Developmental gene regulatory networks in the zebrafish embryo

Chan, Tzu Min; Longabaugh, William J.R.; Bolouri, Hamid; Chen, Hualing; Tseng, Wen-Fang; Chao, Chung-Hao; Jang, Te-Hsuan; Lin, Yu-I; Hung, Shao-Chin; Wang, Horng-Dar; Yuh, Chiou-Hwa

doi:10.1016/j.bbagrm.2008.09.005

Cited by 56 publications

(58 citation statements)

References 126 publications

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“…The complexity of histone PTM profiles reported here reflects the diversity of developmental programs within the embryo, such that not all embryonic genes are expressed in all blastomeres (Rossant and Tam, 2009;Chan et al, 2009). The salt-and-pepper distribution of klf4 transcripts illustrates the differential programming of individual cells and would account for the apparent co-enrichment in H3K4/K27me3 within a single cell (albeit possibly on different alleles) or on a single klf4 promoter sequence, in cells not expressing klf4.…”

Section: Epigenetic States Of Embryonic Genes In Relation To Developmmentioning

confidence: 99%

“…Despite the importance of zebrafish (Danio rerio) as a model organism for studying vertebrate embryogenesis (Aleström et al, 2006) and developmental regulatory networks (Chan et al, 2009), little is known on histone PTMs associated with developmentallyregulated genes in this organism. In zebrafish, chromatin immunoprecipitation (ChIP) (Collas and Dahl, 2008) has been used to investigate the association of H4ac and c-Myc on specific promoters (Havis et al, 2006), map H3K4me3 sites in gastrula-stage embryos (Wardle et al, 2006) and investigate the role of specific transcription factors in hematopoiesis (Hart et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

“…These transcriptional changes result from a pre-determined differentiation program and regulate differentiation. Within the embryo, coordination of transcription in specific blastomeres requires intricate gene regulatory networks (Levine and Davidson, 2005;Chan et al, 2009;Morley et al, 2009). tion of cytosines within CpG dinucleotides is generally associated with gene repression, notably during development and differentiation (Jaenisch and Bird, 2003).…”

Section: Introductionmentioning

confidence: 99%

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Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos

Lindeman¹,

Winata²,

Aanes³

et al. 2010

Int. J. Dev. Biol.

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Embryo development proceeds from a cascade of gene activation and repression events controlled by epigenetic modifications of DNA and histones. Little is known about epigenetic states in the developing zebrafish, despite its importance as a model organism. We report here DNA methylation and histone modification profiles of promoters of developmentallyregulated genes (pou5f1, sox2, sox3, klf4, nnr, otx1b, nes, vasa), as well as tert and bactin2, in zebrafish embryos at the mid-late blastula transition, shortly after embryonic genome activation. We identify four classes of promoters based on the following profiles: (i) those enriched in marks of active genes (H3K9ac, H4ac, H3K4me3) without transcriptionally repressing H3K9me3 or H3K27me3; (ii) those enriched in H3K9ac, H4ac and H3K27me3, without H3K9me3; one such gene was klf4, shown by in situ hybridization to be mosaically expressed, likely accounting for the detection of both activating and repressive marks on its promoter; (iii) those enriched in H3K4me3 and H3K27me3 without acetylation; and (iv) those enriched in all histone modifications examined. Culture of embryo-derived cells under differentiation conditions leads to H3K9 and H4 deacetylation and H3K9 and H3K27 trimethylation on genes that are inactivated, yielding an epigenetic profile similar to those of fibroblasts or muscle. All promoters however retain H3K4me3, indicating an uncoupling of H3K4me3 occupancy and gene expression. All non-CpG island developmentallyregulated promoters are DNA unmethylated in embryos, but hypermethylated in fibroblasts. Our results suggest that differentially expressed embryonic genes are regulated by various patterns of histone modifications on unmethylated DNA, which create a developmentally permissive chromatin state.

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Section: Epigenetic States Of Embryonic Genes In Relation To Developmmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos

Lindeman¹,

Winata²,

Aanes³

et al. 2010

Int. J. Dev. Biol.

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“…[1][2][3] In order to understand and reprogram genetic circuits with the same spatiotemporal resolution, light can be used as an external control element. The installation of light-removable protecting groups on biological macromolecules is a versatile approach to the photochemical regulation of RNA, DNA, and protein activity.…”

Section: Introductionmentioning

confidence: 99%

Genetically Encoded Light-Activated Transcription for Spatiotemporal Control of Gene Expression and Gene Silencing in Mammalian Cells

et al. 2013

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Photocaging provides a method to spatially and temporally control biological function and gene expression with high resolution. Proteins can be photochemically controlled through the sitespecific installation of caging groups on amino acid side chains that are essential for protein function. The photocaging of a synthetic gene network using unnatural amino acid mutagenesis in mammalian cells was demonstrated with an engineered bacteriophage RNA polymerase. A caged T7 RNA polymerase was expressed in cells with an expanded genetic code and used in the photochemical activation of genes under control of an orthogonal T7 promoter, demonstrating tight spatial and temporal control. The synthetic gene expression system was validated with two reporter genes (luciferase and EGFP) and applied to the light-triggered transcription of short hairpin RNA constructs for the induction of RNA interference.

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“…The many advantages to using zebrafish embryos in research include: external fertilization; a transparent "shell" or chorion over the developing zebrafish embryos; embryos that are transparent themselves early in development; and rapid ex utero development. In addition, much is known about normal zebrafish development and zebrafish genetics also are well documented [9][10][11][12]. Also adding to the importance of this model for toxicology research is the ability to directly deliver chemicals to zebrafish embryos as they develop [9,13,14].…”

mentioning

confidence: 99%

Selecting Optimal Animal Models to Investigate Environmental Toxicology

Abbott¹

2013

Poult Fish Wildl Sci

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Developmental gene regulatory networks in the zebrafish embryo

Cited by 56 publications

References 126 publications

Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos

Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos

Genetically Encoded Light-Activated Transcription for Spatiotemporal Control of Gene Expression and Gene Silencing in Mammalian Cells

Selecting Optimal Animal Models to Investigate Environmental Toxicology

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