1 reference

Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay

21 January 2018

1 reference

A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster

21 January 2018

1 reference

A GAL4-driver line resource for Drosophila neurobiology

21 January 2018

1 reference

A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS.

21 January 2018

1 reference

Genome-wide quantitative enhancer activity maps identified by STARR-seq

21 January 2018

1 reference

Function-based identification of mammalian enhancers using site-specific integration

21 January 2018

1 reference

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

21 January 2018

1 reference

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

21 January 2018

1 reference

Composability of regulatory sequences controlling transcription and translation in Escherichia coli

21 January 2018

1 reference

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

21 January 2018

1 reference

Long-range control of gene expression: emerging mechanisms and disruption in disease

21 January 2018

1 reference

The hierarchy of the 3D genome

21 January 2018

1 reference

Genome organization and long-range regulation of gene expression by enhancers

21 January 2018

1 reference

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

21 January 2018

1 reference

Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations

21 January 2018

1 reference

Architectural protein subclasses shape 3D organization of genomes during lineage commitment

21 January 2018

1 reference

Shadow enhancers: frequently asked questions about distributed cis-regulatory information and enhancer redundancy

21 January 2018

1 reference

Determining the specificity of protein-DNA interactions

21 January 2018

1 reference

Functional architecture and evolution of transcriptional elements that drive gene coexpression

31 March 2020

1 reference

A map of nucleosome positions in yeast at base-pair resolution

31 March 2020

1 reference

Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure.

31 March 2020

1 reference

Regulation of cytoplasmic mRNA decay

31 March 2020

1 reference

The eve stripe 2 enhancer employs multiple modes of transcriptional synergy

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24913666

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NRG3684

1 reference

PubMed ID

24913666

Dimensions Publication ID

31 August 2017

0 references

1 reference

PubMed ID

24913666