(Q37593221)

21 August 2017

High-resolution mapping of transcription factor binding sites on native chromatin (English)

1 reference

21 August 2017

Sivakanthan Kasinathan

Sivakanthan Kasinathan

1

0 references

Guillermo A Orsi

Guillermo A Orsi

2

0 references

Gabriel E Zentner

Gabriel E Zentner

3

0 references

Kami Ahmad

4

Kami Ahmad

1 reference

21 August 2017

5

Steven Henikoff

1 reference

21 August 2017

15 December 2013

1 reference

21 August 2017

1 reference

21 August 2017

11

1 reference

21 August 2017

2

1 reference

21 August 2017

203-209

1 reference

https://scigraph.springernature.com/pub.10.1038/nmeth.2766

21 August 2017

0 references

cites work

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Measuring chromatin interaction dynamics on the second time scale at single-copy genes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

ISWI and CHD chromatin remodelers bind promoters but act in gene bodies

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Limitations and possibilities of low cell number ChIP-seq.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

An expansive human regulatory lexicon encoded in transcription factor footprints

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Epigenome characterization at single base-pair resolution.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Identification of functional elements and regulatory circuits by Drosophila modENCODE

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

23 August 2017

Transcription dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Mapping accessible chromatin regions using Sono-Seq

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Impact of chromatin structures on DNA processing for genomic analyses

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Mechanisms that specify promoter nucleosome location and identity

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Where does mediator bind in vivo?

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Genome-wide profiling of salt fractions maps physical properties of chromatin

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Analysis of transcription factor interactions in osteoblasts using competitive chromatin immunoprecipitation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Genome-wide mapping of in vivo protein-DNA interactions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Characteristic low density and shear sensitivity of cross-linked chromatin containing polycomb complexes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Transcriptional regulatory code of a eukaryotic genome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Immunoprecipitation of native chromatin: NChIP.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Pipsqueak and GAGA factor act in concert as partners at homeotic and many other loci

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Discovery of regulatory elements by a computational method for phylogenetic footprinting

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Genome-wide location and function of DNA binding proteins

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

DNA binding sites: representation and discovery

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

GAGA factor binding to DNA via a single trinucleotide sequence element

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Histone H4 acetylation distinguishes coding regions of the human genome from heterochromatin in a differentiation-dependent but transcription-independent manner.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Structure-function analysis of the DNA binding domain of Saccharomyces cerevisiae ABF1.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Isolation of cDNAs encoding the Drosophila GAGA transcription factor

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

REB1, a yeast DNA-binding protein with many targets, is essential for growth and bears some resemblance to the oncogene myb.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

DNAase footprinting a simple method for the detection of protein-DNA binding specificity

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Surveying the epigenomic landscape, one base at a time

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Thermodynamics of ligand-nucleic acid interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

Formaldehyde cross-linking for studying nucleosomal dynamics

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3929178

The specificity of protein-DNA crosslinking by formaldehyde: in vitro and in drosophila embryos

1 September 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

A suppressor of two essential checkpoint genes identifies a novel protein that negatively affects dNTP pools

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

Interactions of Isw2 chromatin remodeling complex with nucleosomal arrays: analyses using recombinant yeast histones and immobilized templates

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

Centromere identity is specified by a single centromeric nucleosome in budding yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

Interaction between the GAGA factor and Mod(mdg4) proteins promotes insulator bypass in Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

H2A.Z nucleosomes enriched over active genes are homotypic

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

BEDTools: a flexible suite of utilities for comparing genomic features

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

MEME-ChIP: motif analysis of large DNA datasets

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

A bipartite DNA-binding domain in yeast Reb1p

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

The REB1 site is an essential component of a terminator for RNA polymerase I in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

The UCSC Genome Browser database: extensions and updates 2013.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

Saccharomyces Genome Database: the genomics resource of budding yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

Getting started with yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

NIH Image to ImageJ: 25 years of image analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

What does our genome encode?

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2766

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NMETH.2766

1 reference

release_psw6mqmhvve2bjwixtyxzatk6a

21 August 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/psw6mqmhvve2bjwixtyxzatk6a

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMCID

3929178

1 reference

21 August 2017

1 reference

PMCID

3929178