Exploring the DNA-recognition potential of homeodomains (Q34249275)

31 July 2017

title

Exploring the DNA-recognition potential of homeodomains (English)

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31 July 2017

Stephanie W Chu

1

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31 July 2017

Marcus B Noyes

2

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31 July 2017

Ryan G Christensen

3

1 reference

31 July 2017

Brian G Pierce

4

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31 July 2017

Lihua J Zhu

5

1 reference

31 July 2017

Zhiping Weng

6

1 reference

31 July 2017

Gary D Stormo

7

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31 July 2017

Scot A Wolfe

8

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31 July 2017

publication date

26 April 2012

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31 July 2017

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31 July 2017

volume

22

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31 July 2017

issue

10

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31 July 2017

page(s)

1889-1898

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Recognition models to predict DNA-binding specificities of homeodomain proteins

31 July 2017

cites work

1 reference

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

28 July 2018

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Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish

28 July 2018

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Quantitative analysis demonstrates most transcription factors require only simple models of specificity

28 July 2018

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An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces

28 July 2018

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Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers.

28 July 2018

1 reference

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28 July 2018

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Genome editing with engineered zinc finger nucleases

28 July 2018

1 reference

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Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function

28 July 2018

1 reference

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Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

28 July 2018

1 reference

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Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination

28 July 2018

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PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice

28 July 2018

1 reference

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Hox specificity unique roles for cofactors and collaborators

28 July 2018

1 reference

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Diversity and complexity in DNA recognition by transcription factors

28 July 2018

1 reference

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Adaptive evolution in zinc finger transcription factors

28 July 2018

1 reference

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Predicting the binding preference of transcription factors to individual DNA k-mers.

28 July 2018

1 reference

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Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Unexpected failure rates for modular assembly of engineered zinc fingers

28 July 2018

1 reference

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A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Inferring protein-DNA dependencies using motif alignments and mutual information.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Cross-species annotation of basic leucine zipper factor interactions: Insight into the evolution of closed interaction networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Ab initio prediction of transcription factor targets using structural knowledge

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Crystal structure of the Msx-1 homeodomain/DNA complex

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Exploring the role of glutamine 50 in the homeodomain-DNA interface: crystal structure of engrailed (Gln50 --> ala) complex at 2.0 A

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

DNA-binding sequence of the human prostate-specific homeodomain protein NKX3.1.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Mutational analysis of the engrailed homeodomain recognition helix by phage display

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

A molecular code dictates sequence-specific DNA recognition by homeodomains.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

A humanized system for pharmacologic control of gene expression

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Differential DNA-binding specificity of the engrailed homeodomain: the role of residue 50.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

The degree of variation in DNA sequence recognition among four Drosophila homeotic proteins.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Understanding the homeodomain

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

A single amino acid can determine the DNA binding specificity of homeodomain proteins.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

The interaction with DNA of wild-type and mutant fushi tarazu homeodomains

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

A Genetic Model for Interaction of the Homeodomain Recognition Helix with DNA

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Homeodomain subtypes and functional diversity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Origins of specificity in protein-DNA recognition.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

The role of DNA shape in protein-DNA recognition

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

A census of human transcription factors: function, expression and evolution

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Predicting DNA recognition by Cys2His2 zinc finger proteins

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Quantitative analysis of protein-RNA interactions by gel mobility shift

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Probabilistic code for DNA recognition by proteins of the EGR family.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Homeodomain determinants of major groove recognition

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Specificity of minor-groove and major-groove interactions in a homeodomain-DNA complex.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3460184

Structure-based design of transcription factors

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22539651

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Lac repressor binding to non-operator DNA: detailed studies and a comparison of eequilibrium and rate competition methods

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22539651

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.139014.112

1 reference

31 July 2017

1 reference

31 July 2017

1 reference