Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
???displayArticle.abstract???
The generation of distinctive cell types that form different tissues and organs requires precise, temporal and spatial control of gene expression. This depends on specific cis-regulatory elements distributed in the noncoding DNA surrounding their target genes. Studies performed on mammalian embryonic stem cells and Drosophila embryos suggest that active enhancers form part of a defined chromatin landscape marked by histone H3 lysine 4 mono-methylation (H3K4me1) and histone H3 lysine 27 acetylation (H3K27ac). Nevertheless, little is known about the dynamics and the potential roles of these marks during vertebrate embryogenesis. Here, we provide genomic maps of H3K4me1/me3 and H3K27ac at four developmental time-points of zebrafish embryogenesis and analyze embryonic enhancer activity. We find that (1) changes in H3K27ac enrichment at enhancers accompany the shift from pluripotency to tissue-specific gene expression, (2) in early embryos, the peaks of H3K27ac enrichment are bound by pluripotent factors such as Nanog, and (3) the degree of evolutionary conservation is higher for enhancers that become marked by H3K27ac at the end of gastrulation, suggesting their implication in the establishment of the most conserved (phylotypic) transcriptome that is known to occur later at the pharyngula stage.
Aday,
Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites.
2011, Pubmed
Aday,
Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites.
2011,
Pubmed
Bauer,
Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration.
2008,
Pubmed
Bessa,
Zebrafish enhancer detection (ZED) vector: a new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish.
2009,
Pubmed
Blader,
Conserved and acquired features of neurogenin1 regulation.
2004,
Pubmed
Blankenberg,
A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.
2007,
Pubmed
Blow,
ChIP-Seq identification of weakly conserved heart enhancers.
2010,
Pubmed
Bonn,
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.
2012,
Pubmed
Chambers,
Nanog safeguards pluripotency and mediates germline development.
2007,
Pubmed
Creyghton,
Histone H3K27ac separates active from poised enhancers and predicts developmental state.
2010,
Pubmed
Dahl,
Histone H3 lysine 27 methylation asymmetry on developmentally-regulated promoters distinguish the first two lineages in mouse preimplantation embryos.
2010,
Pubmed
Domazet-Lošo,
A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns.
2010,
Pubmed
Ernst,
Mapping and analysis of chromatin state dynamics in nine human cell types.
2011,
Pubmed
Gaulton,
A map of open chromatin in human pancreatic islets.
2010,
Pubmed
Grinberg,
Heterozygous deletion of the linked genes ZIC1 and ZIC4 is involved in Dandy-Walker malformation.
2004,
Pubmed
Guo,
Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst.
2010,
Pubmed
Hawkins,
Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency.
2011,
Pubmed
Heintzman,
Histone modifications at human enhancers reflect global cell-type-specific gene expression.
2009,
Pubmed
Heintzman,
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
2007,
Pubmed
Irie,
Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis.
2011,
Pubmed
,
Xenbase
Jowett,
Whole-mount in situ hybridizations on zebrafish embryos using a mixture of digoxigenin- and fluorescein-labelled probes.
1994,
Pubmed
Kalinka,
Gene expression divergence recapitulates the developmental hourglass model.
2010,
Pubmed
Kawakami,
Transgenesis and gene trap methods in zebrafish by using the Tol2 transposable element.
2004,
Pubmed
Keller,
Insights into the evolutionary history of the vertebrate zic3 locus from a teleost-specific zic6 gene in the zebrafish, Danio rerio.
2007,
Pubmed
Kim,
Widespread transcription at neuronal activity-regulated enhancers.
2010,
Pubmed
Kimmel,
Stages of embryonic development of the zebrafish.
1995,
Pubmed
,
Xenbase
Lim,
Zic3 is required for maintenance of pluripotency in embryonic stem cells.
2007,
Pubmed
Nishimoto,
Fibroblast growth factor 13 is essential for neural differentiation in Xenopus early embryonic development.
2007,
Pubmed
,
Xenbase
Ong,
Enhancer function: new insights into the regulation of tissue-specific gene expression.
2011,
Pubmed
Pauli,
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.
2012,
Pubmed
Pekowska,
H3K4 tri-methylation provides an epigenetic signature of active enhancers.
2011,
Pubmed
Rada-Iglesias,
A unique chromatin signature uncovers early developmental enhancers in humans.
2011,
Pubmed
,
Xenbase
Sakabe,
Genome-wide maps of transcription regulatory elements.
2010,
Pubmed
Sandelin,
JASPAR: an open-access database for eukaryotic transcription factor binding profiles.
2004,
Pubmed
Santos-Rosa,
Active genes are tri-methylated at K4 of histone H3.
2002,
Pubmed
Siepel,
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
2005,
Pubmed
Sprague,
The Zebrafish Information Network: the zebrafish model organism database.
2006,
Pubmed
Tang,
Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis.
2010,
Pubmed
Taylor,
Using galaxy to perform large-scale interactive data analyses.
2007,
Pubmed
Tjian,
Transcriptional activation: a complex puzzle with few easy pieces.
1994,
Pubmed
Visel,
ChIP-seq accurately predicts tissue-specific activity of enhancers.
2009,
Pubmed
Wang,
Fibroblast growth factor homologous factor 13 regulates Na+ channels and conduction velocity in murine hearts.
2011,
Pubmed
Wardle,
Zebrafish promoter microarrays identify actively transcribed embryonic genes.
2006,
Pubmed
Ware,
Zic3 is critical for early embryonic patterning during gastrulation.
2006,
Pubmed
Ware,
Identification and functional analysis of ZIC3 mutations in heterotaxy and related congenital heart defects.
2004,
Pubmed
,
Xenbase
Xu,
Nanog-like regulates endoderm formation through the Mxtx2-Nodal pathway.
2012,
Pubmed
Ye,
seqMINER: an integrated ChIP-seq data interpretation platform.
2011,
Pubmed
Zentner,
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions.
2011,
Pubmed
Zhang,
Model-based analysis of ChIP-Seq (MACS).
2008,
Pubmed
