A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals (Q42020759)

15 October 2017

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals (English)

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15 October 2017

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Aviv Regev

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Nir Hacohen

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Raktima Raychowdhury

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Raktima Raychowdhury

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Chad Nusbaum

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Manuel Garber

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Mitchell Guttman

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Ido Amit

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Andreas Gnirke

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Alon Goren

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Bradley E Bernstein

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Nicolas Chevrier

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Nir Yosef

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Anne Thielke

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James Robinson

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Brian Minie

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Zohar Itzhaki

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Ronnie Blecher-Gonen

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Chamutal Bornstein

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Daniela Amann-Zalcenstein

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Assaf Weiner

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Dennis Friedrich

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James Meldrim

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Oren Ram

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Christine Cheng

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Sheila Fisher

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Bang Wong

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30 August 2012

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810-822

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Dimer-specific regulatory mechanisms within the NF-κB family of transcription factors

15 October 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

A transcription factor collective defines cardiac cell fate and reflects lineage history

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Master transcription factors determine cell-type-specific responses to TGF-β signaling

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Computational methods for transcriptome annotation and quantification using RNA-seq

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

A cis-regulatory map of the Drosophila genome.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Integrative genomics viewer

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Identification of functional elements and regulatory circuits by Drosophila modENCODE

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Emerging properties of animal gene regulatory networks

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Inducible gene expression: diverse regulatory mechanisms

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Variation in transcription factor binding among humans

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Forcing cells to change lineages

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Combinatorial binding predicts spatio-temporal cis-regulatory activity

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Finding distal regulatory elements in the human genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Control of inducible gene expression by signal-dependent transcriptional elongation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Fast and accurate short read alignment with Burrows-Wheeler transform

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

TopHat: discovering splice junctions with RNA-Seq

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Structure and function of a transcriptional network activated by the MAPK Hog1.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Genome-wide mapping of in vivo protein-DNA interactions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

High-resolution profiling of histone methylations in the human genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Quantifying similarity between motifs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Transcriptional regulatory code of a eukaryotic genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

5 June 2018

The B7-CD28 superfamily

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

A CDE/CHR tandem element regulates cell cycle-dependent repression of cyclin B2 transcription.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

An advanced culture method for generating large quantities of highly pure dendritic cells from mouse bone marrow

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

The high mobility group protein HMG I(Y) is required for NF-kappa B-dependent virus induction of the human IFN-beta gene

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

A module of negative feedback regulators defines growth factor signaling

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Multilineage transcriptional priming and determination of alternate hematopoietic cell fates.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

GATA transcription factors as potentiators of gut endoderm differentiation.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3873101

Gene regulation. A paradigm for precision

17 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22940246

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.MOLCEL.2012.07.030

1 reference

15 October 2017

1 reference

15 October 2017

PubMed publication ID

22940246

1 reference