Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks. (Q34354921)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23818646%20AND%20SRC:MED&resulttype=core&format=json

4 March 2020

title

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks (English)

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4 March 2020

3

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4 March 2020

author name string

Michael A White

series ordinal

1

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4 March 2020

Connie A Myers

series ordinal

2

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4 March 2020

Barak A Cohen

series ordinal

4

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4 March 2020

language of work or name

English

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publication date

1 July 2013

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Proceedings of the National Academy of Sciences of the United States of America

4 March 2020

published in

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4 March 2020

volume

110

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4 March 2020

issue

29

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4 March 2020

page(s)

11952-11957

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Nucleosome-driven transcription factor binding and gene regulation

4 March 2020

cites work

1 reference

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Complex effects of nucleotide variants in a mammalian cis-regulatory element.

6 July 2018

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

6 July 2018

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An expansive human regulatory lexicon encoded in transcription factor footprints

6 July 2018

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The accessible chromatin landscape of the human genome

6 July 2018

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An integrated encyclopedia of DNA elements in the human genome

6 July 2018

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Functional analysis of transcription factor binding sites in human promoters

6 July 2018

1 reference

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Transcription factors: from enhancer binding to developmental control

6 July 2018

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Inferring direct DNA binding from ChIP-seq

6 July 2018

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Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

6 July 2018

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Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

6 July 2018

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Massively parallel functional dissection of mammalian enhancers in vivo

6 July 2018

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Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins

6 July 2018

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Animal transcription networks as highly connected, quantitative continua

6 July 2018

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A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA.

6 July 2018

1 reference

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DREME: motif discovery in transcription factor ChIP-seq data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718143

MEME-ChIP: motif analysis of large DNA datasets

6 July 2018

1 reference

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FIMO: scanning for occurrences of a given motif

6 July 2018

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Chromatin accessibility pre-determines glucocorticoid receptor binding patterns.

6 July 2018

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Chromatin landscape dictates HSF binding to target DNA elements

6 July 2018

1 reference

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CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718143

Sequence features that drive human promoter function and tissue specificity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718143

Quantitative fine-tuning of photoreceptor cis-regulatory elements through affinity modulation of transcription factor binding sites

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718143

Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.

6 July 2018

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Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718143

High nucleosome occupancy is encoded at human regulatory sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718143

G+C content dominates intrinsic nucleosome occupancy

6 July 2018

1 reference

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Inferring binding energies from selected binding sites

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718143

The role of DNA shape in protein-DNA recognition

6 July 2018

1 reference

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Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

6 July 2018

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The DNA-encoded nucleosome organization of a eukaryotic genome

6 July 2018

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The cis-regulatory logic of the mammalian photoreceptor transcriptional network

6 July 2018

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Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.

6 July 2018

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6 July 2018

1 reference

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Initial sequencing and comparative analysis of the mouse genome

6 July 2018

1 reference

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The human genome browser at UCSC

6 July 2018

1 reference

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Crx, a novel Otx-like paired-homeodomain protein, binds to and transactivates photoreceptor cell-specific genes

6 July 2018

1 reference

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The basic motif-leucine zipper transcription factor Nrl can positively regulate rhodopsin gene expression

6 July 2018

1 reference

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6 July 2018

Identifiers

DOI

10.1073/PNAS.1307449110

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4 March 2020

0 references

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4 March 2020

1 reference

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