Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos. (Q35117051)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25697895%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

title

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos (English)

1 reference

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1 March 2020

0 references

6

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1 March 2020

Hyung Joo Lee

1

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1 March 2020

Bo Zhang

4

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1 March 2020

author name string

Rebecca F Lowdon

2

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1 March 2020

Brett Maricque

3

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1 March 2020

Michael Stevens

5

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1 March 2020

Stephen L Johnson

7

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1 March 2020

Ting Wang

8

1 reference

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1 March 2020

language of work or name

English

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publication date

20 February 2015

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1 March 2020

published in

Nature Communications

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1 March 2020

volume

6

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1 March 2020

page(s)

6315

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Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation

1 March 2020

cites work

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Cdon acts as a Hedgehog decoy receptor during proximal-distal patterning of the optic vesicle

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9 July 2018

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Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

9 July 2018

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9 July 2018

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DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

9 July 2018

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Epigenomic analysis of multilineage differentiation of human embryonic stem cells

9 July 2018

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Transcriptional and epigenetic dynamics during specification of human embryonic stem cells

9 July 2018

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Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos

9 July 2018

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Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern

9 July 2018

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Enhancers: five essential questions

9 July 2018

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9 July 2018

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An integrated encyclopedia of DNA elements in the human genome

9 July 2018

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A map of the cis-regulatory sequences in the mouse genome

9 July 2018

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Functions of DNA methylation: islands, start sites, gene bodies and beyond

9 July 2018

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Enhancers: emerging roles in cell fate specification

9 July 2018

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The Human Epigenome Browser at Washington University

9 July 2018

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Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

9 July 2018

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CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

9 July 2018

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ΦC31 integrase mediates efficient cassette exchange in the zebrafish germline

9 July 2018

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Ascl1 expression defines a subpopulation of lineage-restricted progenitors in the mammalian retina.

9 July 2018

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DNA methylation status predicts cell type-specific enhancer activity.

9 July 2018

1 reference

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Lineage relationship of direct-developing melanocytes and melanocyte stem cells in the zebrafish

9 July 2018

1 reference

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5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells

9 July 2018

1 reference

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TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

9 July 2018

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ZFIN: enhancements and updates to the Zebrafish Model Organism Database

9 July 2018

1 reference

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Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

9 July 2018

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ChIP-Seq identification of weakly conserved heart enhancers

9 July 2018

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ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

9 July 2018

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Conserved role of intragenic DNA methylation in regulating alternative promoters

9 July 2018

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

9 July 2018

1 reference

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

9 July 2018

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GREAT improves functional interpretation of cis-regulatory regions

9 July 2018

1 reference

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Dnmt3 and G9a cooperate for tissue-specific development in zebrafish

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4339225

Human DNA methylomes at base resolution show widespread epigenomic differences

9 July 2018

1 reference

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Genomic views of distant-acting enhancers

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4339225

TopHat: discovering splice junctions with RNA-Seq

9 July 2018

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ChIP-seq accurately predicts tissue-specific activity of enhancers

9 July 2018

1 reference

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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

9 July 2018

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A novel CpG island set identifies tissue-specific methylation at developmental gene loci

9 July 2018

1 reference

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Ultraconservation identifies a small subset of extremely constrained developmental enhancers

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4339225

Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome

9 July 2018

1 reference

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

9 July 2018

1 reference

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Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

9 July 2018

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Analysis of tissue-specific differentially methylated regions (TDMs) in humans

9 July 2018

1 reference

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VISTA Enhancer Browser--a database of tissue-specific human enhancers

9 July 2018

1 reference

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In vivo enhancer analysis of human conserved non-coding sequences

9 July 2018

1 reference

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Zebra fish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development

9 July 2018

1 reference

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Close sequence comparisons are sufficient to identify human cis-regulatory elements.

9 July 2018

1 reference

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Functions and regulations of fibroblast growth factor signaling during embryonic development

9 July 2018

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

9 July 2018

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Highly conserved non-coding sequences are associated with vertebrate development

9 July 2018

1 reference

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Ultraconserved Elements in the Human Genome

9 July 2018

1 reference

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Epigenetic reprogramming in mammalian development

9 July 2018

1 reference

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DNA methylation directs a time-dependent repression of transcription initiation

9 July 2018

1 reference

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Stages of embryonic development of the zebrafish

9 July 2018

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sine oculis is a homeobox gene required for Drosophila visual system development

9 July 2018

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Expression of a β-globin gene is enhanced by remote SV40 DNA sequences

9 July 2018

1 reference

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Sema6a and Plxna2 mediate spatially regulated repulsion within the developing eye to promote eye vesicle cohesion

9 July 2018

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Exploring long-range genome interactions using the WashU Epigenome Browser

27 September 2018

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Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis.

27 September 2018

1 reference

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DNA-binding factors shape the mouse methylome at distal regulatory regions

27 September 2018

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A role for DNA methylation in gastrulation and somite patterning

27 September 2018

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Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish

27 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25697895

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NCOMMS7315

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25697895%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25697895%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

PubMed publication ID

25697895

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25697895%20AND%20SRC:MED&resulttype=core&format=json