Unraveling determinants of transcription factor binding outside the core binding site (Q35793479)

10 August 2017

title

Unraveling determinants of transcription factor binding outside the core binding site (English)

1 reference

Corrigendum: Unraveling determinants of transcription factor binding outside the core binding site

10 August 2017

corrigendum / erratum

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author

Eran Segal

10

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10 August 2017

Michal Levo

1

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10 August 2017

Einat Zalckvar

2

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10 August 2017

Eilon Sharon

3

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10 August 2017

Ana Carolina Dantas Machado

4

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10 August 2017

Yael Kalma

5

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10 August 2017

Maya Lotam-Pompan

6

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10 August 2017

Adina Weinberger

7

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10 August 2017

Zohar Yakhini

8

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10 August 2017

Remo Rohs

9

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10 August 2017

publication date

11 March 2015

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10 August 2017

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10 August 2017

volume

25

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10 August 2017

issue

7

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10 August 2017

page(s)

1018-1029

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Absence of a simple code: how transcription factors read the genome

10 August 2017

cites work

1 reference

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12 July 2018

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TFBSshape: a motif database for DNA shape features of transcription factor binding sites

12 July 2018

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

12 July 2018

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

12 July 2018

1 reference

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

12 July 2018

1 reference

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Determinants of nucleosome positioning

12 July 2018

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High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

12 July 2018

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Probing allostery through DNA

12 July 2018

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DNA-binding specificities of human transcription factors

12 July 2018

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Disentangling the many layers of eukaryotic transcriptional regulation

12 July 2018

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

12 July 2018

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

12 July 2018

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Accurate prediction of inducible transcription factor binding intensities in vivo

12 July 2018

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

12 July 2018

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

12 July 2018

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Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators.

12 July 2018

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Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits.

12 July 2018

1 reference

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

12 July 2018

1 reference

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

12 July 2018

1 reference

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Chromatin Landscape Dictates HSF Binding to Target DNA Elements

12 July 2018

1 reference

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Regularization Paths for Generalized Linear Models via Coordinate Descent

12 July 2018

1 reference

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

12 July 2018

1 reference

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Origins of specificity in protein-DNA recognition.

12 July 2018

1 reference

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Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

12 July 2018

1 reference

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The role of DNA shape in protein-DNA recognition

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484385

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484385

From DNA sequence to transcriptional behaviour: a quantitative approach

12 July 2018

1 reference

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Incorporating nucleosomes into thermodynamic models of transcription regulation

12 July 2018

1 reference

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

12 July 2018

1 reference

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

12 July 2018

1 reference

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

12 July 2018

1 reference

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The DNA-encoded nucleosome organization of a eukaryotic genome

12 July 2018

1 reference

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Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

12 July 2018

1 reference

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Connecting protein structure with predictions of regulatory sites.

12 July 2018

1 reference

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

12 July 2018

1 reference

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

12 July 2018

1 reference

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Genetic regulatory mechanisms in the synthesis of proteins

12 July 2018

2 references

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12 July 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484385

Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484385

Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484385

Poly(dA).poly(dT) is a B-type double helix with a distinctively narrow minor groove

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484385

Saturation mutagenesis of the yeast his3 regulatory site: requirements for transcriptional induction and for binding by GCN4 activator protein

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484385

Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484385

DNA recognition by GAL4: structure of a protein-DNA complex.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484385

The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484385

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4484385

Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure

25 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25762553

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.185033.114

1 reference

10 August 2017

1 reference

10 August 2017

1 reference