Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy (Q36280002)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

title

Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json

Correction for van der Heijden et al., Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy

11 February 2020

corrigendum / erratum

0 references

author

Joke F A van Vugt

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

Colin Logie

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

author name string

Thijn van der Heijden

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

John van Noort

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

language of work or name

English

0 references

publication date

20 August 2012

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json

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

11 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

volume

109

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

issue

38

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

page(s)

E2514-22

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json

Subunit organization of the human INO80 chromatin remodeling complex: an evolutionarily conserved core complex catalyzes ATP-dependent nucleosome remodeling

11 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Mechanism(s) of SWI/SNF-induced nucleosome mobilization

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Nucleosome accessibility governed by the dimer/tetramer interface

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Crystal structures of nucleosome core particles containing the '601' strong positioning sequence

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Nucleosome positioning by genomic excluding-energy barriers

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

10 years of tension on chromatin: results from single molecule force spectroscopy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Nucleosome positioning and gene regulation: advances through genomics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

The DNA-encoded nucleosome organization of a eukaryotic genome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

DNA physical properties determine nucleosome occupancy from yeast to fly.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

nuScore: a web-interface for nucleosome positioning predictions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Nucleosome organization in the Drosophila genome.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Genomic sequence is highly predictive of local nucleosome depletion

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Single-pair FRET microscopy reveals mononucleosome dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

The ins and outs of ATP-dependent chromatin remodeling in budding yeast: biophysical and proteomic perspectives.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

A genomic code for nucleosome positioning

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Measurement of histone-DNA interaction free energy in nucleosomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Dynamic Properties of Nucleosomes during Thermal and ATP-Driven Mobilization

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Nucleosome Repositioning via Loop Formation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

SWI/SNF unwraps, slides, and rewraps the nucleosome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Role of DNA sequence in nucleosome stability and dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Unique translational positioning of nucleosomes on synthetic DNAs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Crystal structure of the nucleosome core particle at 2.8 A resolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

The effect of nucleosome phasing sequences and DNA topology on nucleosome spacing.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Assembly of regularly spaced nucleosome arrays by Drosophila chromatin assembly factor 1 and a 56-kDa histone-binding protein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Entropic elasticity of lambda-phage DNA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

The transactivation domain of Pho4 is required for nucleosome disruption at the PHO5 promoter.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Structural features of a phased nucleosome core particle

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Nucleosome reconstitution on plasmid-inserted poly(dA) . poly(dT)

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Nucleotide sequence of a 5S ribosomal RNA gene in the sea urchin Lytechinus variegatus

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Transcriptionally active SV40 minichromosomes are restriction enzyme sensitive and contain a nucleosome-free origin region

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Nucleosome positioning is determined by the (H3-H4)2 tetramer

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Chromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Nucleosome sequence preferences influence in vivo nucleosome organization

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Direct measurements of the nucleosome-forming preferences of periodic DNA motifs challenge established models

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

DNA bending and its relation to nucleosome positioning.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Sequence periodicities in chicken nucleosome core DNA.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Are nucleosome positions in vivo primarily determined by histone-DNA sequence preferences?

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Dynamics of ATP-dependent chromatin assembly by ACF.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Solution of Percus's equation for the density of hard rods in an external field.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

TGGA repeats impair nucleosome formation.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458375

Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.".

22 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1205659109

Chromatin Fiber Folding: Requirement for the Histone H4 N-terminal Tail

21 January 2018

1 reference

12 December 2020

Chromatin Dynamics: Nucleosomes go Mobile through Twist Defects

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

Thermodynamics of intragenic nucleosome ordering

1 reference

12 December 2020

Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae

1 reference

12 December 2020

A preoccupied position on nucleosomes

1 reference

12 December 2020

Homogeneous reconstituted oligonucleosomes, evidence for salt-dependent folding in the absence of histone H1

1 reference

12 December 2020

Distinguishing between mechanisms of eukaryotic transcriptional activation with bacteriophage T7 RNA polymerase

1 reference

12 December 2020

A 200 base pair region at the 5' end of the chicken adult beta-globin gene is accessible to nuclease digestion

1 reference

12 December 2020

A low resolution structure for the histone core of the nucleosome

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

Identification and characterization of genomic nucleosome-positioning sequences

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

Identifiers

DOI

10.1073/PNAS.1205659109

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json

11 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22908247%20AND%20SRC:MED&resulttype=core&format=json