A genomic code for nucleosome positioning (Q24650238)

https://www.ncbi.nlm.nih.gov/pubmed/?term=16862119

Eran Segal

1

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author name string

Yvonne Fondufe-Mittendorf

2

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Lingyi Chen

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AnnChristine Thåström

4

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Yair Field

5

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Irene K Moore

6

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Ji-Ping Z Wang

7

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Jonathan Widom

Improved alignment of nucleosome DNA sequences using a mixture model

8

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language of work or name

English

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publication date

17 August 2006

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published in

Nature

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volume

442

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page(s)

772-8

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issue

7104

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cites work

1 reference

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Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning

7 April 2017

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Global nucleosome occupancy in yeast

7 April 2017

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Gene ontology: tool for the unification of biology

7 April 2017

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Translating the Histone Code

7 April 2017

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Global analysis of protein expression in yeast

7 April 2017

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Genomic expression programs in the response of yeast cells to environmental changes

7 April 2017

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Transcriptional regulatory code of a eukaryotic genome

7 April 2017

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Functional discovery via a compendium of expression profiles

7 April 2017

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Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization

7 April 2017

1 reference

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A tutorial on hidden Markov models and selected applications in speech recognition

7 April 2017

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Crossref

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Integrated genomic and proteomic analyses of a systematically perturbed metabolic network

22 April 2017

1 reference

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Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Genome-scale identification of nucleosome positions in S. cerevisiae

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Chromatin remodeling complexes: strength in diversity, precision through specialization

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Global role of TATA box-binding protein recruitment to promoters in mediating gene expression profiles

28 September 2017

1 reference

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The structure of DNA in the nucleosome core

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Identification of the binding sites of regulatory proteins in bacterial genomes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Role of DNA sequence in nucleosome stability and dynamics

28 September 2017

1 reference

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating type locus HMLalpha

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Chromatin structure modulation in Saccharomyces cerevisiae by centromere and promoter factor 1.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Sequence-dependent deformational anisotropy of chromatin DNA.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Nucleosomes are positioned with base pair precision adjacent to the alpha 2 operator in Saccharomyces cerevisiae

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Global position and recruitment of HATs and HDACs in the yeast genome.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Nucleosome structure of the yeast CHA1 promoter: analysis of activation-dependent chromatin remodeling of an RNA-polymerase-II-transcribed gene in TBP and RNA pol II mutants defective in vivo in response to acidic activators.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Cell type-specific chromatin organization of the region that governs directionality of yeast mating type switching

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Sequence periodicities in chicken nucleosome core DNA.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Evidence for nucleosome depletion at active regulatory regions genome-wide

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

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

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Identification and distinct regulation of yeast TATA box-containing genes.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Nucleosome structure and repair of N-methylpurines in the GAL1-10 genes of Saccharomyces cerevisiae

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2623244

Identification and characterization of genomic nucleosome-positioning sequences

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16862119

12 December 2020

inferred from PubMed ID database lookup

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16862119

12 December 2020

inferred from PubMed ID database lookup

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16862119

12 December 2020

inferred from PubMed ID database lookup

1 reference

https://api.crossref.org/works/10.1038%2FNATURE04979

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1038/NATURE04979

1 reference

Dimensions Publication ID

396886

1004695015

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396886

1 reference

1 reference

1 reference