Nucleosome-mediated cooperativity between transcription factors (Q34450175)

2 August 2017

title

Nucleosome-mediated cooperativity between transcription factors (English)

1 reference

2 August 2017

Leonid A Mirny

1

1 reference

2 August 2017

language of work or name

English

0 references

publication date

13 December 2010

1 reference

2 August 2017

number of pages

6

1 reference

Proceedings of the National Academy of Sciences of the United States of America

inferred from page(s)

published in

1 reference

2 August 2017

volume

107

1 reference

2 August 2017

issue

52

1 reference

2 August 2017

page(s)

22534-22539

1 reference

High nucleosome occupancy is encoded at human regulatory sequences

2 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

G+C content dominates intrinsic nucleosome occupancy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Different gene regulation strategies revealed by analysis of binding motifs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Incorporating nucleosomes into thermodynamic models of transcription regulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

The DNA-encoded nucleosome organization of a eukaryotic genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

A quantitative model of transcription factor-activated gene expression

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Spontaneous access to DNA target sites in folded chromatin fibers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Chromatin decouples promoter threshold from dynamic range

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Ultrasensitive gene regulation by positive feedback loops in nucleosome modification

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Nucleosome organization in the Drosophila genome.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Interaction of the glucocorticoid receptor with the chromatin landscape

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

A systems view of Drosophila segmentation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

A high-resolution atlas of nucleosome occupancy in yeast

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Nucleosome positioning signals in genomic DNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

An Atomic Model of the Interferon-β Enhanceosome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

The role of chromatin during transcription

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Large-scale turnover of functional transcription factor binding sites in Drosophila

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

A genomic code for nucleosome positioning

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

DNA looping: the consequences and its control.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Allosteric mechanisms of signal transduction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Transcriptional regulation by the numbers: models.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Rapid spontaneous accessibility of nucleosomal DNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Discovery of functional noncoding elements by digital analysis of chromatin structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Adaptive evolution of transcription factor binding sites

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Transcriptional control in the segmentation gene network of Drosophila

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Nucleosomes facilitate their own invasion

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Getting into chromatin: how do transcription factors get past the histones?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Collaborative competition mechanism for gene activation in vivo

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Targeting gene expression to the head: the Drosophila orthodenticle gene is a direct target of the Bicoid morphogen.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

The eve stripe 2 enhancer employs multiple modes of transcriptional synergy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

A single GAL4 dimer can maximally activate transcription under physiological conditions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

The pitch of chromatin DNA is reflected in its nucleotide sequence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Synergistic activation of transcription by multiple binding sites for NF-kappa B even in absence of co-operative factor binding to DNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

How different eukaryotic transcriptional activators can cooperate promiscuously.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Synergistic transcriptional enhancement does not depend on the number of acidic activation domains bound to the promoter

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3012490

Evidence for nucleosome depletion at active regulatory regions genome-wide

6 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0913805107

Dynamics of Replication-Independent Histone Turnover in Budding Yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0913805107

A probabilistic method to detect regulatory modules

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0913805107

Alternative models for describing the acid unfolding of the apomyoglobin folding intermediate

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0913805107

Comparative binding of p53 to its promoter and DNA recognition elements.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0913805107

Automated image analysis of protein localization in budding yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0913805107

Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0913805107

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

21 January 2018

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

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

1 reference

12 December 2020

Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast

1 reference

12 December 2020

Nucleosome positions predicted through comparative genomics

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0913805107

1 reference

2 August 2017

0 references

1 reference

1 reference

2 August 2017

1 reference