(Q42493050)

1 November 2017

Structural constraints in collaborative competition of transcription factors against the nucleosome (English)

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1 November 2017

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Georgette Moyle-Heyrman

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1

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1 November 2017

Hannah S Tims

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2

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1 November 2017

Jonathan Widom

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3

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1 November 2017

language of work or name

English

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publication date

29 July 2011

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1 November 2017

13

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Journal of Molecular Biology

inferred from page(s)

published in

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1 November 2017

412

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1 November 2017

4

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1 November 2017

634-646

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Dynamics of nucleosome invasion by DNA binding proteins

1 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Nucleosome accessibility governed by the dimer/tetramer interface

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Nucleosome-mediated cooperativity between transcription factors

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Different gene regulation strategies revealed by analysis of binding motifs

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Nucleosome disassembly intermediates characterized by single-molecule FRET.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Dynamics and function of compact nucleosome arrays

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

spFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Using DNA mechanics to predict in vitro nucleosome positions and formation energies.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Incorporating nucleosomes into thermodynamic models of transcription regulation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Two strategies for gene regulation by promoter nucleosomes

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Stopped-flow fluorescence resonance energy transfer for analysis of nucleosome dynamics

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

FRET-based methods to study ATP-dependent changes in chromatin structure

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Rapid spontaneous accessibility of nucleosomal DNA.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Interacting models of cooperative gene regulation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Global nucleosome occupancy in yeast

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Nucleosomes facilitate their own invasion

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Measurement of histone-DNA interaction free energy in nucleosomes

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Transcription regulation and animal diversity

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

The structure of DNA in the nucleosome core

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Collaborative competition mechanism for gene activation in vivo

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Identifying regulatory networks by combinatorial analysis of promoter elements

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Structure, dynamics, and function of chromatin in vitro

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Synergistic activation of transcription by physiologically unrelated transcription factors through cooperative DNA-binding

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

The enhanceosome and transcriptional synergy.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Nucleosome-mediated synergism between transcription factors on the mouse mammary tumor virus promoter

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Modulation of promoter occupancy by cooperative DNA binding and activation-domain function is a major determinant of transcriptional regulation by activators in vivo

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Fluorescence resonance energy transfer and nucleic acids

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Nonspecific DNA binding of genome-regulating proteins as a biological control mechanism: Measurement of DNA-bound Escherichia coli lac repressor in vivo

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

A lattice model for transcription factor access to nucleosomal DNA.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Nucleosome stability and accessibility of its DNA to proteins.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Cleavage of LexA repressor.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3534743

Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites

16 August 2018

1 reference

12 December 2020

Lifetime of the histone octamer studied by continuous-flow quasielastic light scattering: test of a model for nucleosome transcription

1 reference

12 December 2020

Kinetic accessibility of buried DNA sites in nucleosomes

1 reference

12 December 2020

Nucleosomal stability and dynamics vary significantly when viewed by internal versus terminal labels

1 reference

12 December 2020

A model for the LexA repressor DNA complex

1 reference

12 December 2020

Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation

1 reference

12 December 2020

A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites

1 reference

12 December 2020

New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning

1 reference

12 December 2020

Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein-protein interactions

1 reference

12 December 2020

Restriction enzymes as probes of nucleosome stability and dynamics

1 reference

12 December 2020

10.1016/J.JMB.2011.07.032

Identifiers

DOI

1 reference

1 November 2017

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1 November 2017

PubMed publication ID

21821044

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