Large-scale structural analysis of the core promoter in mammalian and plant genomes (Q24815290)

4 July 2017

title

Large-scale structural analysis of the core promoter in mammalian and plant genomes (English)

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4 July 2017

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4 July 2017

Yvan Saeys

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Kobe Florquin

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4 July 2017

Sven Degroeve

series ordinal

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4 July 2017

Pierre Rouzé

series ordinal

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4 July 2017

language of work or name

English

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publication date

27 July 2005

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4 July 2017

published in

Nucleic Acids Research

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4 July 2017

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4 July 2017

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4 July 2017

page(s)

4255-4264

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Genome wide analysis of Arabidopsis core promoters

4 July 2017

cites work

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28 September 2017

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Widespread selection for local RNA secondary structure in coding regions of bacterial genes

28 September 2017

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Computational approaches to identify promoters and cis-regulatory elements in plant genomes

28 September 2017

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28 September 2017

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28 September 2017

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The DPE, a core promoter element for transcription by RNA polymerase II.

28 September 2017

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28 September 2017

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Functional annotation of a full-length Arabidopsis cDNA collection

28 September 2017

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Long-range correlations between DNA bending sites: relation to the structure and dynamics of nucleosomes

28 September 2017

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Computational detection and location of transcription start sites in mammalian genomic DNA

28 September 2017

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28 September 2017

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Core promoters: active contributors to combinatorial gene regulation

28 September 2017

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Curved DNA in promoter sequences

28 September 2017

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An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled

28 September 2017

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A-form conformational motifs in ligand-bound DNA structures

28 September 2017

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Insertion site preferences of the P transposable element in Drosophila melanogaster

28 September 2017

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Analysis of large-scale gene expression data

28 September 2017

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Discovery and modeling of transcriptional regulatory regions

28 September 2017

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No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution

28 September 2017

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Exploring expression data: identification and analysis of coexpressed genes

28 September 2017

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CpG islands as genomic footprints of promoters that are associated with replication origins.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

DNA bending and wrapping around RNA polymerase: a "revolutionary" model describing transcriptional mechanisms.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

DNA structure in human RNA polymerase II promoters

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Thermal stability of 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=1181242

DNA bending: the prevalence of kinkiness and the virtues of normality

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot 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=1181242

Eukaryotic Promoter Recognition

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Distal enhancer regulation by promoter derepression in topologically constrained DNA in vitro

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Core promoters and transcriptional control

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Common DNA structural features exhibited by eukaryotic ribosomal gene promoters.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in 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=1181242

Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter 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=1181242

A-Tract bending: insights into experimental structures by computational models

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Helix bending as a factor in protein/DNA recognition.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Clues and consequences of DNA bending in transcription

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Sequence periodicities in chicken nucleosome core DNA.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Content analysis of the core promoter region of human genes.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

The role of DNA deformation energy at individual base steps for the identification of DNA-protein binding sites

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

DNA sequence and structure: direct and indirect recognition in protein-DNA binding

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Adaptive quality-based clustering of gene expression profiles.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Statistical mechanical simulation of polymeric DNA melting with MELTSIM.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Computational applications of DNA structural scales.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Translational positioning of nucleosomes on DNA: the role of sequence-dependent isotropic DNA bending stiffness.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181242

Computer model for recognition of functional transcription start sites in RNA polymerase II promoters of vertebrates

28 November 2018

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12 December 2020

DNA bends in TATA-binding protein-TATA complexes in solution are DNA sequence-dependent

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12 December 2020

Gene-associated CpG islands in plants as revealed by analyses of genomic sequences

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12 December 2020

B-DNA twisting correlates with base-pair morphology.

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12 December 2020

Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena

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12 December 2020

Polarized electronic spectra of Z-DNA single crystals

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12 December 2020

DNA structural variation affects complex formation and promoter melting in ribosomal RNA transcription

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12 December 2020

Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition

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12 December 2020

Identifiers

DOI

10.1093/NAR/GKI737

1 reference

4 July 2017

1 reference

4 July 2017

1 reference