Unknown,Transcriptomics,Genomics,Proteomics

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Mapping of H3K4 and H3K27 trimethylation in zebrafish cells (Gene expression)

ABSTRACT: The genomic distribution of post-translationally modified histones in the zebrafish (Danio rerio) genome remain largely unraveled. The objective of this study was to (1) design a microarray covering all zebrafish gene promoters and 5' end of coding regions, and (ii) using these arrrays, map the genome-wide distribution of trimethylated H3K4 and H3K27 in the embryo derived ZF4 cell line. Specifically, we determined the enrichment profile of H3K4me3, H3K27me3 and of both (co-enriched) modifications in ZF4 cells. We determined average enrichment profiles through metagene analysis, functional terms enriched among genes marked by either modification, pathway analysis, and in relation to gene expression. Gene expression experiments were performed on three biological replicates.

ORGANISM(S): Danio rerio

SUBMITTER: Philippe Collas

PROVIDER: E-GEOD-23679 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays.

Lindeman Leif C LC Reiner Andrew H AH Mathavan Sinnakaruppan S Aleström Peter P Collas Philippe P

PloS one 20101220 12

<h4>Background</h4>Uncovering epigenetic states by chromatin immunoprecipitation and microarray hybridization (ChIP-chip) has significantly contributed to the understanding of gene regulation at the genome-scale level. Many studies have been carried out in mice and humans; however limited high-resolution information exists to date for non-mammalian vertebrate species.<h4>Principal findings</h4>We report a 2.1-million feature high-resolution Nimblegen tiling microarray for ChIP-chip interrogation ...[more]

PMID: 21187971

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Project description:This project aimed at identifying developmental stage specific transcript profiles for catecholaminergic neurons in embryos and early larvae of zebrafish (Danio rerio). Catecholaminergic neurons were labeled using transgenic zebrafish strains to drive expression of GFP. At stages 24, 36, 72 and 96 hrs post fertilization, embryos were dissociated and GFP expressing cells sorted by FACS. Isolated RNAs were processed using either polyA selection and libray generation or NanoCAGE. This is the first effort to determine stage specific mRNA profiles of catecholaminergic neurons in zebrafish. Catecholaminergic neurons were labeled by four different strategies: (1) 24 hrs old embryos: we used the ETvmat2:GFP transgenic line (Wen et al. 2007). Visualization of monoaminergic neurons and neurotoxicity of MPTP in live transgenic zebrafish. Dev Biol. 2008 Vol 314 p84-92) which at this early stage labels catecholaminergic neurons in posterior tuberculum and locus coeruleus; (2) 24 hrs old embryos: we used Tg(otpb.A:egfp)zc48 transgenic line (Fujimoto et al. Identification of a dopaminergic enhancer indicates complexity in vertebrate dopamine neuron phenotype specification. Dev Biol 2011, Vol 352, p393–404) which at this stage label ventral diencephalic dopaminergic neurons and some preoptic neurons. (3) For 72 and 96 hrs old zebrafish larvae we used a th:GFP BAC transgenic lines that labels catecholaminergic neurons (Tay et al., Comprehensive catecholaminergic projectome analysis reveals single-neuron integration of zebrafish ascending and descending dopaminergic systems. Nat Comms 2011 Vol 2, 171; also: T. Leng and W. Driever, unpublished). (4) for the 36 and 48 hrs old zebrafish larvae we used a th:Gal4VP16 driver and UAS:EGFP responder transgenic line system to label catecholaminergic cells (Fernandes et al., Deep brain photoreceptors control light-seeking behavior in zebrafish larvae. Curr Biol. 2012 Vol 22 DOI 10.1016/j.cub.2012.08.016). We used the different transgenic lines, because lines (3) and (4) do not efficiently label catecholaminergic neurons at early stages, while lines (1) and (2) also have GFP expression in several other non-catecholaminergic populations at later stages of development. Embryos were dissociated and catecholaminergic neurons were FACS sorted from GFP-tagged zebrafish (Manoli and Driever, 2012, Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633). RNA was either processed for NanoCAGE, or mRNA was isolated and amplified. cDNA was sequenced by Illumina technique. This data submission is a series of data files consisting of three independent experiments with diffrent RNA-Seq depth: Samples 1-4 (NanoCage): Samples 5-8 (RNA-Seq high read numbers), and SAmples 9-12 (RNA-Seq low read numbers).

Dataset Information

Mapping of H3K4 and H3K27 trimethylation in zebrafish cells (Gene expression)

Publications

Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays.

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