(Q35562092)

8 August 2017

Modeling the relationship of epigenetic modifications to transcription factor binding (English)

1 reference

8 August 2017

Liang Liu

1

1 reference

8 August 2017

Guangxu Jin

series ordinal

2

1 reference

8 August 2017

Xiaobo Zhou

series ordinal

3

1 reference

8 August 2017

language of work or name

English

0 references

publication date

27 March 2015

1 reference

8 August 2017

Nucleic Acids Research

1 reference

8 August 2017

43

1 reference

8 August 2017

8

1 reference

8 August 2017

3873-3885

1 reference

Creative Commons Attribution 4.0 International

8 August 2017

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes

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Transcription factor binding predicts histone modifications in human cell lines

12 July 2018

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Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers.

12 July 2018

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An atlas of active enhancers across human cell types and tissues

12 July 2018

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Effects of cytosine methylation on transcription factor binding sites

12 July 2018

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H3K4me2 reliably defines transcription factor binding regions in different cells

12 July 2018

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Widespread misinterpretable ChIP-seq bias in yeast

12 July 2018

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

12 July 2018

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Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs

12 July 2018

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Regulation of alternative splicing by local histone modifications: potential roles for RNA-guided mechanisms

12 July 2018

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DNA methylation presents distinct binding sites for human transcription factors

12 July 2018

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Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites

12 July 2018

1 reference

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Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis

12 July 2018

1 reference

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The patterns of histone modifications in the vicinity of transcription factor binding sites in human lymphoblastoid cell lines

12 July 2018

1 reference

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Enhancers: five essential questions

12 July 2018

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DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

12 July 2018

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Chromatin organization and transcriptional regulation

12 July 2018

1 reference

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Analysis method of epigenetic DNA methylation to dynamically investigate the functional activity of transcription factors in gene expression

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

12 July 2018

1 reference

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Sequence and chromatin determinants of cell-type-specific transcription factor binding

12 July 2018

1 reference

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Widespread plasticity in CTCF occupancy linked to DNA methylation

12 July 2018

1 reference

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Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

12 July 2018

1 reference

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An integrated encyclopedia of DNA elements in the human genome

12 July 2018

1 reference

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Functional analysis of transcription factor binding sites in human promoters

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Modeling gene expression using chromatin features in various cellular contexts

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Cancer genetics and epigenetics: two sides of the same coin?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Programming of DNA methylation patterns

12 July 2018

1 reference

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ChromHMM: automating chromatin-state discovery and characterization

12 July 2018

1 reference

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Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements

12 July 2018

1 reference

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Evolutionary origins of transcription factor binding site clusters

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

DNA methylation status predicts cell type-specific enhancer activity.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

CpG islands and the regulation of transcription

12 July 2018

1 reference

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Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

12 July 2018

1 reference

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Chromatin higher-order structures and gene regulation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Coordinated histone modifications are associated with gene expression variation within and between species

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

The language of histone crosstalk

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Interplay between DNA methylation and transcription factor availability: implications for developmental activation of the mouse Myogenin gene

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Histone modification levels are predictive for gene expression

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Histone modifications at human enhancers reflect global cell-type-specific gene expression

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Divergent transcription from active promoters

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Crosstalk among Histone Modifications

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Epigenetic interplay between histone modifications and DNA methylation in gene silencing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

A chromatin landmark and transcription initiation at most promoters in human cells

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Transcription factor binding and modified histones in human bidirectional promoters

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

The landscape of histone modifications across 1% of the human genome in five human cell lines

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Epigenetics and aging: the targets and the marks

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

The complex language of chromatin regulation during transcription

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Cancer epigenomics: DNA methylomes and histone-modification maps

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Chromatin modifications and their function

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

12 July 2018

The mammalian epigenome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Suz12 binds to silenced regions of the genome in a cell-type-specific manner

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Histone H4-K16 acetylation controls chromatin structure and protein interactions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Genomic maps and comparative analysis of histone modifications in human and mouse

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Highly conserved non-coding sequences are associated with vertebrate development

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Structure and evolution of transcriptional regulatory networks

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Histone modifications in transcriptional regulation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Transcription of eukaryotic protein-coding genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

The hardwiring of development: organization and function of genomic regulatory systems.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Interplay between chromatin structure and transcription.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Cytosine methylation prevents binding to DNA of a HeLa cell transcription factor required for optimal expression of the adenovirus major late promoter

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Multipartite genetic control elements: communication by DNA loop

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Analysis of CpG methylation and genomic footprinting at the tyrosine aminotransferase gene: DNA methylation alone is not sufficient to prevent protein binding in vivo

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Histone acetyltransferase complexes stabilize swi/snf binding to promoter nucleosomes.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

DNA methylation represses transcription in vivo.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

Going the distance: a current view of enhancer action

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417166

26 September 2018

Identifiers

DOI

10.1093/NAR/GKV255

1 reference

8 August 2017

1 reference

8 August 2017

1 reference