(Q34116983)

31 July 2017

title

Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites (English)

1 reference

31 July 2017

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Joseph T Wade

1

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George M. Church

object named as

George M Church

series ordinal

3

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author name string

Nikos B Reppas

series ordinal

2

1 reference

31 July 2017

Kevin Struhl

series ordinal

4

1 reference

31 July 2017

publication date

1 November 2005

1 reference

31 July 2017

1 reference

31 July 2017

volume

19

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31 July 2017

issue

21

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31 July 2017

page(s)

2619-2630

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Spatial arrangement and macrodomain organization of bacterial chromosomes.

31 July 2017

cites work

1 reference

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5 July 2018

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5 July 2018

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Association of RNA polymerase with transcribed regions in Escherichia coli

5 July 2018

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Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays.

5 July 2018

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The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis

5 July 2018

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Global nucleosome occupancy in yeast

5 July 2018

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Transcriptional regulatory code of a eukaryotic genome

5 July 2018

1 reference

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Topological domain structure of the Escherichia coli chromosome

5 July 2018

1 reference

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WebLogo: A Sequence Logo Generator

5 July 2018

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Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

CREB binds to multiple loci on human chromosome 22.

5 July 2018

1 reference

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Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs

5 July 2018

1 reference

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The Spo0A regulon of Bacillus subtilis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Distribution of NF-kappaB-binding sites across human chromosome 22

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Regulation of gene expression by histone-like proteins in bacteria.

5 July 2018

1 reference

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Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis

5 July 2018

1 reference

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Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

A simple mechanism for co-dependence on two activators at an Escherichia coli promoter

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Histone acetylation at promoters is differentially affected by specific activators and repressors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

RNA expression analysis using a 30 base pair resolution Escherichia coli genome array

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Preferential accessibility of the yeast his3 promoter is determined by a general property of the DNA sequence, not by specific elements

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Identification of additional genes belonging to the LexA regulon in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Fundamentally different logic of gene regulation in eukaryotes and prokaryotes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Alteration of nucleosome structure as a mechanism of transcriptional regulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

The SOS regulatory system of Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Inducible DNA repair systems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Analysis of the regulatory region of the protease III (ptr) gene of Escherichia coli K-12.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Regulated expression of endonuclease EcoRI in Saccharomyces cerevisiae: nuclear entry and biological consequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Eukaryotic proteins expressed in Escherichia coli: An improved thrombin cleavage and purification procedure of fusion proteins with glutathione S-transferase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Evidence for nucleosome depletion at active regulatory regions genome-wide

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Removal of promoter nucleosomes by disassembly rather than sliding in vivo

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

DNA array analysis of gene expression in response to UV irradiation in Escherichia coli

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

Nucleosomes unfold completely at a transcriptionally active promoter

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1276735

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

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16264194

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GAD.1355605

1 reference

31 July 2017

1 reference

31 July 2017

1 reference